1
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Steimann T, Wollborn D, Röck F, Horstmann R, Schmitt E, Christ JJ, Blank LM, Büchs J. Investigation into struvite precipitation: A commonly encountered problem during fermentations on chemically defined media. Biotechnol Bioeng 2024; 121:1076-1089. [PMID: 38151908 DOI: 10.1002/bit.28633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/14/2023] [Accepted: 12/09/2023] [Indexed: 12/29/2023]
Abstract
Chemically defined mineral media are widely used in bioprocesses, as these show less batch to batch variation compared with complex media. Nonetheless, the recommended media formulations often lead to the formation of precipitants at elevated pH values. These precipitates are insoluble and reduce the availability of macronutrients to the cells, which can result in limiting growth rates and lower productivity. They can also damage equipment by clogging pipes, hoses, and spargers in stirred tank fermenters. In this study, the observed precipitate was analyzed via X-ray fluorescence spectroscopy and identified as the magnesium ammonium phosphate salt struvite (MgNH4 PO4 × 6H2 O). The solubility of struvite crystals is known to be extremely low, causing the macronutrients magnesium, phosphate, and ammonium to be bound in the struvite crystals. Here, it was shown that struvite precipitates can be redissolved under common fermentation conditions. Furthermore, it was found that the struvite particle size distribution has a significant effect on the dissolution kinetics, which directly affects macronutrient availability. At a certain particle size, struvite crystals rapidly dissolved and provided unlimiting growth conditions. Therefore, struvite formation should be considered during media and bioprocess development, to ensure that the dissolution kinetics of struvite are faster than the growth kinetics.
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Affiliation(s)
- Thomas Steimann
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - David Wollborn
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Florian Röck
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Rebekka Horstmann
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Elina Schmitt
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | | | - Lars Mathias Blank
- iAMB-Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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2
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Machleid R, Hoehse M, Scholze S, Mazarakis K, Nilsson D, Johansson E, Zehe C, Trygg J, Grimm C, Surowiec I. Feasibility and performance of cross-clone Raman calibration models in CHO cultivation. Biotechnol J 2024; 19:e2300289. [PMID: 38015079 DOI: 10.1002/biot.202300289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
Raman spectroscopy is widely used in monitoring and controlling cell cultivations for biopharmaceutical drug manufacturing. However, its implementation for culture monitoring in the cell line development stage has received little attention. Therefore, the impact of clonal differences, such as productivity and growth, on the prediction accuracy and transferability of Raman calibration models is not yet well described. Raman OPLS models were developed for predicting titer, glucose and lactate using eleven CHO clones from a single cell line. These clones exhibited diverse productivity and growth rates. The calibration models were evaluated for clone-related biases using clone-wise linear regression analysis on cross validated predictions. The results revealed that clonal differences did not affect the prediction of glucose and lactate, but titer models showed a significant clone-related bias, which remained even after applying variable selection methods. The bias was associated with clonal productivity and lead to increased prediction errors when titer models were transferred to cultivations with productivity levels outside the range of their training data. The findings demonstrate the feasibility of Raman-based monitoring of glucose and lactate in cell line development with high accuracy. However, accurate titer prediction requires careful consideration of clonal characteristics during model development.
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Affiliation(s)
- Rafael Machleid
- Sartorius Stedim Biotech GmbH, Göttingen, Germany
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Marek Hoehse
- Sartorius Stedim Biotech GmbH, Göttingen, Germany
| | | | | | - David Nilsson
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | | | | | - Johan Trygg
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
- Sartorius Corporate Research, Umeå, Sweden
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3
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Cordova LT, Dahodwala H, Cooley R, Lee KH. Prediction of CHO cell line stability using expression of DNA repair genes. Biotechnol J 2024; 19:e2300425. [PMID: 37970758 DOI: 10.1002/biot.202300425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/25/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023]
Abstract
Chinese hamster ovary (CHO) cells are essential to biopharmaceutical manufacturing and production instability, the loss of productivity over time, is a long-standing challenge in the industry. Accurate prediction of cell line stability could enable efficient screening to identify clones suitable for manufacturing saving significant time and costs. DNA repair genes may offer biomarkers to address this need. In this study, over 40 cell lines representing various host lineages from three companies/organizations were evaluated for expression of five DNA repair genes (Fam35a, Lig4, Palb2, Pari, and Xrcc6). Expression measured in cells with less than 30 population doubling levels (PDLs) was correlated to stability profiles at 60+ PDL. Principal component analysis identified markers which separate stable and unstable CHO-DG44 cell lines. Notably, two genes, Lig4 and Xrcc6, showed higher expression in unstable CHO-DG44 cell lines with copy number loss identified as the mechanism of production instability. Expression levels across all cell ages showed lower DNA repair gene expression was associated with increased cell age. Collectively, DNA repair genes provide critical insight into long-term behavior of CHO cells and their expression levels have potential to predict cell line stability in certain cases.
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Affiliation(s)
- Lauren T Cordova
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Hussain Dahodwala
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- National Institute for Innovation in Manufacturing Biopharmaceuticals, Newark, Delaware, USA
| | - Rebecca Cooley
- Pfizer, Inc, 875 Chesterfield Pkwy W, Chesterfield, Missouri, USA
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- National Institute for Innovation in Manufacturing Biopharmaceuticals, Newark, Delaware, USA
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4
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Torres AJ. Robust method for chromatogram shape analysis to improve early detection of performance drifts and adverse changes in process parameters during purification column operations. Biotechnol J 2024; 19:e2300271. [PMID: 38012961 DOI: 10.1002/biot.202300271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023]
Abstract
The biopharmaceutical industry is under increased pressure to maximize efficiency, enhance quality compliance, and reduce the cost of drug substance manufacturing. Ways to reduce costs associated with manufacturing of complex biological molecules include maximizing efficiency of chromatography purification steps. For example, process analytical technology (PAT) tools can be employed to improve column resin life, prevent column operating failures, and decrease the time it takes to solve investigations of process deviations. We developed a robust method to probe the shape of the chromatogram for indications of column failure or detrimental changes in the process. The approach herein utilizes raw data obtained from manufacturing followed by a pre-processing routine to align chromatograms and patch together the different chromatogram phases in preparation for multivariate analysis. A principal component analysis (PCA) was performed on the standardized chromatograms to compare different batches, and resulted in the identification specific process change that affected the profile. In addition, changes in the chromatogram peaks were used to create predictive models for impurity clearance. This approach has the potential for early detection of column processing issues, improving timely resolution in large-scale chromatographic operations.
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Affiliation(s)
- Alexis J Torres
- Manufacturing Science and Technology, Pfizer Inc, Sanford, North Carolina, USA
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5
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Chauhan S, Khasa YP. Challenges and Opportunities in the Process Development of Chimeric Vaccines. Vaccines (Basel) 2023; 11:1828. [PMID: 38140232 PMCID: PMC10747103 DOI: 10.3390/vaccines11121828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/22/2023] [Accepted: 08/04/2023] [Indexed: 12/24/2023] Open
Abstract
Vaccines are integral to human life to protect them from life-threatening diseases. However, conventional vaccines often suffer limitations like inefficiency, safety concerns, unavailability for non-culturable microbes, and genetic variability among pathogens. Chimeric vaccines combine multiple antigen-encoding genes of similar or different microbial strains to protect against hyper-evolving drug-resistant pathogens. The outbreaks of dreadful diseases have led researchers to develop economical chimeric vaccines that can cater to a large population in a shorter time. The process development begins with computationally aided omics-based approaches to design chimeric vaccines. Furthermore, developing these vaccines requires optimizing upstream and downstream processes for mass production at an industrial scale. Owing to the complex structures and complicated bioprocessing of evolving pathogens, various high-throughput process technologies have come up with added advantages. Recent advancements in high-throughput tools, process analytical technology (PAT), quality-by-design (QbD), design of experiments (DoE), modeling and simulations, single-use technology, and integrated continuous bioprocessing have made scalable production more convenient and economical. The paradigm shift to innovative strategies requires significant attention to deal with major health threats at the global scale. This review outlines the challenges and emerging avenues in the bioprocess development of chimeric vaccines.
