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Forsberg J, Rasmussen CT, van den Berg FWJ, Engelsen SB, Aru V. Fermentation Analytical Technology (FAT): Monitoring industrial E. coli fermentations using absolute quantitative 1H NMR spectroscopy. Anal Chim Acta 2024; 1311:342722. [PMID: 38816156 DOI: 10.1016/j.aca.2024.342722] [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: 03/04/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND To perform fast, reproducible, and absolute quantitative measurements in an automated manner has become of paramount importance when monitoring industrial processes, including fermentations. Due to its numerous advantages - including its inherent quantitative nature - Proton Nuclear Magnetic Resonance (1H NMR) spectroscopy provides an ideal tool for the time-resolved monitoring of fermentations. However, analytical conditions, including non-automated sample preparation and long relaxation times (T1) of some metabolites, can significantly lengthen the experimental time and make implementation in an industrial set up unfeasible. RESULTS We present a high throughput method based on Standard Operating Procedures (SOPs) and 1H NMR, which lays the foundation for what we call Fermentation Analytical Technology (FAT). Our method was developed for the accurate absolute quantification of metabolites produced during Escherichia coli industrial fermentations. The method includes: (1) a stopped flow system for non-invasive sample collection followed by sample quenching, (2) automatic robot-assisted sample preparation, (3) fast 1H NMR measurements, (4) metabolites quantification using multivariate curve resolution (MCR), and (5) metabolites absolute quantitation using a novel correction factor (k) to compensate for the short recycle delay (D1) employed in the 1H NMR measurements. The quantification performance was tested using two sample types: buffer solutions of chemical standards and real fermentation samples. Five metabolites - glucose, acetate, alanine, phenylalanine and betaine - were quantified. Absolute quantitation ranged between 0.64 and 3.40 mM in pure buffer, and 0.71-7.76 mM in real samples. SIGNIFICANCE The proposed method is generic and can be straight forward implemented to other types of fermentations, such as lactic acid, ethanol and acetic acid fermentations. It provides a high throughput automated solution for monitoring fermentation processes and for quality control through absolute quantification of key metabolites in fermentation broth. It can be easily implemented in an at-line industrial setting, facilitating the optimization of the manufacturing process towards higher yields and more efficient and sustainable use of resources.
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Affiliation(s)
- Jakob Forsberg
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark; Novo Nordisk A/S, Hagedornsvej 1, 2820, Gentofte, Denmark.
| | | | - Frans W J van den Berg
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Søren Balling Engelsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Violetta Aru
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark.
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Krishnamurthy K. Complete Reduction to Amplitude Frequency Table (CRAFT)-A perspective. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:757-791. [PMID: 33486830 DOI: 10.1002/mrc.5135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
The CRAFT (Complete Reduction to Amplitude Frequency Table) technique, based on Bayesian analysis approach, converts FID and/or interferogram (time domain) to a frequency-amplitude table (tabular domain) in a robust, automated, and time-efficient fashion. This mini review/perspective presents an introduction to CRAFT as a processing workflow followed by a discussion of several practical 1D and 2D examples of its applicability and associated benefit. CRAFT provides high quality quantitative results for complex systems without any need for conventional preprocessing steps, such as phase and baseline corrections. Two-dimensional time domain data are typically truncated, particularly in the evolution dimension, and conventional processing after zero-filling and t1max -matched apodization masks potentially available peak resolution. The line broadening introduced by extensive zero-filling and severe apodization functions leads to the lack of clear resolution of cross peaks. CRAFT decimation of interferograms, on the other hand, requires minimal or no apodization prior to extraction of the NMR parameters and significantly improves the spectral linewidth of the cross peaks along F1 dimension compared to conventional (FT) processing. The tabular representation of the CRAFT2d cross peaks information can be visualized in a variety of frequency domain formats for conventional spectral interpretation as well as quantitative applications. A simple workflow to generate in silico oversampled interferogram (iSOS) is presented, and its potential benefit in CRAFT decimation of highly crowded 2D NMR is demonstrated. This report is meant as a collective thesis to present a potentially new paradigm in data processing that questions the need for hitherto unchallenged preprocessing steps, such as phase and baseline correction in 1D and zero-fill/severe apodization in 2D.
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3
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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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4
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Das TK, Narhi LO, Sreedhara A, Menzen T, Grapentin C, Chou DK, Antochshuk V, Filipe V. Stress Factors in mAb Drug Substance Production Processes: Critical Assessment of Impact on Product Quality and Control Strategy. J Pharm Sci 2020; 109:116-133. [DOI: 10.1016/j.xphs.2019.09.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/29/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022]
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5
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Traustason B, Cheeks M, Dikicioglu D. Computer-Aided Strategies for Determining the Amino Acid Composition of Medium for Chinese Hamster Ovary Cell-Based Biomanufacturing Platforms. Int J Mol Sci 2019; 20:E5464. [PMID: 31684012 PMCID: PMC6862603 DOI: 10.3390/ijms20215464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 01/07/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are used for the production of the majority of biopharmaceutical drugs, and thus have remained the standard industry host for the past three decades. The amino acid composition of the medium plays a key role in commercial scale biologics manufacturing, as amino acids constitute the building blocks of both endogenous and heterologous proteins, are involved in metabolic and non-metabolic pathways, and can act as main sources of nitrogen and carbon under certain conditions. As biomanufactured proteins become increasingly complex, the adoption of model-based approaches become ever more popular in complementing the challenging task of medium development. The extensively studied amino acid metabolism is exceptionally suitable for such model-driven analyses, and although still limited in practice, the development of these strategies is gaining attention, particularly in this domain. This paper provides a review of recent efforts. We first provide an overview of the widely adopted practice, and move on to describe the model-driven approaches employed for the improvement and optimization of the external amino acid supply in light of cellular amino acid demand. We conclude by proposing the likely prevalent direction the field is heading towards, providing a critical evaluation of the current state and the future challenges and considerations.
