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Masson HO, Karottki KJLC, Tat J, Hefzi H, Lewis NE. From observational to actionable: rethinking omics in biologics production. Trends Biotechnol 2023; 41:1127-1138. [PMID: 37062598 PMCID: PMC10524802 DOI: 10.1016/j.tibtech.2023.03.009] [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: 01/11/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023]
Abstract
As the era of omics continues to expand with increasing ubiquity and success in both academia and industry, omics-based experiments are becoming commonplace in industrial biotechnology, including efforts to develop novel solutions in bioprocess optimization and cell line development. Omic technologies provide particularly valuable 'observational' insights for discovery science, especially in academic research and industrial R&D; however, biomanufacturing requires a different paradigm to unlock 'actionable' insights from omics. Here, we argue the value of omic experiments in biotechnology can be maximized with deliberate selection of omic approaches and forethought about analysis techniques. We describe important considerations when designing and implementing omic-based experiments and discuss how systems biology analysis strategies can enhance efforts to obtain actionable insights in mammalian-based biologics production.
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Affiliation(s)
- Helen O Masson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Jasmine Tat
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Amgen Inc., Thousand Oaks, CA, USA
| | | | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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Nguyen M, Zimmer A. A reflection on the improvement of Chinese Hamster ovary cell-based bioprocesses through advances in proteomic techniques. Biotechnol Adv 2023; 65:108141. [PMID: 37001570 DOI: 10.1016/j.biotechadv.2023.108141] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Chinese hamster ovary (CHO) cells are the preferred mammalian host for the large-scale production of recombinant proteins in the biopharmaceutical industry. Research endeavors have been directed to the optimization of CHO-based bioprocesses to increase protein quantity and quality, often in an empirical manner. To provide a rationale for those achievements, a myriad of CHO proteomic studies has arisen in recent decades. This review gives an overview of significant advances in LC-MS-based proteomics and sheds light on CHO proteomic studies, with a particular focus on CHO cells with superior bioprocessing phenotypes (growth, viability, titer, productivity and cQA), that have exploited novel proteomic or sub-omic techniques. These proteomic findings expand the current knowledge and understanding about the underlying protein clusters, protein regulatory networks and biological pathways governing such phenotypic changes. The proteomic studies, highlighted herein, will help in the targeted modulation of these cell factories to the desired needs.
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Schulze M, Kumar Y, Rattay M, Niemann J, Wijffels RH, Martens D. Transcriptomic analysis reveals mode of action of butyric acid supplementation in an intensified CHO cell fed‐batch process. Biotechnol Bioeng 2022; 119:2359-2373. [PMID: 35641884 PMCID: PMC9545226 DOI: 10.1002/bit.28150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/17/2022] [Accepted: 05/28/2022] [Indexed: 11/10/2022]
Abstract
Process intensification is increasingly used in the mammalian biomanufacturing industry. The key driver of this trend is the need for more efficient and flexible production strategies to cope with the increased demand for biotherapeutics predicted in the next years. Therefore, such intensified production strategies should be designed, established, and characterized. We established a CHO cell process consisting of an intensified fed‐batch (iFB), which is inoculated by an N‐1 perfusion process that reaches high cell concentrations (100 × 106 c ml−1). We investigated the impact of butyric acid (BA) supplementation in this iFB process. Most prominently, higher cellular productivities of more than 33% were achieved, thus 3.5 g L−1 of immunoglobulin G (IgG) was produced in 6.5 days. Impacts on critical product quality attributes were small. To understand the biological mechanisms of BA in the iFB process, we performed a detailed transcriptomic analysis. Affected gene sets reflected concurrent inhibition of cell proliferation and impact on histone modification. These translate into subsequently enhanced mechanisms of protein biosynthesis: enriched regulation of transcription, messenger RNA processing and transport, ribosomal translation, and cellular trafficking of IgG intermediates. Furthermore, we identified mutual tackling points for optimization by gene engineering. The presented strategy can contribute to meet future requirements in the continuously demanding field of biotherapeutics production.
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Affiliation(s)
- Markus Schulze
- Product Development Cell Culture Technologies, Sartorius Stedim Biotech GmbHAugust‐Spindler‐Str. 1137079GöttingenGermany
- Bioprocess EngineeringWageningen UniversityPO Box 166700 AAWageningenNetherlands
| | - Yadhu Kumar
- Eurofins Genomics Europe Sequencing GmbHJakob‐Stadler‐Platz 7D‐78467KonstanzGermany
| | - Merle Rattay
- Corporate Research Advanced Cell Biology, Sartorius Stedim Cellca GmbHMarie‐Goeppert‐Mayer‐Str. 989081Ulm
| | - Julia Niemann
- Corporate Research BioProcessing Upstream, Sartorius Stedim Biotech GmbHAugust‐Spindler‐Str. 1137079GöttingenGermany
| | - Rene H. Wijffels
- Bioprocess EngineeringWageningen UniversityPO Box 166700 AAWageningenNetherlands
- Biosciences and AquacultureNord UniversityN‐8049BodøNorway
| | - Dirk Martens
- Bioprocess EngineeringWageningen UniversityPO Box 166700 AAWageningenNetherlands
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Li J, Sang Y, Zeng S, Mo S, Zhang Z, He S, Li X, Su G, Liao J, Jiang C. MicrobioSee: A Web-Based Visualization Toolkit for Multi-Omics of Microbiology. Front Genet 2022; 13:853612. [PMID: 35464838 PMCID: PMC9024144 DOI: 10.3389/fgene.2022.853612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
With the upgrade and development of the high-throughput sequencing technology, multi-omics data can be obtained at a low cost. However, mapping tools that existed for microbial multi-omics data analysis cannot satisfy the needs of data description and result in high learning costs, complex dependencies, and high fees for researchers in experimental biology fields. Therefore, developing a toolkit for multi-omics data is essential for microbiologists to save effort. In this work, we developed MicrobioSee, a real-time interactive visualization tool based on web technologies, which could visualize microbial multi-omics data. It includes 17 modules surrounding the major omics data of microorganisms such as the transcriptome, metagenome, and proteome. With MicrobioSee, methods for plotting are simplified in multi-omics studies, such as visualization of diversity, ROC, and enrichment pathways for DEGs. Subsequently, three case studies were chosen to represent the functional application of MicrobioSee. Overall, we provided a concise toolkit along with user-friendly, time-saving, cross-platform, and source-opening for researchers, especially microbiologists without coding experience. MicrobioSee is freely available at https://microbiosee.gxu.edu.cn.
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Affiliation(s)
- JinHui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yimeng Sang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Sen Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Zufan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Sheng He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Birth Defects Prevention and Control Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xinying Li
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Guijiao Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Jianping Liao
- School of Computer and Information Engineering, Nanning Normal University, Nanning, China
- *Correspondence: Chengjian Jiang, ; Jianping Liao,
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
- *Correspondence: Chengjian Jiang, ; Jianping Liao,
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