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Tang X, Quiroz J, Zhang Y, Pan J, Lai Z, Du Z, Liu R. A deep-well plate enabled automated high-throughput cell line development platform. Biotechnol Prog 2024; 40:e3442. [PMID: 38377061 DOI: 10.1002/btpr.3442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/28/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024]
Abstract
Cell line development (CLD) plays a crucial role in the manufacturing process development of therapeutic biologics. Most biologics are produced in Chinese hamster ovary (CHO) cell. Because of the nature of random transgene integration in CHO genome and CHO's inherent plasticity, stable CHO transfectants usually have a vast diversity in productivity, growth, and product quality. Thus, we often must resort to screening a large number of cell pools and clones to increase the probability of identifying the ideal production cell line, which is a very laborious and resource-demanding process. Here we have developed a deep-well plate (DWP) enabled high throughput (DEHT) CLD platform using 24-well DWP (24DWP), liquid handler, and other automation components. This platform has capabilities covering the key steps of CLD including cell passaging, clone imaging and expansion, and fed-batch production. We are the first to demonstrate the suitability of 24DWP for CLD by confirming minimal well-to-well and plate-to-plate variability and the absence of well-to-well cross contamination. We also demonstrated that growth, production, and product quality of 24DWP cultures were comparable to those of conventional shake flask cultures. The DEHT platform enables scientists to screen five times more cultures than the conventional CLD platform, thus significantly decreases the resources needed to identify an ideal production cell line for biologics manufacturing.
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Affiliation(s)
- Xiaoyan Tang
- Process Cell Sciences, MRL, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Jorge Quiroz
- BARDS, Research CMC Statistics, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Yixiao Zhang
- Process Cell Sciences, MRL, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Jessica Pan
- Process Cell Sciences, MRL, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Zhong Lai
- BARDS, Research CMC Statistics, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Zhimei Du
- Process Cell Sciences, MRL, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Ren Liu
- Process Cell Sciences, MRL, Merck & Co., Inc., Rahway, New Jersey, USA
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Neuss A, von Vegesack N, Liepelt R, Büchs J, Barsett Magnus J. Online monitoring of the respiration activity in 96-deep-well microtiter plate Chinese hamster ovary cultures streamlines kill curve experiments. Biotechnol Prog 2024:e3468. [PMID: 38602130 DOI: 10.1002/btpr.3468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Cell line generation of mammalian cells is a time-consuming and labor-intensive process, especially because of challenges in clone selection after transfection. Antibiotics are common selection agents for mammalian cells due to their simplicity of use. However, the optimal antibiotic concentration must be determined with a kill curve experiment before clone selection starts. The traditional kill curve experiments are resource-intensive and time-consuming due to necessary sampling and offline analysis effort. This study, thus, explores the potential of online monitoring the oxygen transfer rate (OTR), as a non-invasive and efficient alternative for kill curve experiments. The OTR is monitored using the Transfer-rate Online Measurement (TOM) system and the micro(μ)-scale Transfer-rate Online Measurement (μTOM) device, which was used for mammalian cells first. It could be shown that the OTR curves for both devices align perfectly, affirming consistent cultivation conditions. The μTOM device proves effective in performing kill curve experiments in 96-deep-well plates without the need for sampling and offline analysis. The streamlined approach reduces medium consumption by 95%, offering a cost-effective and time-efficient solution for kill curve experiments. The study validates the generalizability of the method by applying it to two different CHO cell lines (CHO-K1 and sciCHO) with two antibiotics (puromycin and hygromycin B) each. In conclusion, the broad application of OTR online monitoring for CHO cell cultures in 96-deep-well plates is highlighted. The μTOM device proves as a valuable tool for high-throughput experiments, paving the way for diverse applications, such as media and clone screening, cytotoxicity tests, and scale-up experiments.