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Affiliation(s)
| | - Yogender Pal Khasa
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India;
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6
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Biermann R, Beutel S. Endospore production of Bacillus spp. for industrial use. Eng Life Sci 2023; 23:e2300013. [PMID: 37970521 PMCID: PMC10630785 DOI: 10.1002/elsc.202300013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/02/2023] [Accepted: 10/05/2023] [Indexed: 11/17/2023] Open
Abstract
The increased occurrence of antibiotic resistance and the harmful use of pesticides are a major problem of modern times. A ban on the use of antibiotics as growth promoters in animal breeding has put a focus on the probiotics market. Probiotic food supplements are versatile and show promising results in animal and human nutrition. Chemical pesticides can be substituted by biopesticides, which are very effective against various pests in plants due to increased research. What these fields have in common is the use of spore-forming bacteria. The endospore-forming Bacillus spp. belonging to this group offer an effective solution to the aforementioned problems. Therefore, the biotechnological production of sufficient qualities of such endospores has become an innovative and financially viable field of research. In this review, the production of different Bacillus spp. endospores will be reviewed. For this purpose, the media compositions, cultivation conditions and bioprocess optimization methods of the last 20 years are presented and reflected.
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Affiliation(s)
- Riekje Biermann
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Sascha Beutel
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
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7
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Biermann R, Rösner L, Beyer L, Niemeyer L, Beutel S. Bioprocess development for endospore production by Bacillus coagulans using an optimized chemically defined medium. Eng Life Sci 2023; 23:e2300210. [PMID: 37795343 PMCID: PMC10545977 DOI: 10.1002/elsc.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Abstract
Bacillus coagulans is a promising probiotic, because it combines probiotic properties of Lactobacillus and the ability of Bacillus to form endospores. Due to this hybrid relationship, cultivation of this organism is challenging. As the probiotics market continues to grow, there is a new focus on the production of these microorganisms. In this work, a strain-specific bioprocess for B. coagulans was developed to support growth on one hand and ensure sporulation on the other hand. This circumstance is not trivial, since these two metabolic states are contrary. The developed bioprocess uses a modified chemically defined medium which was further investigated in a one-factor-at-a-time assay after adaptation. A transfer from the shake flask to the bioreactor was successfully demonstrated in the scope of this work. The investigated process parameters included temperature, agitation and pH-control. Especially the pH-control improved the sporulation in the bioreactor when compared to shake flasks. The bioprocess resulted in a sporulation efficiency of 80%-90%. This corresponds to a sevenfold increase in sporulation efficiency due to a transfer to the bioreactor with pH-control. Additionally, a design of experiment (DoE) was conducted to test the robustness of the bioprocess. This experiment validated the beforementioned sporulation efficiency for the developed bioprocess. Afterwards the bioprocess was then scaled up from a 1 L scale to a 10 L bioreactor scale. A comparable sporulation efficiency of 80% as in the small scale was achieved. The developed bioprocess facilitates the upscaling and application to an industrial scale, and can thus help meet the increasing market for probiotics.
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Affiliation(s)
- Riekje Biermann
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Laura Rösner
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Lisa‐Marie Beyer
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Laura Niemeyer
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Sascha Beutel
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
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8
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Dodia H, Sunder AV, Borkar Y, Wangikar PP. Precision fermentation with mass spectrometry-based spent media analysis. Biotechnol Bioeng 2023; 120:2809-2826. [PMID: 37272489 DOI: 10.1002/bit.28450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023]
Abstract
Optimization and monitoring of bioprocesses requires the measurement of several process parameters and quality attributes. Mass spectrometry (MS)-based techniques such as those coupled to gas chromatography (GCMS) and liquid Chromatography (LCMS) enable the simultaneous measurement of hundreds of metabolites with high sensitivity. When applied to spent media, such metabolome analysis can help determine the sequence of substrate uptake and metabolite secretion, consequently facilitating better design of initial media and feeding strategy. Furthermore, the analysis of metabolite diversity and abundance from spent media will aid the determination of metabolic phases of the culture and the identification of metabolites as surrogate markers for product titer and quality. This review covers the recent advances in metabolomics analysis applied to the development and monitoring of bioprocesses. In this regard, we recommend a stepwise workflow and guidelines that a bioprocesses engineer can adopt to develop and optimize a fermentation process using spent media analysis. Finally, we show examples of how the use of MS can revolutionize the design and monitoring of bioprocesses.
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Affiliation(s)
- Hardik Dodia
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | | | - Yogen Borkar
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- Clarity Bio Systems India Pvt. Ltd., Pune, India
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9
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Escandell J, Moura F, Carvalho SB, Silva RJS, Correia R, Roldão A, Gomes-Alves P, Alves PM. Towards a scalable bioprocess for rAAV production using a HeLa stable cell line. Biotechnol Bioeng 2023; 120:2578-2587. [PMID: 37027346 DOI: 10.1002/bit.28394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 04/08/2023]
Abstract
The majority of recombinant adeno-associated viruses (rAAV) approved for clinical use or in clinical trials areproduced by transient transfection using the HEK293 cell line. However, this platform has several manufacturing bottlenecks at commercial scales namely, low product quality (full to empty capsid ratio <20% in most rAAV serotypes), lower productivities obtained after scale-up and the high cost of raw materials, in particular of Good Manufacturing Practice grade plasmid DNA required for transfection. The HeLa-based stable cell line rAAV production system provides a robust and scalable alternative to transient transfection systems. Nevertheless, the time required to generate the producer cell lines combined with the complexity of rAAV production and purification processes still pose several barriers to the use of this platform as a suitable alternative to the HEK293 transient transfection. In this work we streamlined the cell line development and bioprocessing for the HeLaS3-based production of rAAV. By exploring this optimized approach, producer cell lines were generated in 3-4 months, and presented rAAV2 volumetric production (bulk) > 3 × 1011 vg/mL and full to empty capsids ratio (>70%) at 2 L bioreactor scale. Moreover, the established downstream process, based on ion exchange and affinity-based chromatography, efficiently eliminated process related impurities, including the Adenovirus 5 helper virus required for production with a log reduction value of 9. Overall, we developed a time-efficient and robust rAAV bioprocess using a stable producer cell line achieving purified rAAV2 yields > 1 × 1011 vg/mL. This optimized platform may address manufacturing challenges for rAAV based medicines.
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Affiliation(s)
- José Escandell
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipa Moura
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia B Carvalho
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo J S Silva
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo Correia
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Antonio Roldão
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Patrícia Gomes-Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paula M Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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10
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Moço PD, Xu X, Silva CAT, Kamen AA. Production of adeno-associated viral vector serotype 6 by triple transfection of suspension HEK293 cells at higher cell densities. Biotechnol J 2023; 18:e2300051. [PMID: 37337925 DOI: 10.1002/biot.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]
Abstract
In recent years, the use of adeno-associated viruses (AAVs) as vectors for gene and cell therapy has increased, leading to a rise in the amount of AAV vectors required during pre-clinical and clinical trials. AAV serotype 6 (AAV6) has been found to be efficient in transducing different cell types and has been successfully used in gene and cell therapy protocols. However, the number of vectors required to effectively deliver the transgene to one single cell has been estimated at 106 viral genomes (VG), making large-scale production of AAV6 necessary. Suspension cell-based platforms are currently limited to low cell density productions due to the widely reported cell density effect (CDE), which results in diminished production at high cell densities and decreased cell-specific productivity. This limitation hinders the potential of the suspension cell-based production process to increase yields. In this study, we investigated the improvement of the production of AAV6 at higher cell densities by transiently transfecting HEK293SF cells. The results showed that when the plasmid DNA was provided on a cell basis, the production could be carried out at medium cell density (MCD, 4 × 106 cells mL-1 ) resulting in titers above 1010 VG mL-1 . No detrimental effects on cell-specific virus yield or cell-specific functional titer were observed at MCD production. Furthermore, while medium supplementation alleviated the CDE in terms of VG/cell at high cell density (HCD, 10 × 106 cells mL-1 ) productions, the cell-specific functional titer was not maintained, and further studies are necessary to understand the observed limitations for AAV production in HCD processes. The MCD production method reported here lays the foundation for large-scale process operations, potentially solving the current vector shortage in AAV manufacturing.