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Affiliation(s)
- Bergthor Traustason
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK.
| | - Matthew Cheeks
- Cell Sciences, Biopharmaceutical Development, AstraZeneca, Cambridge CB21 6GH, UK.
| | - Duygu Dikicioglu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK.
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6
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Powers DN, Wang Y, Fratz-Berilla EJ, Velugula-Yellela SR, Chavez B, Angart P, Trunfio N, Yoon S, Agarabi C. Real-time quantification and supplementation of bioreactor amino acids to prolong culture time and maintain antibody product quality. Biotechnol Prog 2019; 35:e2894. [PMID: 31425633 PMCID: PMC7003473 DOI: 10.1002/btpr.2894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 01/18/2023]
Abstract
Real‐time monitoring of cell cultures in bioreactors can enable expedited responses necessary to correct potential batch failure perturbations which may normally go undiscovered until the completion of the batch and result in failure. Currently, analytical technologies are dedicated to real‐time monitoring of bioreactor parameters such as pH, dissolved oxygen, and temperature, nutrients such as glucose and glutamine, or metabolites such as lactate. Despite the importance of amino acids as the building blocks of therapeutic protein products, other than glutamine their concentrations are not commonly measured. Here, we present a study into amino acid monitoring, supplementation strategies, and how these techniques may impact the cell growth profiles and product quality. We used preliminary bioreactor runs to establish baselines by determining initial amino acid consumption patterns, the results of which were used to select a pool of amino acids which gets depleted in the bioreactor. These amino acids were combined into blends which were supplemented into bioreactors during a subsequent run, the concentrations of which were monitored using a mass spectrometry based at‐line method we developed to quickly assess amino acid concentrations from crude bioreactor media. We found that these blends could prolong culture life, reversing a viable cell density decrease that was leading to batch death. Additionally, we assessed how these strategies might impact protein product quality, such as the glycan profile. The amino acid consumption data were aligned with the final glycan profiles in principal component analysis to identify which amino acids are most closely associated with glycan outcomes.
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Affiliation(s)
- David N Powers
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Product Quality, Office of Biotechnology Products, Division of Biotechnology Review and Research II, Silver Spring, Maryland
| | - Yifan Wang
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Testing and Research, Division of Product Quality Research, Silver Spring, Maryland
| | - Erica J Fratz-Berilla
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Product Quality, Office of Biotechnology Products, Division of Biotechnology Review and Research II, Silver Spring, Maryland
| | - Sai Rashmika Velugula-Yellela
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Product Quality, Office of Biotechnology Products, Division of Biotechnology Review and Research II, Silver Spring, Maryland
| | - Brittany Chavez
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Product Quality, Office of Biotechnology Products, Division of Biotechnology Review and Research II, Silver Spring, Maryland
| | - Phillip Angart
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Product Quality, Office of Biotechnology Products, Division of Biotechnology Review and Research II, Silver Spring, Maryland
| | - Nicholas Trunfio
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Product Quality, Office of Biotechnology Products, Division of Biotechnology Review and Research II, Silver Spring, Maryland.,Sartorius Stedim North America Inc, Corporate Research, Bohemia, NY
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts, Lowell, Massachusetts
| | - Cyrus Agarabi
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Product Quality, Office of Biotechnology Products, Division of Biotechnology Review and Research II, Silver Spring, Maryland
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7
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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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9
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Park SY, Reimonn TM, Agarabi CD, Brorson KA, Yoon S. Metabolic responses and pathway changes of mammalian cells under different culture conditions with media supplementations. Biotechnol Prog 2018; 34:793-805. [DOI: 10.1002/btpr.2623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/08/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Seo-Young Park
- Dept. of Chemical Engineering; University of Massachusetts; Lowell MA, United States
| | - Thomas M. Reimonn
- Program in Bioinformatics and Integrative Biology; University of Massachusetts Medical School; Worcester MA, United States
| | - Cyrus D. Agarabi
- Division II; Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA; Silver Spring MD, United States
| | - Kurt A. Brorson
- Division II; Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA; Silver Spring MD, United States
| | - Seongkyu Yoon
- Dept. of Chemical Engineering; University of Massachusetts; Lowell MA, United States
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10
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Fouladiha H, Marashi SA, Shokrgozar MA, Farokhi M, Atashi A. Applications of a metabolic network model of mesenchymal stem cells for controlling cell proliferation and differentiation. Cytotechnology 2018; 70:331-338. [PMID: 28980092 PMCID: PMC5809662 DOI: 10.1007/s10616-017-0148-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 09/16/2017] [Indexed: 12/27/2022] Open
Abstract
Mesenchymal stem cells (MSCs) can be isolated from several tissues of adults. In addition, MSCs have the potential of differentiation into several cell types. Therefore, MSCs are very useful in stem cell therapy and regenerative medicine. MSCs have also been used as gene or protein carriers. As a result, maintaining MSCs in a desirable metabolic state has been the subject of several studies. Here, we used a genome scale metabolic network model of bone marrow derived MSCs for exploring the metabolism of these cells. We analyzed metabolic fluxes of the model in order to find ways of increasing stem cell proliferation and differentiation. Consequently, the experimental results were in consistency with computational results. Therefore, analyzing metabolic models was proven to be a promising field in biomedical researches of stem cells.
