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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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2
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Jari M, Abdoli S, Bazi Z, Shamsabadi FT, Roshanmehr F, Shahbazi M. Enhancing protein production and growth in chinese hamster ovary cells through miR-107 overexpression. AMB Express 2024; 14:16. [PMID: 38302631 PMCID: PMC10834913 DOI: 10.1186/s13568-024-01670-y] [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: 10/12/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
Chinese Hamster Ovary (CHO) cells are widely employed as host cells for biopharmaceutical production. The manufacturing of biopharmaceuticals poses several challenges, including restricted growth potential and inadequate productivity of the host cells. MicroRNAs play a crucial role in regulating gene expression and are considered highly promising tools for cell engineering to enhance protein production. Our study aimed to evaluate the effects of miR-107, which is recognized as an onco-miR, on erythropoietin-producing CHO cells (CHO-hEPO). To assess the impact of miR-107 on CHO cells, a DNA plasmid containing miR-107 was introduced to CHO-hEPO cells through transfection. Cell proliferation and viability were assessed using the trypan blue dye exclusion method. Cell cycle analysis was conducted by utilizing propidium iodide (PI) staining. The quantification of EPO was determined using an immunoassay test. Moreover, the impact of miR-107 on the expression of downstream target genes was evaluated using qRT-PCR. Our findings highlight and underscore the substantial impact of transient miR-107 overexpression, which led to a remarkable 2.7-fold increase in EPO titers and a significant 1.6-fold increase in the specific productivity of CHO cells (p < 0.01). Furthermore, this intervention resulted in significant enhancements in cell viability and growth rate (p < 0.05). Intriguingly, the overexpression of miR‑107 was linked to the downregulation of LATS2, PTEN, and TSC1 genes while concurrently driving upregulation in transcript levels of MYC, YAP, mTOR, and S6K genes within transgenic CHO cells. In conclusion, this study collectively underscores the feasibility of utilizing cancer-associated miRNAs as a powerful tool for CHO cell engineering. However, more in-depth exploration is warranted to unravel the precise molecular intricacies of miR-107's effects in the context of CHO cells.
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Affiliation(s)
- Maryam Jari
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Shastkola Road, Falsafi Complex, Gorgan, Zip code: 4934174611, Iran
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Shahriyar Abdoli
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Shastkola Road, Falsafi Complex, Gorgan, Zip code: 4934174611, Iran
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Zahra Bazi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Shastkola Road, Falsafi Complex, Gorgan, Zip code: 4934174611, Iran
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Fatemeh Tash Shamsabadi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Shastkola Road, Falsafi Complex, Gorgan, Zip code: 4934174611, Iran
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Farnaz Roshanmehr
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Shastkola Road, Falsafi Complex, Gorgan, Zip code: 4934174611, Iran
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Majid Shahbazi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Shastkola Road, Falsafi Complex, Gorgan, Zip code: 4934174611, Iran.
- AryaTina Gene (ATG) Biopharmaceutical Company Gorgan, Gorgan, Iran.
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Belliveau J, Papoutsakis ET. The microRNomes of Chinese hamster ovary (CHO) cells and their extracellular vesicles, and how they respond to osmotic and ammonia stress. Biotechnol Bioeng 2023; 120:2700-2716. [PMID: 36788116 DOI: 10.1002/bit.28356] [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: 12/12/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
A new area of focus in Chinese hamster ovary (CHO) biotechnology is the role of small (exosomes) and large (microvesicles or microparticles) extracellular vesicles (EVs). CHO cells in culture exchange large quantities of proteins and RNA through these EVs, yet the content and role of these EVs remain elusive. MicroRNAs (miRs or miRNA) are central to adaptive responses to stress and more broadly to changes in culture conditions. Given that EVs are highly enriched in miRs, and that EVs release large quantities of miRs both in vivo and in vitro, EVs and their miR content likely play an important role in adaptive responses. Here we report the miRNA landscape of CHO cells and their EVs under normal culture conditions and under ammonia and osmotic stress. We show that both cells and EVs are highly enriched in five miRs (among over 600 miRs) that make up about half of their total miR content, and that these highly enriched miRs differ significantly between normal and stress culture conditions. Notable is the high enrichment in miR-92a and miR-23a under normal culture conditions, in contrast to the high enrichment in let-7 family miRs (let-7c, let-7b, and let-7a) under both stress conditions. The latter suggests a preserved stress-responsive function of the let-7 miR family, one of the most highly preserved miR families across species, where among other functions, let-7 miRs regulate core oncogenes, which, depending on the biological context, may tip the balance between cell cycle arrest and apoptosis. While the expected-based on their profound enrichment-important role of these highly enriched miRs remains to be dissected, our data and analysis constitute an important resource for exploring the role of miRs in cell adaptation as well as for synthetic applications.
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Affiliation(s)
- Jessica Belliveau
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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Hong Q, Liu J, Wei Y, Wei X. Application of Baculovirus Expression Vector System (BEVS) in Vaccine Development. Vaccines (Basel) 2023; 11:1218. [PMID: 37515034 PMCID: PMC10386281 DOI: 10.3390/vaccines11071218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Vaccination is one of the most effective strategies to control epidemics. With the deepening of people's awareness of vaccination, there is a high demand for vaccination. Hence, a flexible, rapid, and cost-effective vaccine platform is urgently needed. The baculovirus expression vector system (BEVS) has emerged as a promising technology for vaccine production due to its high safety, rapid production, flexible product design, and scalability. In this review, we introduced the development history of BEVS and the procedures for preparing recombinant protein vaccines using the BEVS platform and summarized the features and limitations of this platform. Furthermore, we highlighted the progress of the BEVS platform-related research, especially in the field of vaccine. Finally, we provided a new prospect for BEVS in future vaccine manufacturing, which may pave the way for future BEVS-derived vaccine development.
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Affiliation(s)
- Qiaonan Hong
- Department of Biotherapy, Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Jian Liu
- Department of Biotherapy, Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Yuquan Wei
- Department of Biotherapy, Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu 610041, China
| | - Xiawei Wei
- Department of Biotherapy, Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu 610041, China
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5
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Bazaz M, Adeli A, Azizi M, Karimipoor M, Mahboudi F, Davoudi N. Overexpression of miR-32 in Chinese hamster ovary cells increases production of Fc-fusion protein. AMB Express 2023; 13:45. [PMID: 37160545 PMCID: PMC10170017 DOI: 10.1186/s13568-023-01540-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/22/2023] [Indexed: 05/11/2023] Open
Abstract
The demand for industrial genetically modified host cells were increased with the growth of the biopharmaceutical market. Numerous studies on improving host cell productivity have shown that altering host cell growth and viability through genetic engineering can increase recombinant protein production. During the last decades, it was demonstrated that overexpression or downregulation of some microRNAs in Chinese Hamster Ovary (CHO) cells as the host cell in biopharmaceutical manufacturing, can improve their productivity. The selection of microRNA targets has been based on their previously identified role in human cancers. MicroRNA-32 (miR-32), which is conserved between humans and hamsters (Crisetulus griseus), was shown to play a role in the regulation of cell proliferation and apoptosis in some human cancers. In this study, we investigated the effect of miR-32 overexpression on the productivity of CHO-VEGF-trap cells. Our results indicated that stable overexpression of miR-32 could dramatically increase the productivity of CHO cells by 1.8-fold. It also significantly increases cell viability, batch culture longevity, and cell growth. To achieve these results, following the construction of a single clone producing an Fc-fusion protein, we transfected cells with a pLexJRed-miR-32 plasmid to stably produce the microRNA and evaluate the impact of mir-32 overexpression on cell productivity, growth and viability in compare with scrambled control. Our findings highlight the application of miRNAs as engineering tools and indicated that miR-32 could be a target for engineering CHO cells to increase cell productivity.