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Affiliation(s)
- Pablo D Moço
- Department of Bioengineering, McGill University, Montreal, Canada
| | - Xingge Xu
- Department of Bioengineering, McGill University, Montreal, Canada
| | - Cristina A T Silva
- Department of Bioengineering, McGill University, Montreal, Canada
- Department of Chemical Engineering, Polytechnique Montréal, Montreal, Canada
| | - Amine A Kamen
- Department of Bioengineering, McGill University, Montreal, Canada
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11
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Wowra K, Hegel E, Scharf A, Grünberger A, Rosenthal K. Estimating environmental impacts of early-stage bioprocesses. Trends Biotechnol 2023; 41:1199-1212. [PMID: 37188575 DOI: 10.1016/j.tibtech.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/09/2023] [Accepted: 03/15/2023] [Indexed: 05/17/2023]
Abstract
The use of bioprocesses in industrial production promises resource- and energy-efficient processes starting from renewable, nonfossil feedstocks. Thus, the environmental benefits must be demonstrated, ideally in the early development phase with standardized methods such as life cycle assessment (LCA). Herein we discuss selected LCA studies of early-stage bioprocesses, highlighting their potential and contribution to estimating environmental impacts and decision support in bioprocess development. However, LCAs are rarely performed among bioprocess engineers due to challenges such as data availability and process uncertainties. To address this issue, recommendations are provided for conducting LCAs of early-stage bioprocesses. Opportunities are identified to facilitate future applicability, for example, by establishing dedicated bioprocess databases that could enable the use of LCAs as standard tools for bioprocess engineers.
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Affiliation(s)
- Karoline Wowra
- Subdivision Biotechnology, Dechema e.V., Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Esther Hegel
- Subdivision Biotechnology, Dechema e.V., Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Andreas Scharf
- Subdivision Biotechnology, Dechema e.V., Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Alexander Grünberger
- Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katrin Rosenthal
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany.
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12
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Helleckes LM, Hemmerich J, Wiechert W, von Lieres E, Grünberger A. Machine learning in bioprocess development: from promise to practice. Trends Biotechnol 2023; 41:817-835. [PMID: 36456404 DOI: 10.1016/j.tibtech.2022.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022]
Abstract
Fostered by novel analytical techniques, digitalization, and automation, modern bioprocess development provides large amounts of heterogeneous experimental data, containing valuable process information. In this context, data-driven methods like machine learning (ML) approaches have great potential to rationally explore large design spaces while exploiting experimental facilities most efficiently. Herein we demonstrate how ML methods have been applied so far in bioprocess development, especially in strain engineering and selection, bioprocess optimization, scale-up, monitoring, and control of bioprocesses. For each topic, we will highlight successful application cases, current challenges, and point out domains that can potentially benefit from technology transfer and further progress in the field of ML.
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Affiliation(s)
- Laura M Helleckes
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; RWTH Aachen University, Templergraben 55, 52062 Aachen, Germany
| | - Johannes Hemmerich
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Wolfgang Wiechert
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; RWTH Aachen University, Templergraben 55, 52062 Aachen, Germany
| | - Eric von Lieres
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; RWTH Aachen University, Templergraben 55, 52062 Aachen, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; Institute of Process Engineering in Life Sciences, Section III: Microsystems in Bioprocess Engineering, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131, Karlsruhe, Germany.
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13
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Rish AJ, Siddiquee K, Huang Z, Xu J, Anderson CA, Borys MC, Khetan A. Strategies for Controlling Afucosylation in Monoclonal Antibodies during Upstream Manufacturing. Biotechnol J 2023:e2200604. [PMID: 37029472 DOI: 10.1002/biot.202200604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Core fucosylation is a highly prevalent and significant feature of N-glycosylation in therapeutic monoclonal antibodies produced by mammalian cells where its absence (afucosylation) plays a key role in treatment safety and efficacy. Notably, even slight changes in the level of afucosylation can have a considerable impact on the antibody-dependent cell-mediated cytotoxicity. Therefore, implementing control over afucosylation levels is important in upstream manufacturing to maintain consistent quality across batches of product, since standard downstream processing does not change afucosylation. In this review, the influences and strategies to control afucosylation are presented. In particular, there is emphasis on upstream manufacturing culture parameters and media supplementation, as these offer particular advantages as control strategies over alternative approaches such as cell line engineering and chemical inhibitors. The review discusses the relationship between the afucosylation influences and the underlying cellular metabolism to promote increased process understanding. Also, briefly highlighted is the value of empirical and mechanistic models in evaluating and designing control methods for core fucosylation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Adam J Rish
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, USA
| | - Khandaker Siddiquee
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Zhuangrong Huang
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Jianlin Xu
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA, USA
| | - Michael C Borys
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Anurag Khetan
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
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14
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Meng X, Liu Y, Yang L, Li R, Wang H, Shen Y, Wei D. Rational identification of a high catalytic efficiency leucine dehydrogenase and process development for efficient synthesis of l-phenylglycine. Biotechnol J 2023; 18:e2200465. [PMID: 36738237 DOI: 10.1002/biot.202200465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/01/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
Enzymatic asymmetric synthesis of chiral amino acids has great industrial potential. However, the low catalytic efficiency of high-concentration substrates limits their industrial application. Herein, using a combination of substrate catalytic efficiency prediction based on "open to closed" conformational change and substrate specificity prediction, a novel leucine dehydrogenase (TsLeuDH), with high substrate catalytic efficiency toward benzoylformic acid (BFA) for producing l-phenylglycine (l-Phg), was directly identified from 4695 putative leucine dehydrogenases in a public database. The specific activity of TsLeuDH was determined to be as high as 4253.8 U mg-1 . Through reaction process optimization, a high-concentration substrate (0.7 m) was efficiently and completely converted within 90 min in a single batch, without any external coenzyme addition. Moreover, a continuous flow-feeding approach was designed using gradient control of the feed rate to reduce substrate accumulation. Finally, the highest overall substrate concentration of up to 1.2 m BFA could be aminated to l-Phg with conversion of >99% in 3 h, demonstrating that this new combination of enzyme process development is promising for large-scale application of l-Phg.
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Affiliation(s)
- Xiangqi Meng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Lin Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Rui Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yaling Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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15
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Perelmuter K, Tiscornia I, Comini MA, Bollati-Fogolín M. Generation and Characterization of Stable Redox-Reporter Mammalian Cell Lines of Biotechnological Relevance. Sensors (Basel) 2022; 22:1324. [PMID: 35214226 DOI: 10.3390/s22041324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022]
Abstract
Cellular functions such as DNA replication and protein translation are influenced by changes in the intracellular redox milieu. Exogenous (i.e., nutrients, deterioration of media components, xenobiotics) and endogenous factors (i.e., metabolism, growth) may alter the redox homeostasis of cells. Thus, monitoring redox changes in real time and in situ is deemed essential for optimizing the production of recombinant proteins. Recently, different redox-sensitive variants of green fluorescent proteins (e.g., rxYFP, roGFP2, and rxmRuby2) have been engineered and proved suitable to detect, in a non-invasive manner, perturbations in the pool of reduced and oxidized glutathione, the major low molecular mass thiol in mammals. In this study, we validate the use of cytosolic rxYFP on two cell lines widely used in biomanufacturing processes, namely, CHO-K1 cells expressing the human granulocyte macrophage colony-stimulating factor (hGM-CSF) and HEK-293. Flow cytometry was selected as the read-out technique for rxYFP signal given its high-throughput and statistical robustness. Growth kinetics and cellular metabolism (glucose consumption, lactate and ammonia production) of the redox reporter cells were comparable to those of the parental cell lines. The hGM-CSF production was not affected by the expression of the biosensor. The redox reporter cell lines showed a sensitive and reversible response to different redox stimuli (reducing and oxidant reagents). Under batch culture conditions, a significant and progressive oxidation of the biosensor occurred when CHO-K1-hGM-CSF cells entered the late-log phase. Medium replenishment restored, albeit partially, the intracellular redox homeostasis. Our study highlights the utility of genetically encoded redox biosensors to guide metabolic engineering or intervention strategies aimed at optimizing cell viability, growth, and productivity.