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Affiliation(s)
- Hamideh Fouladiha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Sayed-Amir Marashi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
| | | | - Mehdi Farokhi
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Amir Atashi
- Stem Cell and Tissue Engineering Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
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11
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Bhatia H, Mehdizadeh H, Drapeau D, Yoon S. In-line monitoring of amino acids in mammalian cell cultures using raman spectroscopy and multivariate chemometrics models. Eng Life Sci 2018; 18:55-61. [PMID: 32624861 PMCID: PMC6999330 DOI: 10.1002/elsc.201700084] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 09/01/2017] [Accepted: 09/25/2017] [Indexed: 12/11/2022] Open
Abstract
The application of PAT for in-line monitoring of biopharmaceutical manufacturing operations has a central role in developing more robust and consistent processes. Various spectroscopic techniques have been applied for collecting real-time data from cell culture processes. Among these, Raman spectroscopy has been shown to have advantages over other spectroscopic techniques, especially in aqueous culture solutions. Measurements of several process parameters such as glucose, lactate, glutamine, glutamate, ammonium, osmolality and VCD using Raman-based chemometrics models have been reported in literature. The application of Raman spectroscopy, coupled with calibration models for amino acid measurement in cell cultures, has been assessed. The developed models cover four amino acids important for cell growth and production: tyrosine, tryptophan, phenylalanine and methionine. The chemometrics models based on Raman spectroscopy data demonstrate the significant potential for the quantification of tyrosine, tryptophan and phenylalanine. The model for methionine would have to be further refined to improve quantification.
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Affiliation(s)
- Hemlata Bhatia
- Department of Biomedical Engineering and BiotechnologyUniversity of Massachusetts LowellLowellMA, USA
| | - Hamidreza Mehdizadeh
- Advanced Manufacturing TechnologyGlobal Technology ServicesPfizer Global SuppliesPfizer‐Inc.PeapackNJ, USA
| | | | - Seongkyu Yoon
- Department of Chemical EngineeringUniversity of Massachusetts LowellLowellMA, USA
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12
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Kiss R, Fizil Á, Szántay C. What NMR can do in the biopharmaceutical industry. J Pharm Biomed Anal 2017; 147:367-377. [PMID: 28760370 DOI: 10.1016/j.jpba.2017.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 11/18/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has a unique capability to probe the primary and higher order molecular structure and the structural dynamics of biomolecules at an atomic resolution, and this capability has been greatly fortified over the last five decades by an astonishing NMR instrumental and methodological development. Because of these factors, NMR has become a primary tool for the structure investigation of biomolecules, spawning a whole scientific subfield dedicated to the subject. This role of NMR is by now well established and broadly appreciated, especially in the context of academic research dealing with proteins that are purified and isotope-labeled in order to facilitate the necessary sophisticated multidimensional NMR measurements. However, the more recent industrial development, manufacturing, and quality control of biopharmaceuticals provide a different framework for NMR. For example, protein drug substances are not isotope-labeled and are present in a medium of excipients, which make structural NMR measurements much more difficult. On the other hand, biotechnology involves many other analytical requirements that can be efficiently addressed by NMR. In this respect the scope and limitations of NMR are less well understood. Having the non-expert reader in mind, herein we wish to highlight the ways in which modern NMR can effectively support biotechnological developments. Our focus will be on biosimilar proteins, pointing out certain cases where its use is probably essential. Based partly on literature data, and partly on our own hands-on experience, this paper is intended to be a guide for choosing the proper NMR approach for analytical questions concerning the structural comparability of therapeutic proteins, monitoring technology-related impurities, protein quantification, analysis of spent media, identification of extractable and leachable components, etc. Also, we focus on critical considerations, particularly those coming from drug authority guidelines, which limit the use of the well-established NMR tools in everyday practice.
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Affiliation(s)
- Róbert Kiss
- Gedeon Richter Plc, Hungary; Spectroscopic Research Department, Hungary
| | - Ádám Fizil
- Gedeon Richter Plc, Hungary; Analytical Department of Biotechnology, Hungary
| | - Csaba Szántay
- Gedeon Richter Plc, Hungary; Spectroscopic Research Department, Hungary.
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13
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Pan X, Streefland M, Dalm C, Wijffels RH, Martens DE. Selection of chemically defined media for CHO cell fed-batch culture processes. Cytotechnology 2017; 69:39-56. [PMID: 27900626 PMCID: PMC5264622 DOI: 10.1007/s10616-016-0036-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/26/2016] [Indexed: 01/17/2023] Open
Abstract
Two CHO cell clones derived from the same parental CHOBC® cell line and producing the same monoclonal antibody (BC-G, a low producing clone; BC-P, a high producing clone) were tested in four basal media in all possible combinations with three feeds (=12 conditions) in fed-batch cultures. Higher amino acid feeding did not always lead to higher mAb production. The two clones showed differences in cell physiology, metabolism and optimal medium-feed combinations. During the phase transitions of all cultures, cell metabolism showed a shift represented by lower specific consumption and production rates, except for the specific glucose consumption rate in cultures fed by Actifeed A/B. The BC-P clone fed by Actifeed A/B showed a threefold cell volume increase and an increase of the specific consumption rate of glucose in the stationary phase. Since feeding was based on glucose this resulted in accumulation of amino acids for this feed, while this did not occur for the poorer feed (EFA/B). The same feed also led to an increase of cell size for the BC-G clone, but to a lesser extent.