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Affiliation(s)
- Masoume Bazaz
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Adeli
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Azizi
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Freidoun Mahboudi
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Noushin Davoudi
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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6
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Kalkan AK, Palaz F, Sofija S, Elmousa N, Ledezma Y, Cachat E, Rios-Solis L. Improving recombinant protein production in CHO cells using the CRISPR-Cas system. Biotechnol Adv 2023; 64:108115. [PMID: 36758652 DOI: 10.1016/j.biotechadv.2023.108115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
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Affiliation(s)
- Ali Kerem Kalkan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Environmental Engineering Department, Gebze Technical University, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Semeniuk Sofija
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nada Elmousa
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Yuri Ledezma
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; Biology Department, Faculty of Pure and Natural Sciences, Universidad Mayor de San Andrés, Bolivia
| | - Elise Cachat
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK; UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Leonardo Rios-Solis
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
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7
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Recent developments in miRNA based recombinant protein expression in CHO. Biotechnol Lett 2022; 44:671-681. [PMID: 35507207 DOI: 10.1007/s10529-022-03250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/30/2022] [Indexed: 11/02/2022]
Abstract
It is widely accepted that the growing demand for recombinant therapeutic proteins has led to the expansion of the biopharmaceutical industry and the development of strategies to increase recombinant protein production in mammalian cell lines such as SP2/0 HEK and particularly Chinese hamster ovary cells. For a long time now, most investigations have been focused on increasing host cell productivity using genetic manipulating of cellular processes like cell cycle, apoptosis, cell growth, protein secretory and other pathways. In recent decades MicroRNAs beside different genetic engineering tools (e.g., TALEN, ZFN, and Crisper/Cas) have attracted further attention as a tool in the genetic engineering of host cells to increase protein expression levels. Their ability to simultaneously target multiple mRNAs involved in one or more cellular processes made them a favorable tool in this field. Accordingly, this study aimed to review the methods of selecting target miRNA for cell line engineering, miRNA gain- or loss-of-function strategies, examples of laboratory and pilot studies in this field and discussed advantages and disadvantages of this technology.
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Liu HN, Dong WH, Lin Y, Zhang ZH, Wang TY. The Effect of microRNA on the Production of Recombinant Protein in CHO Cells and its Mechanism. Front Bioeng Biotechnol 2022; 10:832065. [PMID: 35387297 PMCID: PMC8977551 DOI: 10.3389/fbioe.2022.832065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Recombinant protein production by mammalian cells is the initial step in the manufacture of many therapeutic proteins. Chinese hamster ovary (CHO) cells are the most common host system to produce recombinant therapeutic proteins (RTPs). However, it is still challenging to maintain high productivity ensuring the good quality of RTPs produced by CHO cells. MicroRNAs(miRNAs) are short regulatory non-coding RNAs that can regulate cellular behavior and complex phenotypes. It has been found that miRNAs can enhance the expression level of recombinant proteins in CHO cells by promoting proliferation, resisting apoptosis, and regulating metabolism. miRNAs also can affect the quality of RTPs. In this review, we will discuss the effect and mechanism of miRNA on the expression level and quality of recombinant proteins in CHO cells.
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Affiliation(s)
- Hui-Ning Liu
- The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Wei-Hua Dong
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China.,Department of Biochemistry and Molecular Biology, Basic Medical School, Xinxiang Medical University, Xinxiang, China
| | - Yan Lin
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Zhao-Hui Zhang
- The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China.,Department of Biochemistry and Molecular Biology, Basic Medical School, Xinxiang Medical University, Xinxiang, China
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9
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Raab N, Zeh N, Schlossbauer P, Mathias S, Lindner B, Stadermann A, Gamer M, Fischer S, Holzmann K, Handrick R, Otte K. A blueprint from nature: miRNome comparison of plasma cells and CHO cells to optimize therapeutic antibody production. N Biotechnol 2021; 66:79-88. [PMID: 34710621 DOI: 10.1016/j.nbt.2021.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 12/13/2022]
Abstract
Chinese Hamster Ovary (CHO) cells are the most frequently used biopharmaceutical production hosts, although industry is presently suffering from their variable recombinant product quality, insufficient long-term stability and low productivity. Here, we present an effort to address overall cell line engineering by a novel bottom-up microRNA (miRNA) screening approach. miRNAs are small non-coding RNAs known to regulate global gene expression at the post-transcriptional level and have proved to serve as promising tools for cell line engineering for over a decade. Here the miRNome of plasma cells (PCs) has been analyzed as the natural blueprint for optimized production and secretion of antibodies. Performing comparative miRNome cross-species expression analysis of four murine/human PC-derived (PCD) and two CHO cell lines showed 147 conserved miRNAs to be differentially expressed between PCDs and CHOs. Conducting a targeted miRNA screen of this PC-specific miRNA subset revealed 14 miRNAs to improve bioprocess relevant parameters in CHO cells, among them the PC-characteristic miR-183 cluster. Finally, miRNA target prediction tools and transcriptome analysis were combined to elucidate differentially regulated lysine degradation and fatty acid metabolism pathways in monoclonal antibody (mAb) expressing CHO-DG44 and CHO-K1 cells, respectively. Thus, substantial new insights into molecular and cellular mechanisms of biopharmaceutical production cell lines can be gained by targeted bottom-up miRNA screenings.
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Affiliation(s)
- Nadja Raab
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Nikolas Zeh
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Patrick Schlossbauer
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Sven Mathias
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany; Early Stage Bioprocess Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Benjamin Lindner
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Anna Stadermann
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Martin Gamer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Simon Fischer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | | | - René Handrick
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany.
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High Throughput miRNA Screening Identifies miR-574-3p Hyperproductive Effect in CHO Cells. Biomolecules 2021; 11:biom11081125. [PMID: 34439791 PMCID: PMC8392531 DOI: 10.3390/biom11081125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/11/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022] Open
Abstract
CHO is the cell line of choice for the manufacturing of many complex biotherapeutics. The constant upgrading of cell productivity is needed to meet the growing demand for these life-saving drugs. Manipulation of small non-coding RNAs—miRNAs—is a good alternative to a single gene knockdown approach due to their post-transcriptional regulation of entire cellular pathways without posing translational burden to the production cell. In this study, we performed a high-throughput screening of 2042-human miRNAs and identified several candidates able to increase cell-specific and overall production of Erythropoietin and Etanercept in CHO cells. Some of these human miRNAs have not been found in Chinese hamster cells and yet were still effective in them. We identified miR-574-3p as being able, when overexpressed in CHO cells, to improve overall productivity of Erythropoietin and Etanercept titers from 1.3 to up to 2-fold. In addition, we validated several targets of miR-574-3p and identified p300 as a main target of miR-574-3p in CHO cells. Furthermore, we demonstrated that stable CHO cell overexpressing miRNAs from endogenous CHO pri-miRNA sequences outperform the cells with human pri-miRNA sequences. Our findings highlight the importance of flanking genomic sequences, and their secondary structure features, on pri-miRNA processing offering a novel, cost-effective and fast strategy as a valuable tool for efficient miRNAs engineering in CHO cells.
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11
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Martinez-Lopez JE, Coleman O, Meleady P, Clynes M. Transfection of miR-31* boosts oxidative phosphorylation metabolism in the mitochondria and enhances recombinant protein production in Chinese hamster ovary cells. J Biotechnol 2021; 333:86-96. [PMID: 33940052 DOI: 10.1016/j.jbiotec.2021.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
MicroRNAs are increasingly being used to enhance relevant pathways of interest during CHO cell line development and to optimise biopharmaceutical production processes. Previous studies have demonstrated that genetic manipulation of microRNAs has led to the development of highly productive phenotypes by increasing cell density through modifying the cell cycle, extending the culture lifespan by delaying apoptotic mechanisms, or improving the energetic flux by targeting mitochondrial metabolism. Re-programming mitochondrial metabolism has arisen as a potential area of interest due to the potential to decrease the Warburg effect and increase cell specific productivity with significant impact on the manufacture of recombinant therapeutic proteins. In this study, we have demonstrated a role for miR-31* to enhance specific productivity in CHO cells by boosting oxidative phosphorylation in the mitochondria. A detailed analysis of the mitochondrial metabolism revealed that miR-31* transfection increases basal oxygen consumption and spare respiratory capacity that leads to an increase in ATP production. Additionally, a proteomic analysis unveiled a number of potential targets involved in fatty acid metabolism and the TCA cycle, both implicated in mitochondrial metabolism. This data demonstrates a potential role for miR-31* to reprogramme the mitochondrial energetic metabolism and increase recombinant protein production in CHO cells.