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Affiliation(s)
- Anne Neuss
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Nele von Vegesack
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Raoul Liepelt
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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Ihling N, Berg C, Paul R, Munkler LP, Mäkinen MEL, Chotteau V, Büchs J. Scale-down of CHO cell cultivation from shake flasks based on oxygen mass transfer allows application of parallelized, non-invasive, and time-resolved monitoring of the oxygen transfer rate in 48-well microtiter plates. Biotechnol J 2023; 18:e2300053. [PMID: 37424196 DOI: 10.1002/biot.202300053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Cultivating Chinese hamster ovary (CHO) cells in microtiter plates (MTPs) with time-resolved monitoring of the oxygen transfer rate (OTR) is highly desirable to provide process insights at increased throughput. However, monitoring of the OTR in MTPs has not been demonstrated for CHO cells, yet. Hence, a CHO cultivation process was transferred from shake flasks to MTPs to enable monitoring of the OTR in each individual well of a 48-well MTP. For this, the cultivation of an industrially relevant, antibody-producing cell line was transferred from shake flask to MTP based on the volumetric oxygen mass transfer coefficient (kL a). Culture behavior was well comparable (deviation of the final IgG titer less than 10%). Monitoring of the OTR in 48-well MTPs was then used to derive the cytotoxicity of dimethyl sulfoxide (DMSO) based on a dose-response curve in a single experiment using a second CHO cell line. Logistic fitting of the dose-response curve determined after 100 h was used to determine the DMSO concentration that resulted in a cytotoxicity of 50% (IC50). A DMSO concentration of 2.70% ± 0.25% was determined, which agrees with the IC50 previously determined in shake flasks (2.39% ± 0.1%). Non-invasive, parallelized, and time-resolved monitoring of the OTR of CHO cells in MTPs was demonstrated and offers excellent potential to speed up process development and assess cytotoxicity.
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Affiliation(s)
- Nina Ihling
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Christoph Berg
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Richard Paul
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | | | - Meeri E-L Mäkinen
- KTH Royal Institute of Technology, Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Veronique Chotteau
- KTH Royal Institute of Technology, Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
- AdBIOPRO, Competence Centre for Advanced BioProduction by Continuous Processing, KTH, Stockholm, Sweden
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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Nelson L, Veling M, Farhangdoust F, Cai X, Huhn S, Soloveva V, Chang M. Transcriptomics and cell painting analysis reveals molecular and morphological features associated with fed-batch production performance in CHO recombinant clones. Biotechnol Bioeng 2023; 120:3177-3190. [PMID: 37555462 DOI: 10.1002/bit.28518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023]
Abstract
Stable, highly productive mammalian cells are critical for manufacturing affordable and effective biological medicines. Establishing a rational design of optimal biotherapeutic expression systems requires understanding how cells support the high demand for efficient biologics production. To that end, we performed transcriptomics and high-throughput imaging studies to identify putative genes and morphological features that underpin differences in antibody productivity among clones from a Chinese hamster ovary cell line. During log phase growth, we found that the expression of genes involved in biological processes related to cellular morphology varied significantly between clones with high specific productivity (qP > 35 pg/cell/day) and low specific productivity (qP < 20 pg/cell/day). At Day 10 of a fed-batch production run, near peak viable cell density, differences in gene expression related to metabolism, epigenetic regulation, and proliferation became prominent. Furthermore, we identified a subset of genes whose expression predicted overall productivity, including glutathione synthetase (Gss) and lactate dehydrogenase A (LDHA). Finally, we demonstrated the feasibility of cell painting coupled with high-throughput imaging to assess the morphological properties of intracellular organelles in relation to growth and productivity in fed-batch production. Our efforts lay the groundwork for systematic elucidation of clone performance using a multiomics approach that can guide future process design strategies.
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Affiliation(s)
| | | | | | - Xuezhu Cai
- Merck & Co., Inc., Rahway, New Jersey, USA
| | - Steve Huhn
- Merck & Co., Inc., Rahway, New Jersey, USA
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Sun M, Gao AX, Liu X, Yang Y, Ledesma-Amaro R, Bai Z. High-throughput process development from gene cloning to protein production. Microb Cell Fact 2023; 22:182. [PMID: 37715258 PMCID: PMC10503041 DOI: 10.1186/s12934-023-02184-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/19/2023] [Indexed: 09/17/2023] Open
Abstract
In the post-genomic era, the demand for faster and more efficient protein production has increased, both in public laboratories and industry. In addition, with the expansion of protein sequences in databases, the range of possible enzymes of interest for a given application is also increasing. Faced with peer competition, budgetary, and time constraints, companies and laboratories must find ways to develop a robust manufacturing process for recombinant protein production. In this review, we explore high-throughput technologies for recombinant protein expression and present a holistic high-throughput process development strategy that spans from genes to proteins. We discuss the challenges that come with this task, the limitations of previous studies, and future research directions.