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Affiliation(s)
- Xiao Pan
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Mathieu Streefland
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Ciska Dalm
- Synthon Biopharmaceuticals BV, Upstream Process Development, PO Box 7071, 6503 GN, Nijmegen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Dirk E Martens
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
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14
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Solution state nuclear magnetic resonance spectroscopy for biological metabolism and pathway intermediate analysis. Essays Biochem 2016; 60:419-428. [PMID: 27980092 DOI: 10.1042/ebc20160044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 11/17/2022]
Abstract
Using nuclear magnetic resonance (NMR) spectroscopy in the study of metabolism has been immensely popular in medical- and health-related research but has yet to be widely applied to more fundamental biological problems. This review provides some NMR background relevant to metabolism, describes why 1H NMR spectra are complex as well as introducing relevant terminology and definitions. The applications and practical considerations of NMR metabolic profiling and 13C NMR-based flux analyses are discussed together with the elegant 'enzyme trap' approach for identifying novel metabolic pathway intermediates. The importance of sample preparation and data analysis are also described and explained with reference to data precision and multivariate analysis to introduce researchers unfamiliar with NMR and metabolism to consider this technique for their research interests. Finally, a brief glance into the future suggests NMR-based metabolism has room to expand in the 21st century through new isotope labels, and NMR technologies and methodologies.
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Pan X, Streefland M, Dalm C, Wijffels RH, Martens DE. Selection of chemically defined media for CHO cell fed-batch culture processes. Cytotechnology 2016. [PMID: 27900626 DOI: 10.1007/s10616‐016‐0036‐5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Two CHO cell clones derived from the same parental CHOBC® cell line and producing the same monoclonal antibody (BC-G, a low producing clone; BC-P, a high producing clone) were tested in four basal media in all possible combinations with three feeds (=12 conditions) in fed-batch cultures. Higher amino acid feeding did not always lead to higher mAb production. The two clones showed differences in cell physiology, metabolism and optimal medium-feed combinations. During the phase transitions of all cultures, cell metabolism showed a shift represented by lower specific consumption and production rates, except for the specific glucose consumption rate in cultures fed by Actifeed A/B. The BC-P clone fed by Actifeed A/B showed a threefold cell volume increase and an increase of the specific consumption rate of glucose in the stationary phase. Since feeding was based on glucose this resulted in accumulation of amino acids for this feed, while this did not occur for the poorer feed (EFA/B). The same feed also led to an increase of cell size for the BC-G clone, but to a lesser extent.
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Affiliation(s)
- Xiao Pan
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Mathieu Streefland
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Ciska Dalm
- Synthon Biopharmaceuticals BV, Upstream Process Development, PO Box 7071, 6503 GN, Nijmegen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands.,Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Dirk E Martens
- Bioprocess Engineering, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
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Agarabi CD, Chavez BK, Lute SC, Read EK, Rogstad S, Awotwe-Otoo D, Brown MR, Boyne MT, Brorson KA. Exploring the linkage between cell culture process parameters and downstream processing utilizing a plackett-burman design for a model monoclonal antibody. Biotechnol Prog 2016; 33:163-170. [DOI: 10.1002/btpr.2402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/16/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Cyrus D. Agarabi
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Brittany K. Chavez
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Scott C. Lute
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Erik K. Read
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Sarah Rogstad
- Div. of Pharmaceutical Analysis; Office of Testing and Research, OPQ, CDER, FDA; Silver Spring MD
| | - David Awotwe-Otoo
- Div. of Post Marketing Activities II; OPQ, CDER, FDA; Silver Spring MD
| | - Matthew R. Brown
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Michael T. Boyne
- Div. of Pharmaceutical Analysis; Office of Testing and Research, OPQ, CDER, FDA; Silver Spring MD
| | - Kurt A. Brorson
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
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Bhatia H, Read E, Agarabi C, Brorson K, Lute S, Yoon S. Hybridoma cell-culture and glycan profile dataset at various bioreactor conditions. Data Brief 2016; 9:676-678. [PMID: 27790631 PMCID: PMC5071535 DOI: 10.1016/j.dib.2016.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/21/2016] [Accepted: 10/05/2016] [Indexed: 11/15/2022] Open
Abstract
This is an “11 factor-2 level-12 run” Plackett-Burman experimental design dataset. The dataset includes 11 engineering bioreactor parameters as input variables. These 11 factors were varied at 2 levels and 23 response variables that are glycan profile attributes, were measured “A Design Space Exploration for Control of Critical Quality Attributes of mAb” (H. Bhatia, E.K. Read, C.D. Agarabi, K.A. Brorson, S.C. Lute, S. Yoon S, 2016) [2].