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16
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Blombach B, Grünberger A, Centler F, Wierckx N, Schmid J. Exploiting unconventional prokaryotic hosts for industrial biotechnology. Trends Biotechnol 2021; 40:385-397. [PMID: 34482995 DOI: 10.1016/j.tibtech.2021.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
Developing cost-efficient biotechnological processes is a major challenge in replacing fossil-based industrial production processes. The remarkable progress in genetic engineering ensures efficient and fast tailoring of microbial metabolism for a wide range of bioconversions. However, improving intrinsic properties such as tolerance, handling, growth, and substrate consumption rates is still challenging. At the same time, synthetic biology tools are becoming easier applicable and transferable to nonmodel organisms. These trends have resulted in the exploitation of new and unconventional microbial systems with sophisticated properties, which render them promising hosts for the bio-based industry. Here, we highlight the metabolic and cellular capabilities of representative prokaryotic newcomers and discuss the potential and drawbacks of these hosts for industrial application.
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Affiliation(s)
- Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany; SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | | | - Florian Centler
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Nick Wierckx
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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17
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Sharma A, Noda M, Sugiyama M, Kaur B, Ahmad A. Metabolic Engineering of Pediococcus acidilactici BD16 for Heterologous Expression of Synthetic alaD Gene Cassette and L-Alanine Production in the Recombinant Strain Using Fed-Batch Fermentation. Foods 2021; 10:1964. [PMID: 34441741 DOI: 10.3390/foods10081964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/21/2022] Open
Abstract
Metabolic engineering substantially aims at the development of more efficient, robust and industrially competitive microbial strains for the potential applications in food, fermentation and pharmaceutical industries. An efficient lab scale bioprocess was developed for high level fermentative production of L-alanine using metabolically engineered Pediococcus acidilactici BD16 (alaD+). Computational biology tools assisted the designing of a synthetic alaD gene cassette, which was further cloned in shuttle vector pLES003 and expressed using an auto-inducible P289 promoter. Further, L-alanine production in the recombinant P. acidilactici BD16 (alaD+) strain was carried out using fed-batch fermentation under oxygen depression conditions, which significantly enhanced L-alanine levels. The recombinant strain expressing the synthetic alaD gene produced 229.12 g/L of L-alanine after 42 h of fed-batch fermentation, which is the second highest microbial L-alanine titer reported so far. After extraction and crystallization, 95% crystal L-alanine (217.54 g/L) was recovered from the culture broth with an enantiomeric purity of 97%. The developed bioprocess using recombinant P. acidilactici BD16 (alaD+) is suggested as the best alternative to chemical-based commercial synthesis of L-alanine for potential industrial applications.
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18
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Hutter C, von Stosch M, Cruz Bournazou MN, Butté A. Knowledge transfer across cell lines using hybrid Gaussian process models with entity embedding vectors. Biotechnol Bioeng 2021; 118:4389-4401. [PMID: 34383309 DOI: 10.1002/bit.27907] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/06/2021] [Accepted: 07/23/2021] [Indexed: 11/06/2022]
Abstract
To date, a large number of experiments are performed to develop a biochemical process. The generated data is used only once, to take decisions for development. Could we exploit data of already developed processes to make predictions for a novel process, we could significantly reduce the number of experiments needed. Processes for different products exhibit differences in behaviour, typically only a subset behave similar. Therefore, effective learning on multiple product spanning process data requires a sensible representation of the product identity. We propose to represent the product identity (a categorical feature) by embedding vectors that serve as input to a Gaussian process regression model. We demonstrate how the embedding vectors can be learned from process data and show that they capture an interpretable notion of product similarity. The improvement in performance is compared to traditional one-hot encoding on a simulated cross product learning task. All in all, the proposed method could render possible significant reductions in wet-lab experiments.
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Affiliation(s)
- Clemens Hutter
- DataHow AG, Zurich, Switzerland.,Chair for Mathematical Information Science, ETH Zurich
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19
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Tevelev B, Patel H, Shields K, Wei W, Cooley C, Zhang S, Bitzas G, Duan W, Khetemenee L, Jackobek R, D'Antona A, Sievers A, King A, Tam A, Zhang Y, Sousa E, Cohen J, Wroblewska L, Marshall J, Jackson M, Scarcelli JJ. Genetic rearrangement during site specific integration event facilitates cell line development of a bispecific molecule. Biotechnol Prog 2021; 37:e3158. [PMID: 33891804 PMCID: PMC8459265 DOI: 10.1002/btpr.3158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022]
Abstract
Site specific integration (SSI) expression systems offer robust means of generating highly productive and stable cell lines for traditional monoclonal antibodies. As complex modalities such as antibody‐like molecules comprised of greater than two peptides become more prevalent, greater emphasis needs to be placed on the ability to produce appreciable quantities of the correct product of interest (POI). The ability to screen several transcript stoichiometries could play a large role in ensuring high amounts of the correct POI. Here we illustrate implementation of an SSI expression system with a single site of integration for development and production of a multi‐chain, bi‐specific molecule. A SSI vector with a single copy of all of the genes of interest was initially selected for stable Chinese hamster ovary transfection. While the resulting transfection pools generated low levels of the desired heterodimer, utilizing an intensive clone screen strategy, we were able to identify clones having significantly higher levels of POI. In‐depth genotypic characterization of clones having the desirable phenotype revealed that a duplication of the light chain within the landing pad was responsible for producing the intended molecule. Retrospective transfection pool analysis using a vector configuration mimicking the transgene configuration found in the clones, as well as other vector configurations, yielded more favorable results with respect to % POI. Overall, the study demonstrated that despite the theoretical static nature of the SSI expression system, enough heterogeneity existed to yield clones having significantly different transgene phenotypes/genotypes and support production of a complex multi‐chain molecule.