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Affiliation(s)
- Jesus E Martinez-Lopez
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland
| | - Orla Coleman
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland.
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland
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12
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Kumar S, Dhara VG, Orzolek LD, Hao H, More AJ, Lau EC, Betenbaugh MJ. Elucidating the impact of cottonseed hydrolysates on CHO cell culture performance through transcriptomic analysis. Appl Microbiol Biotechnol 2020; 105:271-285. [PMID: 33201275 DOI: 10.1007/s00253-020-10972-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 01/08/2023]
Abstract
In order to evaluate the impact of plant-based hydrolysates on CHO cells, a transcriptomic study was undertaken using cottonseed hydrolysate and Illumina's NextSeq transcriptomics profiling for 2 days of a batch cell culture. While cottonseed hydrolysate extended cell growth and increased antibody titer, significant effects were seen on transcriptomic signatures of supplemented cultures when compared to untreated cultures, evaluated using fold change, gene ontology (GO), and KEGG pathway analysis. Transcription and other factors commonly associated with cell growth such as those of the Atf family and homeobox proteins were upregulated while genes in the Hippo signaling pathway were downregulated. Genes involved in anabolic pathways such as gluconeogenesis and those involving protein folding and translation elongation were upregulated. GO analysis of biological processes for cottonseed-supplemented cultures indicated enrichments in DNA replication, protein processing, and unfolded protein response while molecular functions associated with growth such as GTPases, ATP binding, and aminoacyl t-RNA ligase activity were also enriched. Cellular components associated with structural integrity such as actin cytoskeleton, microtubules, mitochondrion, and Lewy body were enriched. Enriched KEGG pathways include growth-associated pathways such as cell cycle, pI3K-AKT-mTOR, and cancer-related pathways as well as those enhancing glycan metabolism, purine metabolism, amino acid biosynthesis, and protein processing in the endoplasmic reticulum (ER). These transcriptomic profiles provide insights into the roles that hydrolysates such as cottonseed can play in altering CHO cell growth and other physiological characteristics as well as suggesting ways in which CHO cell culture may be modified for enhancing performance in biotechnology applications. KEY POINTS: • Hydrolysate-supplemented cultures increased mammalian cell growth and productivity. • Fold-change analysis revealed upregulation in transcription and translation. • Enriched GOs and KEGG pathways including cell cycle and metabolism were observed.
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Affiliation(s)
- Swetha Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Venkata Gayatri Dhara
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Linda D Orzolek
- Transcriptomics and Deep Sequencing Core, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Haiping Hao
- Transcriptomics and Deep Sequencing Core, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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13
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Abstract
Following the success of and the high demand for recombinant protein-based therapeutics during the last 25 years, the pharmaceutical industry has invested significantly in the development of novel treatments based on biologics. Mammalian cells are the major production systems for these complex biopharmaceuticals, with Chinese hamster ovary (CHO) cell lines as the most important players. Over the years, various engineering strategies and modeling approaches have been used to improve microbial production platforms, such as bacteria and yeasts, as well as to create pre-optimized chassis host strains. However, the complexity of mammalian cells curtailed the optimization of these host cells by metabolic engineering. Most of the improvements of titer and productivity were achieved by media optimization and large-scale screening of producer clones. The advances made in recent years now open the door to again consider the potential application of systems biology approaches and metabolic engineering also to CHO. The availability of a reference genome sequence, genome-scale metabolic models and the growing number of various “omics” datasets can help overcome the complexity of CHO cells and support design strategies to boost their production performance. Modular design approaches applied to engineer industrially relevant cell lines have evolved to reduce the time and effort needed for the generation of new producer cells and to allow the achievement of desired product titers and quality. Nevertheless, important steps to enable the design of a chassis platform similar to those in use in the microbial world are still missing. In this review, we highlight the importance of mammalian cellular platforms for the production of biopharmaceuticals and compare them to microbial platforms, with an emphasis on describing novel approaches and discussing still open questions that need to be resolved to reach the objective of designing enhanced modular chassis CHO cell lines.
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14
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Wang TY, Guo X. Expression vector cassette engineering for recombinant therapeutic production in mammalian cell systems. Appl Microbiol Biotechnol 2020; 104:5673-5688. [PMID: 32372203 DOI: 10.1007/s00253-020-10640-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Human tissue plasminogen activator was the first recombinant therapy protein that successfully produced in Chinese hamster ovary cells in 1986 and approved for clinical use. Since then, more and more therapeutic proteins are being manufactured in mammalian cells, and the technologies for recombinant protein production in this expression system have developed rapidly, with the optimization of both upstream and downstream processes. One of the most promising strategies is expression vector cassette optimization based on the expression vector cassette. In this review paper, these approaches and developments are summarized, and the future strategy on the utilizing of expression cassettes for the production of recombinant therapeutic proteins in mammalian cells is discussed.
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Affiliation(s)
- Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
| | - Xiao Guo
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- Perildicals Publishing House, Xinxiang Medical University, Xinxiang, Henan, China
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15
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Amadi IM, Agrawal V, Christianson T, Bardliving C, Shamlou P, LeBowitz JH. Inhibition of endogenous miR-23a/miR-377 in CHO cells enhances difficult-to-express recombinant lysosomal sulfatase activity. Biotechnol Prog 2020; 36:e2974. [PMID: 31990124 DOI: 10.1002/btpr.2974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/11/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022]
Abstract
Difficult-to-express (DTE) recombinant proteins such as multi-specific proteins, DTE monoclonal antibodies, and lysosomal enzymes have seen difficulties in manufacturability using Chinese hamster ovary (CHO) cells or other mammalian cells as production platforms. CHO cells are preferably used for recombinant protein production for their ability to secrete human-like recombinant proteins with posttranslational modification, resistance to viral infection, and familiarity with drug regulators. However, despite huge progress made in engineering CHO cells for high volumetric productivity, DTE proteins like recombinant lysosomal sulfatase represent one of the poorly understood proteins. Furthermore, there is growing interest in the use of microRNA (miRNA) to engineer CHO cells expressing DTE proteins to improve cell performance of relevant bioprocess phenotypes. To our knowledge, no research has been done to improve CHO cell production of DTE recombinant lysosomal sulfatase using miRNA. We identified miR-23a and miR-377 as miRNAs predicted to target SUMF1, an activator of sulfatases, using in silico prediction tools. Transient inhibition of CHO endogenous miR-23a/miR-377 significantly enhanced recombinant sulfatase enzyme-specific activity by ~15-21% compared to scramble without affecting cell growth. Though inhibition of miR-23a/miR-377 had no significant effect on the mRNA and protein levels of SUMF1, overexpression of miR-23a/377 caused ~30% and ~27-29% significant reduction in endogenous SUMF1 protein and mRNA expression levels, respectively. In summary, our data demonstrate the importance of using miRNA to optimize the CHO cell line secreting DTE recombinant lysosomal sulfatase.