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Affiliation(s)
- Hemlata Bhatia
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, USA
| | - Erik Read
- Division II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA, Silver Springs, MD, USA
| | - Cyrus Agarabi
- Division II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA, Silver Springs, MD, USA
| | - Kurt Brorson
- Division II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA, Silver Springs, MD, USA
| | - Scott Lute
- Division II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA, Silver Springs, MD, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, USA
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18
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A design space exploration for control of Critical Quality Attributes of mAb. Int J Pharm 2016; 512:242-252. [DOI: 10.1016/j.ijpharm.2016.08.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 08/15/2016] [Accepted: 08/24/2016] [Indexed: 01/19/2023]
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19
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An omics approach to rational feed. J Biotechnol 2016; 234:127-138. [DOI: 10.1016/j.jbiotec.2016.07.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 07/12/2016] [Accepted: 07/29/2016] [Indexed: 12/23/2022]
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20
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Reimonn TM, Park SY, Agarabi CD, Brorson KA, Yoon S. Effect of amino acid supplementation on titer and glycosylation distribution in hybridoma cell cultures-Systems biology-based interpretation using genome-scale metabolic flux balance model and multivariate data analysis. Biotechnol Prog 2016; 32:1163-1173. [PMID: 27452371 DOI: 10.1002/btpr.2335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/17/2016] [Indexed: 01/24/2023]
Abstract
Genome-scale flux balance analysis (FBA) is a powerful systems biology tool to characterize intracellular reaction fluxes during cell cultures. FBA estimates intracellular reaction rates by optimizing an objective function, subject to the constraints of a metabolic model and media uptake/excretion rates. A dynamic extension to FBA, dynamic flux balance analysis (DFBA), can calculate intracellular reaction fluxes as they change during cell cultures. In a previous study by Read et al. (2013), a series of informed amino acid supplementation experiments were performed on twelve parallel murine hybridoma cell cultures, and this data was leveraged for further analysis (Read et al., Biotechnol Prog. 2013;29:745-753). In order to understand the effects of media changes on the model murine hybridoma cell line, a systems biology approach is applied in the current study. Dynamic flux balance analysis was performed using a genome-scale mouse metabolic model, and multivariate data analysis was used for interpretation. The calculated reaction fluxes were examined using partial least squares and partial least squares discriminant analysis. The results indicate media supplementation increases product yield because it raises nutrient levels extending the growth phase, and the increased cell density allows for greater culture performance. At the same time, the directed supplementation does not change the overall metabolism of the cells. This supports the conclusion that product quality, as measured by glycoform assays, remains unchanged because the metabolism remains in a similar state. Additionally, the DFBA shows that metabolic state varies more at the beginning of the culture but less by the middle of the growth phase, possibly due to stress on the cells during inoculation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1163-1173, 2016.
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Affiliation(s)
- Thomas M Reimonn
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell
| | - Seo-Young Park
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell
| | - Cyrus D Agarabi
- Division II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA, Silver Springs, MD, USA
| | - Kurt A Brorson
- Division II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER, FDA, Silver Springs, MD, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell.
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21
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Improved Stability of a Model IgG3 by DoE-Based Evaluation of Buffer Formulations. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2074149. [PMID: 27042659 PMCID: PMC4794585 DOI: 10.1155/2016/2074149] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/20/2015] [Accepted: 11/29/2015] [Indexed: 02/03/2023]
Abstract
Formulating appropriate storage conditions for biopharmaceutical proteins is essential for ensuring their stability and thereby their purity, potency, and safety over their shelf-life. Using a model murine IgG3 produced in a bioreactor system, multiple formulation compositions were systematically explored in a DoE design to optimize the stability of a challenging antibody formulation worst case. The stability of the antibody in each buffer formulation was assessed by UV/VIS absorbance at 280 nm and 410 nm and size exclusion high performance liquid chromatography (SEC) to determine overall solubility, opalescence, and aggregate formation, respectively. Upon preliminary testing, acetate was eliminated as a potential storage buffer due to significant visible precipitate formation. An additional 24 full factorial DoE was performed that combined the stabilizing effect of arginine with the buffering capacity of histidine. From this final DoE, an optimized formulation of 200 mM arginine, 50 mM histidine, and 100 mM NaCl at a pH of 6.5 was identified to substantially improve stability under long-term storage conditions and after multiple freeze/thaw cycles. Thus, our data highlights the power of DoE based formulation screening approaches even for challenging monoclonal antibody molecules.
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22
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Zalai D, Hevér H, Lovász K, Molnár D, Wechselberger P, Hofer A, Párta L, Putics Á, Herwig C. A control strategy to investigate the relationship between specific productivity and high-mannose glycoforms in CHO cells. Appl Microbiol Biotechnol 2016; 100:7011-24. [PMID: 26910040 PMCID: PMC4947490 DOI: 10.1007/s00253-016-7380-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/26/2022]
Abstract
The integration of physiological knowledge into process control strategies is a cornerstone for the improvement of biopharmaceutical cell culture technologies. The present contribution investigates the applicability of specific productivity as a physiological control parameter in a cell culture process producing a monoclonal antibody (mAb) in CHO cells. In order to characterize cell physiology, the on-line oxygen uptake rate (OUR) was monitored and the time-resolved specific productivity was calculated as physiological parameters. This characterization enabled to identify the tight link between the deprivation of tyrosine and the decrease in cell respiration and in specific productivity. Subsequently, this link was used to control specific productivity by applying different feeding profiles. The maintenance of specific productivity at various levels enabled to identify a correlation between the rate of product formation and the relative abundance of high-mannose glycoforms. An increase in high mannose content was assumed to be the result of high specific productivity. Furthermore, the high mannose content as a function of cultivation pH and specific productivity was investigated in a design of experiment approach. This study demonstrated how physiological parameters could be used to understand interactions between process parameters, physiological parameters, and product quality attributes.