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Affiliation(s)
- Barbara Tevelev
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Himakshi Patel
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Kathleen Shields
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Wei Wei
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Cecilia Cooley
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Sam Zhang
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | | | - Weili Duan
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Lam Khetemenee
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Ryan Jackobek
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Aaron D'Antona
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Annette Sievers
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Amy King
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Amy Tam
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Yan Zhang
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Eric Sousa
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Justin Cohen
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Lila Wroblewska
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Jeffrey Marshall
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Martha Jackson
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - John J Scarcelli
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
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20
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Castro LS, Lobo GS, Pereira P, Freire MG, Neves MC, Pedro AQ. Interferon-Based Biopharmaceuticals: Overview on the Production, Purification, and Formulation. Vaccines (Basel) 2021; 9:328. [PMID: 33915863 PMCID: PMC8065594 DOI: 10.3390/vaccines9040328] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022] Open
Abstract
The advent of biopharmaceuticals in modern medicine brought enormous benefits to the treatment of numerous human diseases and improved the well-being of many people worldwide. First introduced in the market in the early 1980s, the number of approved biopharmaceutical products has been steadily increasing, with therapeutic proteins, antibodies, and their derivatives accounting for most of the generated revenues. The success of pharmaceutical biotechnology is closely linked with remarkable developments in DNA recombinant technology, which has enabled the production of proteins with high specificity. Among promising biopharmaceuticals are interferons, first described by Isaacs and Lindenmann in 1957 and approved for clinical use in humans nearly thirty years later. Interferons are secreted autocrine and paracrine proteins, which by regulating several biochemical pathways have a spectrum of clinical effectiveness against viral infections, malignant diseases, and multiple sclerosis. Given their relevance and sustained market share, this review provides an overview on the evolution of interferon manufacture, comprising their production, purification, and formulation stages. Remarkable developments achieved in the last decades are herein discussed in three main sections: (i) an upstream stage, including genetically engineered genes, vectors, and hosts, and optimization of culture conditions (culture media, induction temperature, type and concentration of inducer, induction regimens, and scale); (ii) a downstream stage, focusing on single- and multiple-step chromatography, and emerging alternatives (e.g., aqueous two-phase systems); and (iii) formulation and delivery, providing an overview of improved bioactivities and extended half-lives and targeted delivery to the site of action. This review ends with an outlook and foreseeable prospects for underdeveloped aspects of biopharma research involving human interferons.
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Affiliation(s)
- Leonor S. Castro
- CICECO–Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (L.S.C.); (G.S.L.); (M.G.F.)
| | - Guilherme S. Lobo
- CICECO–Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (L.S.C.); (G.S.L.); (M.G.F.)
| | - Patrícia Pereira
- Centre for Mechanical Engineering, Materials and Processes, Department of Chemical Engineering, University of Coimbra, Rua Sílvio Lima-Polo II, 3030-790 Coimbra, Portugal;
| | - Mara G. Freire
- CICECO–Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (L.S.C.); (G.S.L.); (M.G.F.)
| | - Márcia C. Neves
- CICECO–Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (L.S.C.); (G.S.L.); (M.G.F.)
| | - Augusto Q. Pedro
- CICECO–Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (L.S.C.); (G.S.L.); (M.G.F.)
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21
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Feary M, Moffat MA, Casperson GF, Allen MJ, Young RJ. CHOK1SV GS-KO SSI expression system: A combination of the Fer1L4 locus and glutamine synthetase selection. Biotechnol Prog 2021; 37:e3137. [PMID: 33609084 DOI: 10.1002/btpr.3137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/03/2021] [Accepted: 02/07/2021] [Indexed: 12/11/2022]
Abstract
There are an ever-increasing number of biopharmaceutical candidates in clinical trials fueling an urgent need to streamline the cell line development process. A critical part of the process is the methodology used to generate and screen candidate cell lines compatible with GMP manufacturing processes. The relatively large amount of clone phenotypic variation observed from conventional "random integration" (RI)-based cell line construction is thought to be the result of a combination of the position variegation effect, genome plasticity and clonal variation. Site-specific integration (SSI) has been used by several groups to temper the influence of the position variegation effect and thus reduce variability in expression of biopharmaceutical candidates. Following on from our previous reports on the application of the Fer1L4 locus for SSI in CHOK1SV (10E9), we have combined this locus and a CHOK1SV glutamine synthetase knockout (GS-KO) host to create an improved expression system. The host, CHOK1SV GS-KO SSI (HD7876), was created by homology directed integration of a targetable landing pad flanked with incompatible Frt sequences in the Fer1L4 gene. The targeting vector contains a promoterless GS expression cassette and monoclonal antibody (mAb) expression cassettes, flanked by Frt sites compatible with equivalent sites flanking the landing pad in the host cell line. SSI clones expressing four antibody candidates, selected in a streamlined cell line development process, have mAb titers which rival RI (1.0-4.5 g/L) and robust expression stability (100% of clones stable through the 50 generation "manufacturing window" which supports commercial manufacturing at 12,000 L bioreactor scale).
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Affiliation(s)
- Marc Feary
- R&D Cell Engineering, Lonza Biologics, Little Chesterford, UK
| | - Mark A Moffat
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Gerald F Casperson
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Martin J Allen
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Robert J Young
- R&D Cell Engineering, Lonza Biologics, Little Chesterford, UK
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22
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Totaro D, Radoman B, Schmelzer B, Rothbauer M, Steiger MG, Mayr T, Sauer M, Ertl P, Mattanovich D. Microscale Perfusion-Based Cultivation for Pichia pastoris Clone Screening Enables Accelerated and Optimized Recombinant Protein Production Processes. Biotechnol J 2020; 16:e2000215. [PMID: 32935449 DOI: 10.1002/biot.202000215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/28/2020] [Indexed: 11/06/2022]
Abstract
Pichia pastoris has emerged in the past years as a promising host for recombinant protein and biopharmaceutical production. In the establishment of high cell density fed-batch biomanufacturing, screening phase and early bioprocess development (based on microplates and shake flasks) still represent a bottleneck due to high-cost and time-consuming procedures as well as low experiment complexity. In the present work, a screening protocol developed for P. pastoris clone selection is implemented in a multiplexed microfluidic device with 15 μL cultivation chambers able to operate in perfusion mode and monitor dissolved oxygen content in the culture in a non-invasive way. The setup allowed us to establish carbon-limited conditions and evaluate strain responses to different input variables. Results from micro-scale perfusion cultures are then compared with 1L fed-batch fermentation. The best producer in terms of titer and productivity is rapidly identified after 12 h from inoculation and the results confirmed by lab-scale fermentation. Moreover, the physiological analyses of the strains under different conditions suggested how more complex experimental conditions are achievable despite the relatively easy, straight-forward, and cost-effective experimental setup. Implementation and standardization of these micro-scale protocols could reduce the demand for lab-scale bioreactor cultivations thus accelerating the development of protein production processes.
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Affiliation(s)
- Damiano Totaro
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, Vienna, 1060, Austria
| | - Bojana Radoman
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bernhard Schmelzer
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Mario Rothbauer
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, Vienna, 1060, Austria
| | - Matthias G Steiger
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Getreidemarkt 9/166 A, Vienna, 1060, Austria
| | - Torsten Mayr
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9 / II + III, Graz, 8010, Austria
| | - Michael Sauer
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Ertl
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, Vienna, 1060, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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23
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Hamaker NK, Lee KH. A Site-Specific Integration Reporter System That Enables Rapid Evaluation of CRISPR/Cas9-Mediated Genome Editing Strategies in CHO Cells. Biotechnol J 2020; 15:e2000057. [PMID: 32500600 DOI: 10.1002/biot.202000057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/09/2020] [Indexed: 12/12/2022]
Abstract
Targeted gene knockout and site-specific integration (SSI) are powerful genome editing techniques to improve the development of industrially relevant Chinese hamster ovary (CHO) cell lines. However, past efforts to perform SSI in CHO cells are characterized by low efficiencies. Moreover, numerous strategies proposed to boost SSI efficiency in mammalian cell types have yet to be evaluated head to head or in combination to appreciably boost efficiencies in CHO. To enable systematic and rapid optimization of genome editing methods, the SSIGNAL (site-specific integration and genome alteration) reporter system is developed. This tool can analyze CRISPR (clustered regularly interspaced palindromic repeats)/Cas9 (CRISPR-associated protein 9)-mediated disruption activity alone or in conjunction with SSI efficiency. The reporter system uses green and red dual-fluorescence signals to indicate genotype states within four days following transfection, facilitating rapid data acquisition via standard flow cytometry instrumentation. In addition to describing the design and development of the system, two of its applications are demonstrated by first comparing transfection conditions to maximize CRISPR/Cas9 activity and subsequently assessing the efficiency of several promising SSI strategies. Due to its sensitivity and versatility, the SSIGNAL reporter system may serve as a tool to advance genome editing technology.