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Affiliation(s)
- Ifeanyi Michael Amadi
- BioMarin Pharmaceutical Inc., Novato, California.,Keck Graduate Institute, Claremont, California
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16
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Chevallier V, Andersen MR, Malphettes L. Oxidative stress-alleviating strategies to improve recombinant protein production in CHO cells. Biotechnol Bioeng 2019; 117:1172-1186. [PMID: 31814104 PMCID: PMC7078918 DOI: 10.1002/bit.27247] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 11/11/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022]
Abstract
Large scale biopharmaceutical production of biologics relies on the overexpression of foreign proteins by cells cultivated in stirred tank bioreactors. It is well recognized and documented fact that protein overexpression may impact host cell metabolism and that factors associated with large scale culture, such as the hydrodynamic forces and inhomogeneities within the bioreactors, may promote cellular stress. The metabolic adaptations required to support the high‐level expression of recombinant proteins include increased energy production and improved secretory capacity, which, in turn, can lead to a rise of reactive oxygen species (ROS) generated through the respiration metabolism and the interaction with media components. Oxidative stress is defined as the imbalance between the production of free radicals and the antioxidant response within the cells. Accumulation of intracellular ROS can interfere with the cellular activities and exert cytotoxic effects via the alternation of cellular components. In this context, strategies aiming to alleviate oxidative stress generated during the culture have been developed to improve cell growth, productivity, and reduce product microheterogeneity. In this review, we present a summary of the different approaches used to decrease the oxidative stress in Chinese hamster ovary cells and highlight media development and cell engineering as the main pathways through which ROS levels may be kept under control.
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Affiliation(s)
- Valentine Chevallier
- Upstream Process Sciences, Biotech Sciences, UCB Nordic A/S, Copenhagen, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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17
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Pairawan MS, Bolhassani A, Rahimpour A. Enhanced transient expression of an anti-CD52 monoclonal antibody in CHO cells through utilization of miRNA sponge technology. Res Pharm Sci 2019; 14:335-342. [PMID: 31516510 PMCID: PMC6714117 DOI: 10.4103/1735-5362.263626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are the dominant mammalian host system for the production of recombinant therapeutic proteins. Improving the viable cell density during culture of recombinant CHO cells can greatly affect the production yield. MicroRNAs (miRs) -15a and 16-1 are known as negative regulators of multiple genes involved in cell cycle progression and apoptotic inhibition. miR sponges, which act as decoy targets, are transcripts which contain complementary binding sites to the seed region of related miRs. Stably expressed miR sponges are known as efficient tools for miR loss of function studies. In this study, stable CHO cell pools and clones expressing miRs-15a and 16-1 specific decoy transcript downstream of an enhanced green fluorescent protein reporter gene was developed. Analysis of cell growth during 12 days of batch culture indicated improved maximum viable cell density of CHO cells and clones expressing the decoy transcript. In addition, transient expression of a recombinant anti-CD52 monoclonal antibody was significantly improved in a decoy harboring CHO cell clone, representing a 3.37-fold increase in yield after 4 days of culture. Our results indicated that miR sponge technology can be successfully applied for the improvement of cell viability and transient monoclonal antibody expression in CHO host cells.
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Affiliation(s)
- Morvarid Sadat Pairawan
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, I.R. Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran.,Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
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18
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Inwood S, Abaandou L, Betenbaugh M, Shiloach J. Improved protein expression in HEK293 cells by over-expressing miR-22 and knocking-out its target gene, HIPK1. N Biotechnol 2019; 54:28-33. [PMID: 31425885 DOI: 10.1016/j.nbt.2019.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/01/2019] [Accepted: 08/15/2019] [Indexed: 02/08/2023]
Abstract
Stable cell lines can continuously produce a recombinant protein without the need to repeatedly engineer the genome. In a previous study HIPK1, Homeodomain-interacting Protein Kinase 1, was found to be a target of the microRNA miR-22 that, when repressed, improved expression of both an intracellular and a secreted protein. In this report, HEK293 cells stably over-expressing miR-22 were compared with HEK293 with knockout of HIPK1, executed by CRISPR/Cas9, for their ability to improve recombinant protein expression. In this model case of luciferase, over-expression of miR-22 improved overall activity 2.4-fold while the HIPK1 knockout improved overall activity 4.7-fold.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA; Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Laura Abaandou
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA.
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19
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Zhu J, Hatton D. New Mammalian Expression Systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 165:9-50. [PMID: 28585079 DOI: 10.1007/10_2016_55] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There are an increasing number of recombinant antibodies and proteins in preclinical and clinical development for therapeutic applications. Mammalian expression systems are key to enabling the production of these molecules, and Chinese hamster ovary (CHO) cell platforms continue to be central to delivery of the stable cell lines required for large-scale production. Increasing pressure on timelines and efficiency, further innovation of molecular formats and the shift to new production systems are driving developments of these CHO cell line platforms. The availability of genome and transcriptome data coupled with advancing gene editing tools are increasing the ability to design and engineer CHO cell lines to meet these challenges. This chapter aims to give an overview of the developments in CHO expression systems and some of the associated technologies over the past few years.
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Affiliation(s)
- Jie Zhu
- MedImmune, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Diane Hatton
- MedImmune, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK.
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20
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21
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Hong JK, Lakshmanan M, Goudar C, Lee DY. Towards next generation CHO cell line development and engineering by systems approaches. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Lim SM, Park SH, Lee JH, Kim SH, Kim JY, Min JK, Lee GM, Kim YG. Differential expression of microRNAs in recombinant Chinese hamster ovary cells treated with sodium butyrate using digital RNA counting. J Biotechnol 2018; 283:37-42. [PMID: 30012463 DOI: 10.1016/j.jbiotec.2018.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 04/13/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023]
Abstract
Sodium butyrate (NaBu) is an efficient supplement for increasing recombinant protein production in Chinese hamster ovary (CHO) cell culture. To elucidate the effects of NaBu on miRNA expression profile in recombinant CHO (rCHO) cells, differentially expressed miRNAs in NaBu-treated rCHO cells were assessed by NanoString nCounter analysis. This result showed that eight mature mouse miRNAs (let-7b, let-7d, miR-15b, miR-25, miR-27a, miR-99a, miR-125a-5p, and miR-125b-5p) were differentially expressed. Furthermore, quantitative real-time RT-PCR analysis of eight mature CHO miRNAs, annotated using a miRBase database, confirmed the transcriptomic findings. Among the potential corresponding target mRNAs for the selected mature miRNAs, seven cell growth-related target genes (e2f2, akt2, mtor, bcl-2, bim, p38α, and bmf) and five N-glycosylation-related target genes (neu1, b4galt3, gale, man1b1 and mgat4a) were selected by considering the effectiveness of NaBu on rCHO cell culture. The altered expression patterns of the 12 target mRNAs were inversely correlated with those of the selected mature miRNAs. Altogether, NanoString nCounter analysis may be useful for identifying differentially expressed miRNAs in rCHO cells.
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Affiliation(s)
- Sung-Min Lim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea
| | - Sun-Hye Park
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea
| | - Joo-Hyoung Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Sun Hong Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Jee Yon Kim
- Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Jeong-Ki Min
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon,South Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea.
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23
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Dangi AK, Sinha R, Dwivedi S, Gupta SK, Shukla P. Cell Line Techniques and Gene Editing Tools for Antibody Production: A Review. Front Pharmacol 2018; 9:630. [PMID: 29946262 PMCID: PMC6006397 DOI: 10.3389/fphar.2018.00630] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/16/2022] Open
Abstract
The present day modern formulation practices for drugs are based on newer tools and techniques toward effective utilization. The methods of antibody formulations are to be revolutionized based on techniques of cell engineering and gene editing. In the present review, we have discussed innovations in cell engineering toward production of novel antibodies for therapeutic applications. Moreover, this review deciphers the use of RNAi, ribozyme engineering, CRISPR-Cas-based techniques for better strategies for antibody production. Overall, this review describes the multidisciplinary aspects of the production of therapeutic proteins that has gained more attention due to its increasing demand.