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Affiliation(s)
- Dénes Zalai
- Department of Biotechnology, Gedeon Richter Plc., 19-21, Gyömrői út, Budapest, 1103, Hungary.,Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Helga Hevér
- Spectroscopic Research Department, Gedeon Richter Plc., 19-21, Gyömrői út, Budapest, 1103, Hungary
| | - Krisztina Lovász
- Department of Biotechnology, Gedeon Richter Plc., 19-21, Gyömrői út, Budapest, 1103, Hungary
| | - Dóra Molnár
- Department of Biotechnology, Gedeon Richter Plc., 19-21, Gyömrői út, Budapest, 1103, Hungary
| | - Patrick Wechselberger
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.,CD Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
| | - Alexandra Hofer
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - László Párta
- Department of Biotechnology, Gedeon Richter Plc., 19-21, Gyömrői út, Budapest, 1103, Hungary
| | - Ákos Putics
- Department of Biotechnology, Gedeon Richter Plc., 19-21, Gyömrői út, Budapest, 1103, Hungary
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria. .,CD Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria.
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23
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Rathore AS, Singh SK. Production of Protein Therapeutics in the Quality by Design (QbD) Paradigm. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2015_5004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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24
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Torkashvand F, Vaziri B, Maleknia S, Heydari A, Vossoughi M, Davami F, Mahboudi F. Designed Amino Acid Feed in Improvement of Production and Quality Targets of a Therapeutic Monoclonal Antibody. PLoS One 2015; 10:e0140597. [PMID: 26480023 PMCID: PMC4610691 DOI: 10.1371/journal.pone.0140597] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/27/2015] [Indexed: 11/18/2022] Open
Abstract
Cell culture feeds optimization is a critical step in process development of pharmaceutical recombinant protein production. Amino acids are the basic supplements of mammalian cell culture feeds with known effect on their growth promotion and productivity. In this study, we reported the implementation of the Plackett-Burman (PB) multifactorial design to screen the effects of amino acids on the growth promotion and productivity of a Chinese hamster ovary DG-44 (CHO-DG44) cell line producing bevacizumab. After this screening, the amino acid combinations were optimized by the response surface methodology (RSM) to determine the most effective concentration in feeds. Through this strategy, the final monoclonal antibody (mAb) titre was enhanced by 70%, compared to the control group. For this particular cell line, aspartic acid, glutamic acid, arginine and glycine had the highest positive effects on the final mAb titre. Simultaneously, the impact of the designed amino acid feed on some critical quality attributes of bevacizumab was examined in the group with highest productivity. The product was analysed for N-glycan profiles, charge variant distribution, and low molecular weight forms. The results showed that the target product quality has been improved using this feeding strategy. It was shown how this strategy could significantly diminish the time and number of experiments in identifying the most effective amino acids and related concentrations in target product enhancement. This model could be successfully applied to other components of culture media and feeds.
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Affiliation(s)
| | - Behrouz Vaziri
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- * E-mail: (BV); (FM)
| | - Shayan Maleknia
- Process Development Department, Aryogen Biopharma Inc., Alborz, Iran
| | - Amir Heydari
- Department of Chemical & Petroleum Engineering, Biochemical & Bioenvironmental Research Center Sharif University of Technology, Tehran, Iran
| | - Manouchehr Vossoughi
- Department of Chemical & Petroleum Engineering, Biochemical & Bioenvironmental Research Center Sharif University of Technology, Tehran, Iran
| | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fereidoun Mahboudi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- * E-mail: (BV); (FM)
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25
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Wu H, Read E, White M, Chavez B, Brorson K, Agarabi C, Khan M. Real time monitoring of bioreactor mAb IgG3 cell culture process dynamics via Fourier transform infrared spectroscopy: Implications for enabling cell culture process analytical technology. Front Chem Sci Eng 2015. [DOI: 10.1007/s11705-015-1533-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Sokolenko S, Aucoin MG. A correction method for systematic error in (1)H-NMR time-course data validated through stochastic cell culture simulation. BMC SYSTEMS BIOLOGY 2015; 9:51. [PMID: 26335002 PMCID: PMC4558828 DOI: 10.1186/s12918-015-0197-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/13/2015] [Indexed: 01/24/2023]
Abstract
Background The growing ubiquity of metabolomic techniques has facilitated high frequency time-course data collection for an increasing number of applications. While the concentration trends of individual metabolites can be modeled with common curve fitting techniques, a more accurate representation of the data needs to consider effects that act on more than one metabolite in a given sample. To this end, we present a simple algorithm that uses nonparametric smoothing carried out on all observed metabolites at once to identify and correct systematic error from dilution effects. In addition, we develop a simulation of metabolite concentration time-course trends to supplement available data and explore algorithm performance. Although we focus on nuclear magnetic resonance (NMR) analysis in the context of cell culture, a number of possible extensions are discussed. Results Realistic metabolic data was successfully simulated using a 4-step process. Starting with a set of metabolite concentration time-courses from a metabolomic experiment, each time-course was classified as either increasing, decreasing, concave, or approximately constant. Trend shapes were simulated from generic functions corresponding to each classification. The resulting shapes were then scaled to simulated compound concentrations. Finally, the scaled trends were perturbed using a combination of random and systematic errors. To detect systematic errors, a nonparametric fit was applied to each trend and percent deviations calculated at every timepoint. Systematic errors could be identified at time-points where the median percent deviation exceeded a threshold value, determined by the choice of smoothing model and the number of observed trends. Regardless of model, increasing the number of observations over a time-course resulted in more accurate error estimates, although the improvement was not particularly large between 10 and 20 samples per trend. The presented algorithm was able to identify systematic errors as small as 2.5 % under a wide range of conditions. Conclusion Both the simulation framework and error correction method represent examples of time-course analysis that can be applied to further developments in 1H-NMR methodology and the more general application of quantitative metabolomics. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0197-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stanislav Sokolenko
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, N2L 3G1, ON, Canada
| | - Marc G Aucoin
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, N2L 3G1, ON, Canada.