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Affiliation(s)
- Nathaniel K Hamaker
- Biopharmaceutical Innovation Center, Newark, DE, 19713, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Kelvin H Lee
- Biopharmaceutical Innovation Center, Newark, DE, 19713, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
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24
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Whitehead TA, Banta S, Bentley WE, Betenbaugh MJ, Chan C, Clark DS, Hoesli CA, Jewett MC, Junker B, Koffas M, Kshirsagar R, Lewis A, Li CT, Maranas C, Terry Papoutsakis E, Prather KLJ, Schaffer S, Segatori L, Wheeldon I. The importance and future of biochemical engineering. Biotechnol Bioeng 2020; 117:2305-2318. [PMID: 32343367 DOI: 10.1002/bit.27364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 02/06/2023]
Abstract
Today's Biochemical Engineer may contribute to advances in a wide range of technical areas. The recent Biochemical and Molecular Engineering XXI conference focused on "The Next Generation of Biochemical and Molecular Engineering: The role of emerging technologies in tomorrow's products and processes". On the basis of topical discussions at this conference, this perspective synthesizes one vision on where investment in research areas is needed for biotechnology to continue contributing to some of the world's grand challenges.
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Affiliation(s)
- Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California
| | - Corinne A Hoesli
- Department of Chemical Engineering & Department of Biological and Biomedical Engineering, McGill University, Montreal, Québec, Canada
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois
| | - Beth Junker
- BioProcess Advantage LLC, Middesex, New Jersey
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | | | | | - Chien-Ting Li
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - E Terry Papoutsakis
- Department of Chemical & Biomolecular Engineering & the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Laura Segatori
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, California
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25
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Totaro D, Rothbauer M, Steiger MG, Mayr T, Wang HY, Lin YS, Sauer M, Altvater M, Ertl P, Mattanovich D. Downscaling screening cultures in a multifunctional bioreactor array-on-a-chip for speeding up optimization of yeast-based lactic acid bioproduction. Biotechnol Bioeng 2020; 117:2046-2057. [PMID: 32190900 PMCID: PMC7317386 DOI: 10.1002/bit.27338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/21/2020] [Accepted: 03/17/2020] [Indexed: 01/09/2023]
Abstract
A key challenge for bioprocess engineering is the identification of the optimum process conditions for the production of biochemical and biopharmaceutical compounds using prokaryotic as well as eukaryotic cell factories. Shake flasks and bench-scale bioreactor systems are still the golden standard in the early stage of bioprocess development, though they are known to be expensive, time-consuming, and labor-intensive as well as lacking the throughput for efficient production optimizations. To bridge the technological gap between bioprocess optimization and upscaling, we have developed a microfluidic bioreactor array to reduce time and costs, and to increase throughput compared with traditional lab-scale culture strategies. We present a multifunctional microfluidic device containing 12 individual bioreactors (Vt = 15 µl) in a 26 mm × 76 mm area with in-line biosensing of dissolved oxygen and biomass concentration. Following initial device characterization, the bioreactor lab-on-a-chip was used in a proof-of-principle study to identify the most productive cell line for lactic acid production out of two engineered yeast strains, evaluating whether it could reduce the time needed for collecting meaningful data compared with shake flasks cultures. Results of the study showed significant difference in the strains' productivity within 3 hr of operation exhibiting a 4- to 6-fold higher lactic acid production, thus pointing at the potential of microfluidic technology as effective screening tool for fast and parallelizable industrial bioprocess development.
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Affiliation(s)
- Damiano Totaro
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Faculty of Technical Chemistry, Vienna University of Technology, Vienna, Austria
| | - Mario Rothbauer
- Faculty of Technical Chemistry, Vienna University of Technology, Vienna, Austria
| | - Matthias G Steiger
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Torsten Mayr
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Graz, Austria
| | - Hsiang-Yu Wang
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Sheng Lin
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Michael Sauer
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Martin Altvater
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Ertl
- Faculty of Technical Chemistry, Vienna University of Technology, Vienna, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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26
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Ongey EL, Santolin L, Waldburger S, Adrian L, Riedel SL, Neubauer P. Bioprocess Development for Lantibiotic Ruminococcin-A Production in Escherichia coli and Kinetic Insights Into LanM Enzymes Catalysis. Front Microbiol 2019; 10:2133. [PMID: 31572338 PMCID: PMC6753504 DOI: 10.3389/fmicb.2019.02133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/30/2019] [Indexed: 11/13/2022] Open
Abstract
Ruminococcin-A (RumA) is a peptide antibiotic with post-translational modifications including thioether cross-links formed from non-canonical amino acids, called lanthionines, synthesized by a dedicated lanthionine-generating enzyme RumM. RumA is naturally produced by Ruminococcus gnavus, which is part of the normal bacterial flora in the human gut. High activity of RumA against pathogenic Clostridia has been reported, thus allowing potential exploitation of RumA for clinical applications. However, purifying RumA from R. gnavus is challenging due to low production yields (<1 μg L-1) and difficulties to cultivate the obligately anaerobic organism. We recently reported the reconstruction of the RumA biosynthesis machinery in Escherichia coli where the fully modified and active peptide was expressed as a fusion protein together with GFP. In the current study we developed a scale-up strategy for the biotechnologically relevant heterologous production of RumA, aimed at overproducing the peptide under conditions comparable with those in industrial production settings. To this end, glucose-limited fed-batch cultivation was used. Firstly, parallel cultivations were performed in 24-microwell plates using the enzyme-based automated glucose-delivery cultivation system EnPresso® B to determine optimal conditions for IPTG induction. We combined the bioprocess development with ESI-MS and tandem ESI-MS to monitor modification of the precursor peptide (preRumA) during bioreactor cultivation. Dehydration of threonine and serine residues in the core peptide, catalyzed by RumM, occurs within 1 h after IPTG induction while formation of thioether cross-bridges occur around 2.5 h after induction. Our data also supplies important information on modification kinetics especially with respect to the fluctuations observed in the various dehydrated precursor peptide versions or intermediates produced at different time points during bioreactor cultivation. Overall, protein yields obtained from the bioreactor cultivations were >120 mg L-1 for the chimeric construct and >150 mg L-1 for RumM. The correlation observed between microscale and lab-scale bioreactor cultivations suggests that the process is robust and realistically applicable to industrial-scale conditions.
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Affiliation(s)
- Elvis L Ongey
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lara Santolin
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Saskia Waldburger
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany.,Chair of Geobiotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sebastian L Riedel
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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27
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Tsakona S, Papadaki A, Kopsahelis N, Kachrimanidou V, Papanikolaou S, Koutinas A. Development of a Circular Oriented Bioprocess for Microbial Oil Production Using Diversified Mixed Confectionery Side-Streams. Foods 2019; 8:E300. [PMID: 31370368 PMCID: PMC6723147 DOI: 10.3390/foods8080300] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023] Open
Abstract
Diversified mixed confectionery waste streams were utilized in a two-stage bioprocess to formulate a nutrient-rich fermentation media for microbial oil production. Solid-state fermentation was conducted for the production of crude enzyme consortia to be subsequently applied in hydrolytic reactions to break down starch, disaccharides, and proteins into monosaccharides, amino acids, and peptides. Crude hydrolysates were evaluated in bioconversion processes using the red yeast Rhodosporidium toruloides DSM 4444 both in batch and fed-batch mode. Under nitrogen-limiting conditions, during fed-batch cultures, the concentration of microbial lipids reached 16.6-17 g·L-1 with the intracellular content being more than 40% (w/w) in both hydrolysates applied. R. toruloides was able to metabolize mixed carbon sources without catabolite repression. The fatty acid profile of the produced lipids was altered based on the substrate employed in the bioconversion process. Microbial lipids were rich in polyunsaturated fatty acids, with oleic acid being the major fatty acid (61.7%, w/w). This study showed that mixed food side-streams could be valorized for the production of microbial oil with high unsaturation degree, pointing towards the potential to produce tailor-made lipids for specific food applications. Likewise, the proposed process conforms unequivocally to the principles of the circular economy, as the entire quantity of confectionery by-products are implemented to generate added-value compounds that will find applications in the same original industry, thus closing the loop.