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Affiliation(s)
- Arun K. Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | | | - Shailja Dwivedi
- Advanced Biotech Lab, Ipca Laboratories Limited, Mumbai, India
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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24
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Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng 2018; 115:2087-2100. [PMID: 29704459 PMCID: PMC6045439 DOI: 10.1002/bit.26722] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/13/2018] [Accepted: 04/25/2018] [Indexed: 12/20/2022]
Abstract
Accurate and complete genome sequences are essential in biotechnology to facilitate genome‐based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short‐read‐based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing and merged this with Illumina‐based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28‐fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up‐ and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.
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Affiliation(s)
- Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Madolyn L MacDonald
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware.,Delaware Biotechnology Institute, Newark, Delaware
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, California.,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California
| | - Heena Dhiman
- Austrian Center of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Shawn Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware.,Delaware Biotechnology Institute, Newark, Delaware
| | - Sven Griep
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Kelley Heffner
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Inmaculada Hernandez
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Karina Brinkrolf
- Department of Biorescources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Vienna, Austria
| | - Mojtaba Samoudi
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California.,Department of Pediatrics, University of California, San Diego, California
| | - Haiping Hao
- Johns Hopkins University Deep Sequencing and Microarray Core, Johns Hopkins University, Baltimore, Maryland
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Michael J Betenbaugh
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, California.,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California.,Department of Pediatrics, University of California, San Diego, California
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kelvin H Lee
- Delaware Biotechnology Institute, Newark, Delaware.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
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25
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Eisenhut P, Klanert G, Weinguny M, Baier L, Jadhav V, Ivansson D, Borth N. A CRISPR/Cas9 based engineering strategy for overexpression of multiple genes in Chinese hamster ovary cells. Metab Eng 2018; 48:72-81. [PMID: 29852271 DOI: 10.1016/j.ymben.2018.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 12/23/2022]
Abstract
Manipulation of multiple genes to engineer Chinese Hamster Ovary (CHO) cells for better performance in production processes of biopharmaceuticals has recently become more and more popular. Yet, identification of useful genes and the unequivocally assessment of their effect alone and in combination(s) on the cellular phenotype is difficult due to high variation between subclones. Here, we present development and proof-of-concept of a novel engineering strategy using multiplexable activation of artificially repressed genes (MAARGE). This strategy will allow faster screening of overexpression of multiple genes in all possible combinations. MAARGE, in its here presented installment, comprises four different genes of interest that can all be stably integrated into the genome from one plasmid in a single transfection. Three of the genes are initially repressed by a repressor element (RE) that is integrated between promoter and translation start site. We show that an elongated 5'-UTR with an additional transcription termination (poly(A)) signal most efficiently represses protein expression. Distinct guide RNA (gRNA) targets flanking the REs for each gene then allow to specifically delete the RE by CRISPR/Cas9 and thus to activate the expression of the corresponding gene(s). We show that both individual and multiplexed activation of the genes of interest in a stably transfected CHO cell line is possible. Also, upon transfection of this stable cell line with all three gRNAs together, it was possible to isolate cells that express all potential gene combinations in a single experiment.
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Key Words
- BFP, Blue Fluorescent Protein
- BP, Bandpass
- CD, Chemically defined
- CHO, Chinese Hamster ovary
- CRISPR, Clustered regularly interspaced palindromic repeats
- CRISPR/Cas9
- Cas9, CRISPR-associated protein 9
- Cell line engineering
- Chinese Hamster
- Fluorescent proteins
- GFP, Green Fluorescent Protein
- MAARGE, Multiplexable Activation of Artificially Repressed Genes
- MFI, Mean fluorescence intensity
- Ovary cells CHO
- Pathway engineering
- RE, Repressor element
- REST, Repressor element 1 silencing transcription factor
- RFP, Red Fluorescent protein
- RFP657, Red Fluorescent protein 657
- bp, Base pairs
- gRNA, Guide RNA
- poly(A), Poly Adenylation signal
- rpm, Rotations per minute
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Affiliation(s)
- Peter Eisenhut
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Klanert
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marcus Weinguny
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Laurenz Baier
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vaibhav Jadhav
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Nicole Borth
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
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26
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Weis BL, Guth N, Fischer S, Wissing S, Fradin S, Holzmann KH, Handrick R, Otte K. Stable miRNA overexpression in human CAP cells: Engineering alternative production systems for advanced manufacturing of biologics using miR-136 and miR-3074. Biotechnol Bioeng 2018; 115:2027-2038. [PMID: 29665036 DOI: 10.1002/bit.26715] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 04/09/2018] [Indexed: 01/06/2023]
Abstract
Chinese hamster ovary (CHO) cells still represent the major production host for therapeutic proteins. However, multiple limitations have been acknowledged leading to the search for alternative expression systems. CEVEC's amniocyte production (CAP) cells are human production cells demonstrated to enable efficient overexpression of recombinant proteins with human glycosylation pattern. However, CAP cells have not yet undergone any engineering approaches to optimize process parameters for a cheaper and more sustainable production of biopharmaceuticals. Thus, we assessed the possibility to enhance CAP cell production capacity via cell engineering using miRNA technology. Based on a previous high-content miRNA screen in CHO-SEAP cells, selected pro-productive miRNAs including, miR-99b-3p, 30a-5p, 329-3p, 483-3p, 370-3p, 219-1-3p, 3074-5p, 136-3p, 30e-5p, 1a-3p, and 484-5p, were shown to act pro-productive and product independent upon transient transfection in CAP and CHO antibody expressing cell lines. Stable expression of miRNAs established seven CAP cell pools with an overexpression of the pro-productive miRNA strand. Subsequent small-scale screening as well as upscaling batch experiments identified miR-136 and miR-3074 to significantly increase final mAb concentration in CAP-mAb cells. Transcriptomic changes analyzed by microarrays identified several lncRNAs as well as growth and apoptosis-related miRNAs to be differentially regulated in CAP-mAb-miR-136 and -miR-3074. This study presents the first engineering approach to optimize the alternative human expression system of CAP-cells.
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Affiliation(s)
- Benjamin L Weis
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nadine Guth
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Simon Fischer
- Boehringer Ingelheim Pharma GmbH & Co KG, Cell Culture Development CMB, Biberach, Germany
| | | | | | | | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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27
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Kamachi Y, Omasa T. Development of hyper osmotic resistant CHO host cells for enhanced antibody production. J Biosci Bioeng 2018; 125:470-478. [DOI: 10.1016/j.jbiosc.2017.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/29/2017] [Accepted: 11/06/2017] [Indexed: 12/28/2022]
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28
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RNA interference technology to improve the baculovirus-insect cell expression system. Biotechnol Adv 2018; 36:443-451. [DOI: 10.1016/j.biotechadv.2018.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/11/2017] [Accepted: 01/13/2018] [Indexed: 02/02/2023]
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29
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Costello A, Lao N, Clynes M, Barron N. Conditional Knockdown of Endogenous MicroRNAs in CHO Cells Using TET-ON-SanDI Sponge Vectors. Methods Mol Biol 2018; 1603:87-100. [PMID: 28493125 DOI: 10.1007/978-1-4939-6972-2_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs of about 22 nucleotides in length and have proven to be useful targets for genetic modifications for desirable phenotype in the biotech industry. The use of constitutively expressed "miRNA sponge" vectors in which multiple, tandem miRNA binding sites containing transcripts are transcriptionally regulated by a constitutive promoter for down regulating the levels of endogenous microRNAs in Chinese hamster ovary (CHO) cells has shown to be more advantageous than using synthetic antisense oligonucleotides. The application of miRNA sponges in biotechnological processes, however, could be more effective, if expression of miRNA sponges could be tuned. In this chapter, we present a method for the generation of stable CHO cell lines expressing a TET-ON-SanDI-miRNA-sponge that is in theory expressed only in the presence of an inducer.