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27
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Rathore AS, Kumar Singh S, Pathak M, Read EK, Brorson KA, Agarabi CD, Khan M. Fermentanomics: Relating quality attributes of a monoclonal antibody to cell culture process variables and raw materials using multivariate data analysis. Biotechnol Prog 2015; 31:1586-99. [DOI: 10.1002/btpr.2155] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 07/24/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Anurag S. Rathore
- Dept. of Chemical Engineering; Indian Inst. of Technology; Hauz Khas New Delhi India
| | - Sumit Kumar Singh
- Dept. of Chemical Engineering; Indian Inst. of Technology; Hauz Khas New Delhi India
| | - Mili Pathak
- Dept. of Chemical Engineering; Indian Inst. of Technology; Hauz Khas New Delhi India
| | - Erik K. Read
- Div. of Monoclonal Antibodies; Office of Biotechnology Products, Food and Drug Administration; Silver Spring MD 20903
| | - Kurt A. Brorson
- Div. of Monoclonal Antibodies; Office of Biotechnology Products, Food and Drug Administration; Silver Spring MD 20903
| | - Cyrus D. Agarabi
- Div. of Product Quality Research; Office of Testing and Research, Food and Drug Administration; Silver Spring MD 20903
| | - Mansoor Khan
- Div. of Product Quality Research; Office of Testing and Research, Food and Drug Administration; Silver Spring MD 20903
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28
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Agarabi CD, Schiel JE, Lute SC, Chavez BK, Boyne MT, Brorson KA, Khan M, Read EK. Bioreactor process parameter screening utilizing a Plackett-Burman design for a model monoclonal antibody. J Pharm Sci 2015; 104:1919-1928. [PMID: 25762022 DOI: 10.1002/jps.24420] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/13/2015] [Accepted: 02/10/2015] [Indexed: 01/05/2023]
Abstract
Consistent high-quality antibody yield is a key goal for cell culture bioprocessing. This endpoint is typically achieved in commercial settings through product and process engineering of bioreactor parameters during development. When the process is complex and not optimized, small changes in composition and control may yield a finished product of less desirable quality. Therefore, changes proposed to currently validated processes usually require justification and are reported to the US FDA for approval. Recently, design-of-experiments-based approaches have been explored to rapidly and efficiently achieve this goal of optimized yield with a better understanding of product and process variables that affect a product's critical quality attributes. Here, we present a laboratory-scale model culture where we apply a Plackett-Burman screening design to parallel cultures to study the main effects of 11 process variables. This exercise allowed us to determine the relative importance of these variables and identify the most important factors to be further optimized in order to control both desirable and undesirable glycan profiles. We found engineering changes relating to culture temperature and nonessential amino acid supplementation significantly impacted glycan profiles associated with fucosylation, β-galactosylation, and sialylation. All of these are important for monoclonal antibody product quality.
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Affiliation(s)
- Cyrus D Agarabi
- Division of Product Quality Research, Office of Testing and Research, OPS, CDER, FDA, Silver Spring, Maryland
| | - John E Schiel
- Biomolecular Measurement Division, Bioanalytical Science Group, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Scott C Lute
- Division of Monoclonal Antibodies, Office of Biotechnology Products, OPS, CDER, FDA Silver Spring, Maryland
| | - Brittany K Chavez
- Division of Monoclonal Antibodies, Office of Biotechnology Products, OPS, CDER, FDA Silver Spring, Maryland
| | - Michael T Boyne
- Division of Pharmaceutical Analysis, Office of Testing and Research, OPS, CDER, FDA, St. Louis, Missouri
| | - Kurt A Brorson
- Division of Monoclonal Antibodies, Office of Biotechnology Products, OPS, CDER, FDA Silver Spring, Maryland
| | - Mansoora Khan
- Division of Product Quality Research, Office of Testing and Research, OPS, CDER, FDA, Silver Spring, Maryland.