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Affiliation(s)
- Sofia Tsakona
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Aikaterini Papadaki
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
- Department of Food Science and Technology, Ionian University, 28100 Argostoli, Greece.
| | - Nikolaos Kopsahelis
- Department of Food Science and Technology, Ionian University, 28100 Argostoli, Greece
| | | | - Seraphim Papanikolaou
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Apostolis Koutinas
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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28
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Papadaki A, Diamantopoulou P, Papanikolaou S, Philippoussis A. Evaluation of Biomass and Chitin Production of Morchella Mushrooms Grown on Starch-Based Substrates. Foods 2019; 8:E239. [PMID: 31266266 DOI: 10.3390/foods8070239] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
Morchella sp. is one of the most expensive mushrooms with a high nutritional profile. In this study, the polysaccharide content of Morchella species was investigated. Specifically, mycelium growth rate, biomass production, sclerotia formation, and glucosamine and total polysaccharides content of six Morchella species grown on a starch-based media were evaluated. Submerged fermentations in potato dextrose broth resulted in a glucosamine content of around 3.0%. In solid-state fermentations (SSF), using potato dextrose agar, a high linear growth rate (20.6 mm/day) was determined. Increased glucosamine and total polysaccharides content were observed after the formation of sclerotia. Biomass and glucosamine content were correlated, and the equations were used for the indirect estimation of biomass in SSF with agro-industrial starch-based materials. Wheat grains (WG), potato peels (PP), and a mixture of 1:1 of them (WG-PP) were evaluated as substrates. Results showed that the highest growth rate of 9.05 mm/day was determined on WG and the maximum biomass yield (407 mg/g) on WG-PP. The total polysaccharide content reached up to 18.4% of dried biomass in WG-PP. The results of the present study proved encouraging for the efficient bioconversion of potato and other starch-based agro-industrial waste streams to morel biomass and sclerotia eliciting nutritional and bioactive value.
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29
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Mandenius CF. Conceptual Design of Micro-Bioreactors and Organ-on-Chips for Studies of Cell Cultures. Bioengineering (Basel) 2018; 5:E56. [PMID: 30029542 PMCID: PMC6164921 DOI: 10.3390/bioengineering5030056] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 01/19/2023] Open
Abstract
Engineering design of microbioreactors (MBRs) and organ-on-chip (OoC) devices can take advantage of established design science theory, in which systematic evaluation of functional concepts and user requirements are analyzed. This is commonly referred to as a conceptual design. This review article compares how common conceptual design principles are applicable to MBR and OoC devices. The complexity of this design, which is exemplified by MBRs for scaled-down cell cultures in bioprocess development and drug testing in OoCs for heart and eye, is discussed and compared with previous design solutions of MBRs and OoCs, from the perspective of how similarities in understanding design from functionality and user purpose perspectives can more efficiently be exploited. The review can serve as a guideline and help the future design of MBR and OoC devices for cell culture studies.
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30
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Reinhart D, Damjanovic L, Kaisermayer C, Sommeregger W, Gili A, Gasselhuber B, Castan A, Mayrhofer P, Grünwald-Gruber C, Kunert R. Bioprocessing of Recombinant CHO-K1, CHO-DG44, and CHO-S: CHO Expression Hosts Favor Either mAb Production or Biomass Synthesis. Biotechnol J 2018; 14:e1700686. [PMID: 29701329 DOI: 10.1002/biot.201700686] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/26/2018] [Indexed: 01/02/2023]
Abstract
Chinese hamster ovary (CHO) cells comprise a variety of lineages including CHO-DXB11, CHO-K1, CHO-DG44, and CHO-S. Despite all CHO cell lines sharing a common ancestor, extensive mutagenesis, and clonal selection has resulted in substantial genetic heterogeneity among them. Data from sequencing show that different genes are missing in individual CHO cell lines and each cell line harbors a unique set of mutations with relevance to the bioprocess. However, not much literature is available about the influence of genetic differences of CHO on the performance of bioprocess operations. In this study, the host cell-specific differences among three widely used CHO cell lines (CHO-K1, CHO-S, and CHO-DG44) and recombinantly expressed the same monoclonal antibody (mAb) in an isogenic format by using bacterial artificial chromosomes (BACs) as transfer vector in all cell lines is examined. Cell-specific growth and product formation are studied in batch, fed-batch, and semi-continuous perfusion cultures. Further, two different cell culture media are used to investigate their effects. The authors find CHO cell line-specific preferences for mAb production or biomass synthesis that are determined by the host cell line. Additionally, quality attributes of the expressed mAb are influenced by the host cell line and media.
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Affiliation(s)
- David Reinhart
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Lukas Damjanovic
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| | | | - Wolfgang Sommeregger
- Bilfinger Industrietechnik Salzburg GmbH, Urstein Nord 31, 5412 Puch bei Hallein, Austria
| | - Andreas Gili
- Polymun Scientific Immunbiologische Forschung GmbH, Donaustraße 99, 3400 Klosterneuburg, Austria
| | - Bernhard Gasselhuber
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Andreas Castan
- GE Healthcare Life Sciences AB, Björkgatan 30, 75184 Uppsala, Sweden
| | - Patrick Mayrhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Renate Kunert
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
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31
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Kalonia CK, Heinrich F, Curtis JE, Raman S, Miller MA, Hudson SD. Protein Adsorption and Layer Formation at the Stainless Steel-Solution Interface Mediates Shear-Induced Particle Formation for an IgG1 Monoclonal Antibody. Mol Pharm 2018; 15:1319-1331. [PMID: 29425047 PMCID: PMC5997281 DOI: 10.1021/acs.molpharmaceut.7b01127] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Passage of specific protein solutions through certain pumps, tubing, and/or filling nozzles can result in the production of unwanted subvisible protein particles (SVPs). In this work, surface-mediated SVP formation was investigated. Specifically, the effects of different solid interface materials, interfacial shear rates, and protein concentrations on SVP formation were measured for the National Institute of Standards and Technology monoclonal antibody (NISTmAb), a reference IgG1 monoclonal antibody (mAb). A stainless steel rotary piston pump was used to identify formulation and process parameters that affect aggregation, and a flow cell (alumina or stainless steel interface) was used to further investigate the effect of different interface materials and/or interfacial shear rates. SVP particles produced were monitored using flow microscopy or flow cytometry. Neutron reflectometry and a quartz crystal microbalance with dissipation monitoring were used to characterize adsorption and properties of NISTmAb at the stainless steel interface. Pump/shear cell experiments showed that the NISTmAb concentration and interface material had a significant effect on SVP formation, while the effects of interfacial shear rate and passage number were less important. At the higher NISTmAb concentrations, the adsorbed protein became structurally altered at the stainless steel interface. The primary adsorbed layer remained largely undisturbed during flow, suggesting that SVP formation at high NISTmAb concentration was caused by the disruption of patches and/or secondary interactions.