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Affiliation(s)
- Alan Costello
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.
| | - Nga Lao
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Niall Barron
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
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30
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Jazayeri SH, Amiri-Yekta A, Bahrami S, Gourabi H, Sanati MH, Khorramizadeh MR. Vector and Cell Line Engineering Technologies Toward Recombinant Protein Expression in Mammalian Cell Lines. Appl Biochem Biotechnol 2018; 185:986-1003. [PMID: 29396733 DOI: 10.1007/s12010-017-2689-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/29/2017] [Indexed: 11/26/2022]
Abstract
The rapid growth of global biopharmaceutical market in the recent years has been a good indication of its significance in biotechnology industry. During a long period of time in recombinant protein production from 1980s, optimizations in both upstream and downstream processes were launched. In this regard, one of the most promising strategies is expression vector engineering technology based on incorporation of DNA opening elements found in the chromatin border regions of vectors as well as targeting gene integration. Along with these approaches, cell line engineering has revealed convenient outcomes in isolating high-producing clones. According to the fact that more than 50% of the approved therapeutic proteins is being manufactured in mammalian cell lines, in this review, we focus on several approaches and developments in vector and cell line engineering technologies in mammalian cell culture.
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Affiliation(s)
- Seyedeh Hoda Jazayeri
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Amir Amiri-Yekta
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Salahadin Bahrami
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Mohammad Hossein Sanati
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran.
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
| | - Mohammad Reza Khorramizadeh
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, P.O. Box: 1411413137, Tehran, Iran.
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31
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Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells. Genes (Basel) 2018; 9:genes9010025. [PMID: 29315258 PMCID: PMC5793178 DOI: 10.3390/genes9010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 12/27/2022] Open
Abstract
The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO) cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK), while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.
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32
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Li Q, Wang Q, Wang O, Shao K, Lin H, Lei Y. A simple and scalable hydrogel-based system for culturing protein-producing cells. PLoS One 2018; 13:e0190364. [PMID: 29293594 PMCID: PMC5749782 DOI: 10.1371/journal.pone.0190364] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/13/2017] [Indexed: 01/08/2023] Open
Abstract
Recombinant protein therapeutics have become important components of the modern medicine. Majority of them are produced with mammalian cells that are cultured either through adherent culturing, in which cells are cultured on substrates, or suspension culturing, in which cells are suspended and cultured in agitated cell culture medium in a culture vessel. The adherent cell culturing method is limited by its low yield. In suspension culturing, cells need extensive genetic manipulation to grow as single cells at high density, which is time- and labor-consuming. Here, we report a new method, which utilizes a thermoreversible hydrogel as the scaffold for culturing protein-expressing cells. The hydrogel scaffolds not only provide 3D spaces for the cells, but also act as physical barriers to prevent excessive cellular agglomeration and protect cells from the hydrodynamic stresses. As a result, cells can grow at high viability, high growth rate, and extremely high yield even without genetic manipulations. The cell yield in the hydrogels is around 20 times of the suspension culturing. In addition, the protein productivity per cell per day in the hydrogel is higher than the adherent culturing method. This new method is simple, scalable and defined. It will be of great value for both the research laboratories and pharmaceutical industry for producing proteins.
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Affiliation(s)
- Qiang Li
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, Nebraska, United States of America
- Biomedical Engineering Program, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Qiaofeng Wang
- Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ou Wang
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, Nebraska, United States of America
- Biomedical Engineering Program, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Kaifeng Shao
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Haishuang Lin
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Yuguo Lei
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, Nebraska, United States of America
- Biomedical Engineering Program, University of Nebraska, Lincoln, Nebraska, United States of America
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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33
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Inwood S, Betenbaugh MJ, Lal M, Shiloach J. Genome-Wide High-Throughput RNAi Screening for Identification of Genes Involved in Protein Production. Methods Mol Biol 2018; 1850:209-219. [PMID: 30242689 PMCID: PMC9563094 DOI: 10.1007/978-1-4939-8730-6_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
With an increasing number of blockbuster drugs being recombinant mammalian proteins, protein production platforms that focus on mammalian proteins have had a profound impact in many areas of basic and applied research. Many groups, both academic and industrial, have been focusing on developing cost-effective methods to improve the production of mammalian proteins that would support potential therapeutic applications. As it stands, while a wide range of platforms have been successfully developed for laboratory use, the majority of biologicals are still produced in mammalian cell lines due to the requirement for posttranslational modification and the biosynthetic complexity of target proteins. An unbiased high-throughput RNAi screening approach can be an efficient tool to identify target genes involved in recombinant protein production. Here we describe the process of optimizing the transfection conditions, performing the genome-wide siRNA screen, the activity and cell viability assays and the validation transfection to identify genes involved with protein expression.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Madhu Lal
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, MD, USA.
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34
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Kellner K, Solanki A, Amann T, Lao N, Barron N. Targeting miRNAs with CRISPR/Cas9 to Improve Recombinant Protein Production of CHO Cells. Methods Mol Biol 2018; 1850:221-235. [PMID: 30242690 DOI: 10.1007/978-1-4939-8730-6_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs with their unique ability to target hundreds of genes have been highlighted as powerful tools to improve bioprocess behavior of cells. The common approaches to stably deplete miRNAs are the use of sponge decoy transcripts or shRNA inhibitors, which requires the introduction and expression of extra genetic material. As an alternative, we implemented the CRISPR/Cas9 system in our laboratory to generate Chinese hamster ovary (CHO) cells which lack the expression of a specific miRNA for the purpose of functional studies. To implement the system, miR-27a/b was chosen as it has been shown to be upregulated during hypothermic conditions and therefore may be involved in controlling CHO cell growth and recombinant protein productivity. In this chapter, we present a protocol for targeting miRNAs in CHO cells using CRISPR/Cas9 and the analysis of the resulting phenotype, using miR-27 as an example. We showed that it is possible to target miRNAs in CHO cells and achieved ≥80% targeting efficiency. Indel analysis and TOPO-TA cloning combined with Sanger sequencing showed a range of different indels. Furthermore, it was possible to identify clones with no detectable expression of mature miR-27b. Depletion of miR-27b led to improved viability in late stages of batch and fed-batch cultures making it a potentially interesting target to improve bioprocess performance of CHO cells.
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Affiliation(s)
- Kevin Kellner
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland.
| | - Ankur Solanki
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Thomas Amann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nga Lao
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Niall Barron
- National Institute for Bioprocessing Research and Training, Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
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35
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Stolfa G, Smonskey MT, Boniface R, Hachmann AB, Gulde P, Joshi AD, Pierce AP, Jacobia SJ, Campbell A. CHO-Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction. Biotechnol J 2017; 13:e1700227. [PMID: 29072373 DOI: 10.1002/biot.201700227] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 01/07/2023]
Abstract
CHO cells are the most prevalent platform for modern bio-therapeutic production. Currently, there are several CHO cell lines used in bioproduction with distinct characteristics and unique genotypes and phenotypes. These differences limit advances in productivity and quality that can be achieved by the most common approaches to bioprocess optimization and cell line engineering. Incorporating omics-based approaches into current bioproduction processes will complement traditional methodologies to maximize gains from CHO engineering and bioprocess improvements. In order to highlight the utility of omics technologies in CHO bioproduction, the authors discuss current applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, lipidomics, fluxomics, glycomics, and multi-omics approaches and the potential they hold for the future of bioproduction. Multiple omics approaches are currently being used to improve CHO bioprocesses; however, the application of these technologies is still limited. As more CHO-omic datasets become available and integrated into systems models, the authors expect significant gains in product yield and quality. While individual omics technologies provide incremental improvements in bioproduction, the authors will likely see the most significant gains by applying multi-omics and systems biology approaches to individual CHO cell lines.