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Affiliation(s)
- Manman Sun
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Alex Xiong Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China.
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
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Marcianò D, Toffolatti SL. Methods for Fungicide Efficacy Screenings: Multiwell Testing Procedures for the Oomycetes Phytophthora infestans and Pythium ultimum. Microorganisms 2023; 11:microorganisms11020350. [PMID: 36838315 PMCID: PMC9959339 DOI: 10.3390/microorganisms11020350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Oomycetes-borne diseases represent a serious problem for agriculture sustainability due to the high use of chemical products employed for their control. In recent years, increasing concerns on side effects associated with fungicide utilization have led to the reduction of the permissible modes of action, with the remaining ones continuously threatened by the increase of resistant strains in the pathogen populations. In this context, it is mandatory to develop new generation fungicides characterized by high specificity towards the target species and low environmental impact to guarantee the sustainability, productivity, and quality of food production. Fungicide discovery is a lengthy and costly process, and despite these urgent needs, poor description and formalization of high-throughput methodologies for screening the efficacy of active compounds are commonly reported for these kinds of organisms. In this study, a comprehensive picture of two high-throughput practices for efficient fungicide screening against plant-pathogenic oomycetes has been provided. Different protocols using multiwell plates were validated on approved crop protection products using Phytophthora infestans and Pythium ultimum as the model species. In addition, detailed statistical inputs useful for the analysis of data related to the efficacy of screenings are included.
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Wang Q, Chen Y, Fu J, Yang Q, Feng L. High-throughput screening of lycopene-overproducing mutants of Blakeslea trispora by combining ARTP mutation with microtiter plate cultivation and transcriptional changes revealed by RNA-seq. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107664] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bowman EK, Alper HS. Microdroplet-Assisted Screening of Biomolecule Production for Metabolic Engineering Applications. Trends Biotechnol 2020; 38:701-714. [DOI: 10.1016/j.tibtech.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 12/19/2022]
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Markert S, Torkler S, Hohmann K, Popp O. Traces matter: Targeted optimization of monoclonal antibody N-glycosylation based on/by implementing automated high-throughput trace element screening. Biotechnol Prog 2020; 36:e3042. [PMID: 32583628 DOI: 10.1002/btpr.3042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 01/02/2023]
Abstract
The use of high-throughput systems in cell culture process optimization offers various opportunities in biopharmaceutical process development. Here we describe the potential for acceleration and enhancement of product quality optimization and de novo bioprocess design regarding monoclonal antibody N-glycosylation by using an iterative statistical Design of Experiments (DoE) strategy based on our automated microtiter plate-based system for suspension cell culture. In our example, the combination of an initial screening of trace metal building blocks with a comprehensive DoE-based screening of 13 different trace elemental ions at three concentration levels in one run revealed most effective levers for N-glycan processing and biomass formation. Obtained results served to evaluate optimal concentration ranges and the right supplementation timing of relevant trace elements at shake flask and 2 L bioreactor scale. This setup identified manganese, copper, zinc, and iron as major factors. Manganese and copper acted as inverse key players in N-glycosylation, showing a positive effect of manganese and a negative effect of copper on glycan maturation in a zinc-dependent manner. Zinc and iron similarly improved cell growth and biomass formation. These findings allowed determining optimal concentration ranges for all four trace elements to establish control on desired product quality attributes regarding premature afucosylated and mature galactosylated glycan species. Our results demonstrates the power of combining robotics with DoE screening to enhance product quality optimization and to improve process understanding, thus, enabling targeted product quality control.
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Affiliation(s)
- Sven Markert
- Pharmaceutical Biotech Production and Development, Roche Diagnostics GmbH, Pharmaceutical Biotech Production and Development, Penzberg, Germany
| | - Stephanie Torkler
- Cell Culture Research, Roche Diagnostics GmbH, Cell Culture Research, Pharma Research and Early Development, Roche Innovation Center Munich, pRED, LMR, Penzberg, Germany
| | - Katharina Hohmann
- Cell Culture Research, Roche Diagnostics GmbH, Cell Culture Research, Pharma Research and Early Development, Roche Innovation Center Munich, pRED, LMR, Penzberg, Germany
| | - Oliver Popp
- Cell Culture Research, Roche Diagnostics GmbH, Cell Culture Research, Pharma Research and Early Development, Roche Innovation Center Munich, pRED, LMR, Penzberg, Germany
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