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Affiliation(s)
- Cavan K. Kalonia
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
- Formulation Sciences Department, MedImmune Inc., Gaithersburg, Maryland 20878, United States
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Joseph E. Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sid Raman
- Formulation Sciences Department, MedImmune Inc., Gaithersburg, Maryland 20878, United States
| | - Maria A. Miller
- Formulation Sciences Department, MedImmune Inc., Gaithersburg, Maryland 20878, United States
| | - Steven D. Hudson
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
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32
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Reichelt WN, Haas F, Sagmeister P, Herwig C. Bioprocess development workflow: Transferable physiological knowledge instead of technological correlations. Biotechnol Prog 2016; 33:261-270. [PMID: 27690336 DOI: 10.1002/btpr.2377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 09/28/2016] [Indexed: 11/06/2022]
Abstract
Microbial bioprocesses need to be designed to be transferable from lab scale to production scale as well as between setups. Although substantial effort is invested to control technological parameters, usually the only true constant parameter is the actual producer of the product: the cell. Hence, instead of solely controlling technological process parameters, the focus should be increasingly laid on physiological parameters. This contribution aims at illustrating a workflow of data life cycle management with special focus on physiology. Information processing condenses the data into physiological variables, while information mining condenses the variables further into physiological descriptors. This basis facilitates data analysis for a physiological explanation for observed phenomena in productivity. Targeting transferability, we demonstrate this workflow using an industrially relevant Escherichia coli process for recombinant protein production and substantiate the following three points: (1) The postinduction phase is independent in terms of productivity and physiology from the preinduction variables specific growth rate and biomass at induction. (2) The specific substrate uptake rate during induction phase was found to significantly impact the maximum specific product titer. (3) The time point of maximum specific titer can be predicted by an easy accessible physiological variable: while the maximum specific titers were reached at different time points (19.8 ± 7.6 h), those maxima were reached all within a very narrow window of cumulatively consumed substrate dSn (3.1 ± 0.3 g/g). Concluding, this contribution provides a workflow on how to gain a physiological view on the process and illustrates potential benefits. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:261-270, 2017.
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Affiliation(s)
- Wieland N Reichelt
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/166, Vienna, A-1060, Austria
| | - Florian Haas
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1A/166-4, Vienna, 1060, Austria
| | - Patrick Sagmeister
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1A/166-4, Vienna, 1060, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/166, Vienna, A-1060, Austria
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33
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Silber J, Kramer A, Labes A, Tasdemir D. From Discovery to Production: Biotechnology of Marine Fungi for the Production of New Antibiotics. Mar Drugs 2016; 14:md14070137. [PMID: 27455283 PMCID: PMC4962027 DOI: 10.3390/md14070137] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/06/2016] [Accepted: 07/12/2016] [Indexed: 02/02/2023] Open
Abstract
Filamentous fungi are well known for their capability of producing antibiotic natural products. Recent studies have demonstrated the potential of antimicrobials with vast chemodiversity from marine fungi. Development of such natural products into lead compounds requires sustainable supply. Marine biotechnology can significantly contribute to the production of new antibiotics at various levels of the process chain including discovery, production, downstream processing, and lead development. However, the number of biotechnological processes described for large-scale production from marine fungi is far from the sum of the newly-discovered natural antibiotics. Methods and technologies applied in marine fungal biotechnology largely derive from analogous terrestrial processes and rarely reflect the specific demands of the marine fungi. The current developments in metabolic engineering and marine microbiology are not yet transferred into processes, but offer numerous options for improvement of production processes and establishment of new process chains. This review summarises the current state in biotechnological production of marine fungal antibiotics and points out the enormous potential of biotechnology in all stages of the discovery-to-development pipeline. At the same time, the literature survey reveals that more biotechnology transfer and method developments are needed for a sustainable and innovative production of marine fungal antibiotics.
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Affiliation(s)
- Johanna Silber
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
| | - Annemarie Kramer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
| | - Antje Labes
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
| | - Deniz Tasdemir
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
- Faculty of Mathematics and Natural Sciences, University of Kiel, Christian-Albrechts-Platz 4, Kiel 24118, Germany.
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Abstract
Pichia pastoris is a widely used host organism for the recombinant production of proteins. It is attracting increasing interest for the production of biopharmaceuticals, due to its capability of performing posttranslational modifications. Traditionally, production processes with P. pastoris describe fed-batch processes based on feed forward regimes with a constant specific growth rate. However, this strategy does not consider physiological changes of the organism, bearing the risk of overfeeding and thus harming the cells. Recently, we introduced the specific substrate uptake rate as a novel physiological parameter to design fed-batch strategies for P. pastoris. We showed that by doing dynamic batch experiments strain specific parameters, which are needed to set up respective feeding profiles, can be easily determined. Furthermore we proved that dynamics during feeding directly affects productivity and product purity. Here, we sum up our findings regarding dynamics in bioprocess development for P. pastoris.
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Affiliation(s)
- Oliver Spadiut
- a Vienna University of Technology; Institute of Chemical Engineering ; Research Area Biochemical Engineering ; Vienna , Austria
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35
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Markely LRA, Kurt L, Lau J, Mane S, Guan B, Ryll T, Estes S, Prajapati S, Bakhshayeshi M, Pieracci J. High-throughput ion exchange purification of positively charged recombinant protein in the presence of negatively charged dextran sulfate. Biotechnol Prog 2014; 30:516-20. [PMID: 24449619 DOI: 10.1002/btpr.1873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/10/2013] [Accepted: 01/17/2014] [Indexed: 11/10/2022]
Abstract
Product quality analyses are critical for developing cell line and bioprocess producing therapeutic proteins with desired critical product quality attributes. To facilitate these analyses, a high-throughput small-scale protein purification (SSP) is required to quickly purify many samples in parallel. Here we develop an SSP using ion exchange resins to purify a positively charged recombinant growth factor P1 in the presence of negatively charged dextran sulfate supplemented to improve the cell culture performance. The major challenge in this work is that the strong ionic interaction between P1 and dextran sulfate disrupts interaction between P1 and chromatography resins. To solve this problem, we develop a two-step SSP using Q Sepharose Fast Flow (QFF) and SP Sepharose XL (SPXL) resins to purify P1. The overall yield of this two-step SSP is 78%. Moreover, the SSP does not affect the critical product quality attributes. The SSP was critical for developing the cell line and process producing P1.
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Affiliation(s)
- Lam Raga A Markely
- Cell Culture Development Dept. - High-Throughput Analytical Group, Biogen Idec Inc., 15 Cambridge Center, Cambridge, MA, 02142
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Rohe P, Venkanna D, Kleine B, Freudl R, Oldiges M. An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform. Microb Cell Fact 2012; 11:144. [PMID: 23113930 PMCID: PMC3526558 DOI: 10.1186/1475-2859-11-144] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 10/29/2012] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND High-throughput methods are widely-used for strain screening effectively resulting in binary information regarding high or low productivity. Nevertheless achieving quantitative and scalable parameters for fast bioprocess development is much more challenging, especially for heterologous protein production. Here, the nature of the foreign protein makes it impossible to predict the, e.g. best expression construct, secretion signal peptide, inductor concentration, induction time, temperature and substrate feed rate in fed-batch operation to name only a few. Therefore, a high number of systematic experiments are necessary to elucidate the best conditions for heterologous expression of each new protein of interest. RESULTS To increase the throughput in bioprocess development, we used a microtiter plate based cultivation system (Biolector) which was fully integrated into a liquid-handling platform enclosed in laminar airflow housing. This automated cultivation platform was used for optimization of the secretory production of a cutinase from Fusarium solani pisi with Corynebacterium glutamicum. The online monitoring of biomass, dissolved oxygen and pH in each of the microtiter plate wells enables to trigger sampling or dosing events with the pipetting robot used for a reliable selection of best performing cutinase producers. In addition to this, further automated methods like media optimization and induction profiling were developed and validated. All biological and bioprocess parameters were exclusively optimized at microtiter plate scale and showed perfect scalable results to 1 L and 20 L stirred tank bioreactor scale. CONCLUSIONS The optimization of heterologous protein expression in microbial systems currently requires extensive testing of biological and bioprocess engineering parameters. This can be efficiently boosted by using a microtiter plate cultivation setup embedded into a liquid-handling system, providing more throughput by parallelization and automation. Due to improved statistics by replicate cultivations, automated downstream analysis, and scalable process information, this setup has superior performance compared to standard microtiter plate cultivation.
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Affiliation(s)
- Peter Rohe
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Deepak Venkanna
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Britta Kleine
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic Microbiology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Roland Freudl
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic Microbiology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
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