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Affiliation(s)
- Gino Stolfa
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Ryan Boniface
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Paul Gulde
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Atul D Joshi
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Anson P Pierce
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Scott J Jacobia
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Andrew Campbell
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
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36
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Inwood S, Buehler E, Betenbaugh M, Lal M, Shiloach J. Identifying HIPK1 as Target of miR-22-3p Enhancing Recombinant Protein Production From HEK 293 Cell by Using Microarray and HTP siRNA Screen. Biotechnol J 2017; 13. [PMID: 28987030 DOI: 10.1002/biot.201700342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/11/2017] [Indexed: 01/20/2023]
Abstract
Protein expression from human embryonic kidney cells (HEK 293) is an important tool for structural and clinical studies. It is previously shown that microRNAs (small, noncoding RNAs) are effective means for improved protein expression from these cells, and by conducting a high-throughput screening of the human microRNA library, several microRNAs are identified as potential candidates for improving expression. From these, miR-22-3p is chosen for further study since it increased the expression of luciferase, two membrane proteins and a secreted fusion protein with minimal effect on the cells' growth and viability. Since each microRNA can interact with several gene targets, it is of interest to identify the repressed genes for understanding and exploring the improved expression mechanism for further implementation. Here, the authors describe a novel approach for identification of the target genes by integrating the differential gene expression analysis with information obtained from our previously conducted high-throughput siRNA screening. The identified genes were validated as being involved in improving luciferase expression by using siRNA and qRT-PCR. Repressing the target gene, HIPK1, is found to increase luciferase and GPC3 expression 3.3- and 2.2-fold, respectively.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland 20892, USA.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Eugen Buehler
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Madhu Lal
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland 20892, USA
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37
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Griffith A, Kelly PS, Vencken S, Lao NT, Greene CM, Clynes M, Barron N. miR-CATCH Identifies Biologically Active miRNA Regulators of the Pro-Survival Gene XIAP, in Chinese Hamster Ovary Cells. Biotechnol J 2017; 13:e1700299. [PMID: 28976632 DOI: 10.1002/biot.201700299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/18/2017] [Indexed: 01/01/2023]
Abstract
Genetic engineering of mammalian cells is of interest as a means to boost bio-therapeutic protein yield. X-linked inhibitor of apoptosis (XIAP) overexpression has previously been shown to enhance CHO cell growth and prolong culture longevity while additionally boosting productivity. The authors confirmed this across a range of recombinant products (SEAP, EPO, and IgG). However, stable overexpression of an engineering transgene competes for the cells translational machinery potentially compromising product titre. MicroRNAs are attractive genetic engineering candidates given their non-coding nature and ability to regulate multiple genes simultaneously, thereby relieving the translational burden associated with stable overexpression of a protein-encoding gene. The large number of potential targets of a single miRNA, falsely predicted in silico, presents difficulties in identifying those that could be useful engineering tools. The authors explored the identification of direct miRNA regulators of the pro-survival endogenous XIAP gene in CHO-K1 cells by using a miR-CATCH protocol. A biotin-tagged antisense DNA oligonucleotide for XIAP mRNA is designed and used to pull down and capture bound miRNAs. Two miRNAs are chosen out of the 14 miRNAs identified for further validation, miR-124-3p and miR-19b-3p. Transient transfection of mimics for both results in the diminished translation of endogenous CHO XIAP protein whereas their inhibition increases XIAP protein levels. A 3'UTR reporter assay confirms miR-124-3p to be a bona fide regulator of XIAP in CHO-K1 cells. This method demonstrates a useful approach to finding miRNA candidates for CHO cell engineering without competing for the cellular translational machinery.
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Affiliation(s)
- Alan Griffith
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paul S Kelly
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Sebastian Vencken
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Nga T Lao
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Catherine M Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Niall Barron
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,National Institute for Bioprocessing Research and Training, Fosters Ave, Dublin 4, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin 4, Ireland
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38
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Brown AJ, Kalsi D, Fernandez-Martell A, Cartwright J, Barber NOW, Patel YD, Turner R, Bryant CL, Johari YB, James DC. Expression Systems for Recombinant Biopharmaceutical Production by Mammalian Cells in Culture. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1002/9783527699124.ch13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Adam J. Brown
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Devika Kalsi
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | | | - Joe Cartwright
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Nicholas O. W. Barber
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Yash D. Patel
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | | | - Claire L. Bryant
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Yusuf B. Johari
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - David C. James
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
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39
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Lalonde ME, Durocher Y. Therapeutic glycoprotein production in mammalian cells. J Biotechnol 2017; 251:128-140. [DOI: 10.1016/j.jbiotec.2017.04.028] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 04/12/2017] [Accepted: 04/23/2017] [Indexed: 12/12/2022]
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40
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Meyer HJ, Reilly D, Martin SE, Wong AW. Identification of a novel miRNA that increases transient protein expression in combination with valproic acid. Biotechnol Prog 2017; 33:1139-1145. [DOI: 10.1002/btpr.2488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/18/2017] [Indexed: 12/29/2022]
Affiliation(s)
| | - Dorothea Reilly
- Dept. of Early Stage Cell Culture; 1 DNA Way South San Francisco CA 94080
| | - Scott E. Martin
- Department of Discovery Oncology; Genentech; 1 DNA Way South San Francisco CA 94080
| | - Athena W. Wong
- Dept. of Early Stage Cell Culture; 1 DNA Way South San Francisco CA 94080
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41
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Schoellhorn M, Fischer S, Wagner A, Handrick R, Otte K. miR-143 targets MAPK7 in CHO cells and induces a hyperproductive phenotype to enhance production of difficult-to-express proteins. Biotechnol Prog 2017; 33:1046-1058. [DOI: 10.1002/btpr.2475] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 03/24/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Melanie Schoellhorn
- Inst. of Applied Biotechnology, University of Applied Sciences Biberach; Hubertus-Liebrecht-Strasse 35 Biberach 88400 Germany
| | - Simon Fischer
- Inst. of Applied Biotechnology, University of Applied Sciences Biberach; Hubertus-Liebrecht-Strasse 35 Biberach 88400 Germany
| | - Andreas Wagner
- Inst. of Applied Biotechnology, University of Applied Sciences Biberach; Hubertus-Liebrecht-Strasse 35 Biberach 88400 Germany
| | - René Handrick
- Inst. of Applied Biotechnology, University of Applied Sciences Biberach; Hubertus-Liebrecht-Strasse 35 Biberach 88400 Germany
| | - Kerstin Otte
- Inst. of Applied Biotechnology, University of Applied Sciences Biberach; Hubertus-Liebrecht-Strasse 35 Biberach 88400 Germany
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42
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Fischer S, Marquart KF, Pieper LA, Fieder J, Gamer M, Gorr I, Schulz P, Bradl H. miRNA engineering of CHO cells facilitates production of difficult-to-express proteins and increases success in cell line development. Biotechnol Bioeng 2017; 114:1495-1510. [PMID: 28262952 PMCID: PMC6084326 DOI: 10.1002/bit.26280] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/25/2017] [Accepted: 03/01/2017] [Indexed: 01/05/2023]
Abstract