| | - Erik K Read
- Division of Monoclonal Antibodies, Office of Biotechnology Products, OPS, CDER, FDA Silver Spring, Maryland
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29
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30
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Kyriakopoulos S, Kontoravdi C. A framework for the systematic design of fed-batch strategies in mammalian cell culture. Biotechnol Bioeng 2014; 111:2466-76. [PMID: 24975682 DOI: 10.1002/bit.25319] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 06/10/2014] [Accepted: 06/17/2014] [Indexed: 01/20/2023]
Abstract
A methodology to calculate the required amount of amino acids (a.a.) and glucose in feeds for animal cell culture from monitoring their levels in batch experiments is presented herein. Experiments with the designed feeds on an antibody-producing Chinese hamster ovary cell line resulted in a 3-fold increase in titer compared to batch culture. Adding 40% more nutrients to the same feed further increases the yield to 3.5 higher than in batch culture. Our results show that above a certain threshold there is no linear correlation between nutrient addition and the integral of viable cell concentration. In addition, although high ammonia levels hinder cell growth, they do not appear to affect specific antibody productivity, while we hypothesize that high extracellular lactate concentration is the cause for the metabolic shift towards lactate consumption for the cell line used. Overall, the performance of the designed feeds is comparable to that of a commercial feed that was tested in parallel. Expanding this approach to more nutrients, as well as changing the ratio of certain amino acids as informed by flux balance analysis, could achieve even higher yields.
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Affiliation(s)
- Sarantos Kyriakopoulos
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
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31
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Hmiel LK, Brorson KA, Boyne MT. Post-translational structural modifications of immunoglobulin G and their effect on biological activity. Anal Bioanal Chem 2014; 407:79-94. [DOI: 10.1007/s00216-014-8108-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/08/2014] [Accepted: 08/11/2014] [Indexed: 12/15/2022]
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32
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Xu P, Dai XP, Graf E, Martel R, Russell R. Effects of glutamine and asparagine on recombinant antibody production using CHO-GS cell lines. Biotechnol Prog 2014; 30:1457-68. [PMID: 25079388 DOI: 10.1002/btpr.1957] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 07/11/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Ping Xu
- Global Manufacturing and Supply, Bristol-Myers Squibb Company; 519 Route 173 West Bloomsbury NJ 08804
| | - Xiao-Ping Dai
- Global Manufacturing and Supply, Bristol-Myers Squibb Company; 519 Route 173 West Bloomsbury NJ 08804
| | - Erica Graf
- Global Manufacturing and Supply, Bristol-Myers Squibb Company; 519 Route 173 West Bloomsbury NJ 08804
| | - Richard Martel
- Global Manufacturing and Supply, Bristol-Myers Squibb Company; 519 Route 173 West Bloomsbury NJ 08804
| | - Reb Russell
- Global Manufacturing and Supply, Bristol-Myers Squibb Company; 519 Route 173 West Bloomsbury NJ 08804
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33
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Sokolenko S, Blondeel EJM, Azlah N, George B, Schulze S, Chang D, Aucoin MG. Profiling convoluted single-dimension proton NMR spectra: a Plackett-Burman approach for assessing quantification error of metabolites in complex mixtures with application to cell culture. Anal Chem 2014; 86:3330-7. [PMID: 24555717 DOI: 10.1021/ac4033966] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Single-dimension hydrogen, or proton, nuclear magnetic resonance spectroscopy (1D-(1)H NMR) has become an attractive option for characterizing the full range of components in complex mixtures of small molecular weight compounds due to its relative simplicity, speed, spectral reproducibility, and noninvasive sample preparation protocols compared to alternative methods. One challenge associated with this method is the overlap of NMR resonances leading to "convoluted" spectra. While this can be mitigated through "targeted profiling", there is still the possibility of increased quantification error. This work presents the application of a Plackett-Burman experimental design for the robust estimation of precision and accuracy of 1D-(1)H NMR compound quantification in synthetic mixtures, with application to mammalian cell culture supernatant. A single, 20 sample experiment was able to provide a sufficient estimate of bias and variability at different metabolite concentrations. Two major sources of bias were identified: incorrect interpretation of singlet resonances and the quantification of resonances from protons in close proximity to labile protons. Furthermore, decreases in measurement accuracy and precision could be observed with decreasing concentration for a small fraction of the components as a result of their particular convolution patterns. Finally, the importance of a priori concentration estimates is demonstrated through the example of interpreting acetate metabolite trends from a bioreactor cultivation of Chinese hamster ovary cells expressing a recombinant antibody.
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Affiliation(s)
- Stanislav Sokolenko
- Waterloo Institute for Nanotechnology, Department of Chemical Engineering, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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34
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Li B, Shanahan M, Calvet A, Leister KJ, Ryder AG. Comprehensive, quantitative bioprocess productivity monitoring using fluorescence EEM spectroscopy and chemometrics. Analyst 2014; 139:1661-71. [DOI: 10.1039/c4an00007b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Using fluorescence excitation-emission matrix spectroscopy and chemometric methods we demonstrate an effective and rapid method for quantitative monitoring of a mammalian cell culture based manufacturing process.
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Affiliation(s)
- Boyan Li
- Nanoscale Biophotonics Laboratory
- School of Chemistry
- National University of Ireland
- Galway, Ireland
| | - Michael Shanahan
- Nanoscale Biophotonics Laboratory
- School of Chemistry
- National University of Ireland
- Galway, Ireland
| | - Amandine Calvet
- Nanoscale Biophotonics Laboratory
- School of Chemistry
- National University of Ireland
- Galway, Ireland
| | - Kirk J. Leister
- Bristol-Myers Squibb
- Process Analytical Sciences
- Syracuse, USA
| | - Alan G. Ryder
- Nanoscale Biophotonics Laboratory
- School of Chemistry
- National University of Ireland
- Galway, Ireland
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