In recent years, coherent with growing biologics portfolios also the number of complex and thus difficult-to-express (DTE) therapeutic proteins has increased considerably. DTE proteins challenge bioprocess development and can include various therapeutic protein formats such as monoclonal antibodies (mAbs), multi-specific affinity scaffolds (e.g., bispecific antibodies), cytokines, or fusion proteins. Hence, the availability of robust and versatile Chinese hamster ovary (CHO) host cell factories is fundamental for high-yielding bioprocesses. MicroRNAs (miRNAs) have emerged as potent cell engineering tools to improve process performance of CHO manufacturing cell lines. However, there has not been any report demonstrating the impact of beneficial miRNAs on industrial cell line development (CLD) yet. To address this question, we established novel CHO host cells constitutively expressing a pro-productive miRNA: miR-557. Novel host cells were tested in two independent CLD campaigns using two different mAb candidates including a normal as well as a DTE antibody. Presence of miR-557 significantly enhanced each process step during CLD in a product independent manner. Stable expression of miR-557 increased the probability to identify high-producing cell clones. Furthermore, production cell lines derived from miR-557 expressing host cells exhibited significantly increased final product yields in fed-batch cultivation processes without compromising product quality. Strikingly, cells co-expressing miR-557 and a DTE antibody achieved a twofold increase in product titer compared to clones co-expressing a negative control miRNA. Thus, host cell engineering using miRNAs represents a promising tool to overcome limitations in industrial CLD especially with regard to DTE proteins. Biotechnol. Bioeng. 2017;114: 1495-1510. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Simon Fischer
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany.,Cell Culture Development CMB, Boehringer Ingelheim GmbH & Co. KG, Biberach, Germany
| | - Kim F Marquart
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Lisa A Pieper
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Juergen Fieder
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Martin Gamer
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Ingo Gorr
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Patrick Schulz
- Cell Culture Development CMB, Boehringer Ingelheim GmbH & Co. KG, Biberach, Germany
| | - Harald Bradl
- Cell Culture Development CMB, Boehringer Ingelheim GmbH & Co. KG, Biberach, Germany
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Pieper LA, Strotbek M, Wenger T, Gamer M, Olayioye MA, Hausser A. Secretory pathway optimization of CHO producer cells by co-engineering of the mitosRNA-1978 target genes CerS2 and Tbc1D20. Metab Eng 2017; 40:69-79. [PMID: 28088541 DOI: 10.1016/j.ymben.2017.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/23/2016] [Accepted: 01/09/2017] [Indexed: 12/13/2022]
Abstract
Chinese Hamster Ovary (CHO) cells are the most commonly used host for the production of biopharmaceuticals. Although transcription and translation engineering strategies have been employed to generate high-producer cell clones, the secretory pathway still remains a bottleneck in cellular productivity. In this study we show that ectopic expression of a human mitochondrial genome-encoded small RNA (mitosRNA-1978) in an IgG expressing CHO cell line strongly improved specific productivity by functioning in a microRNA-like fashion. By next generation sequencing we identified two endoplasmic reticulum (ER)-localized proteins, Ceramide Synthase 2 (CerS2) and the Rab1 GAP Tbc domain family member 20 (Tbc1D20), as target genes of mitosRNA-1978. Combined transient siRNA-mediated knockdown of CerS2 and Tbc1D20 resulted in increased specific productivity of CHO-IgG cells, thus recapitulating the mitosRNA-1978 phenotype. In support of a function in vesicular trafficking at the level of the ER, we provide evidence for altered cellular ceramide composition upon CerS2 knockdown and increased activity of Rab1 in CHO-IgG cells depleted of Tbc1D20. Importantly, in a fed-batch process, the combined stable knockdown of CerS2 and Tbc1D20 in CHO-IgG cells resulted in dramatically increased antibody production which was accompanied by enhanced cell growth. Thus, by identifying mitosRNA-1978 target genes in combination with an informed shRNA-mediated co-engineering approach we successfully optimized the secretory capacity of CHO producer cells used for the manufacturing of therapeutic proteins.
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Affiliation(s)
- Lisa A Pieper
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany
| | - Michaela Strotbek
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany
| | - Till Wenger
- Boehringer Ingelheim Pharma GmbH & Co.KG, Birkendorfer Str. 65, 88400 Biberach an der Riß, Germany
| | - Martin Gamer
- Boehringer Ingelheim Pharma GmbH & Co.KG, Birkendorfer Str. 65, 88400 Biberach an der Riß, Germany
| | - Monilola A Olayioye
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany; Stuttgart Research Center Systems Biology, University of Stuttgart, Germany.
| | - Angelika Hausser
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany; Stuttgart Research Center Systems Biology, University of Stuttgart, Germany.
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Ritter A, Rauschert T, Oertli M, Piehlmaier D, Mantas P, Kuntzelmann G, Lageyre N, Brannetti B, Voedisch B, Geisse S, Jostock T, Laux H. Disruption of the gene C12orf35
leads to increased productivities in recombinant CHO cell lines. Biotechnol Bioeng 2016; 113:2433-42. [DOI: 10.1002/bit.26009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/08/2016] [Accepted: 05/09/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Anett Ritter
- Novartis Institutes for BioMedical Research; Basel Switzerland
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | | | - Mevion Oertli
- Novartis Institutes for BioMedical Research; Basel Switzerland
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | - Daniel Piehlmaier
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | - Panagiotis Mantas
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | | | - Nadine Lageyre
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | | | - Bernd Voedisch
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | - Sabine Geisse
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | - Thomas Jostock
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | - Holger Laux
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
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45
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A signature of 12 microRNAs is robustly associated with growth rate in a variety of CHO cell lines. J Biotechnol 2016; 235:150-61. [PMID: 26993211 DOI: 10.1016/j.jbiotec.2016.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 12/25/2022]
Abstract
As Chinese Hamster Ovary (CHO) cells are the cell line of choice for the production of human-like recombinant proteins, there is interest in genetic optimization of host cell lines to overcome certain limitations in their growth rate and protein secretion. At the same time, a detailed understanding of these processes could be used to advantage by identification of marker transcripts that characterize states of performance. In this context, microRNAs (miRNAs) that exhibit a robust correlation to the growth rate of CHO cells were determined by analyzing miRNA expression profiles in a comprehensive collection of 46 samples including CHO-K1, CHO-S and CHO-DUKXB11, which were adapted to various culture conditions, and analyzed in different growth stages using microarrays. By applying Spearman or Pearson correlation coefficient criteria of>|0.6|, miRNAs with high correlation to the overall growth, or growth rates observed in exponential, serum-free, and serum-free exponential phase were identified. An overlap of twelve miRNAs common for all sample sets was revealed, with nine positively and three negatively correlating miRNAs. The here identified panel of miRNAs can help to understand growth regulation in CHO cells and contains putative engineering targets as well as biomarkers for cell lines with advantageous growth characteristics.
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46
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The art of CHO cell engineering: A comprehensive retrospect and future perspectives. Biotechnol Adv 2015; 33:1878-96. [DOI: 10.1016/j.biotechadv.2015.10.015] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/21/2015] [Accepted: 10/30/2015] [Indexed: 12/14/2022]
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47
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Harreither E, Hackl M, Pichler J, Shridhar S, Auer N, Łabaj PP, Scheideler M, Karbiener M, Grillari J, Kreil DP, Borth N. Microarray profiling of preselected CHO host cell subclones identifies gene expression patterns associated with increased production capacity. Biotechnol J 2015; 10:1625-38. [PMID: 26315449 DOI: 10.1002/biot.201400857] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 06/22/2015] [Accepted: 08/21/2015] [Indexed: 01/02/2023]
Abstract
Over the last three decades, product yields from CHO cells have increased dramatically, yet specific productivity (qP) remains a limiting factor. In a previous study, using repeated cell-sorting, we have established different host cell subclones that show superior transient qP over their respective parental cell lines (CHO-K1, CHO-S). The transcriptome of the resulting six cell lines in different biological states (untransfected, mock transfected, plasmid transfected) was first explored by hierarchical clustering and indicated that gene activity associated with increased qP did not stem from a certain cellular state but seemed to be inherent for a high qP host line. We then performed a novel gene regression analysis identifying drivers for an increase in qP. Genes significantly implicated were first systematically tested for enrichment of GO terms using a Bayesian approach incorporating the hierarchical structure of the GO term tree. Results indicated that specific cellular components such as nucleus, ER, and Golgi are relevant for cellular productivity. This was complemented by targeted GSA that tested functionally homogeneous, manually curated subsets of KEGG pathways known to be involved in transcription, translation, and protein processing. Significantly implicated pathways included mRNA surveillance, proteasome, protein processing in the ER and SNARE interactions in vesicular transport.
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Affiliation(s)
- Eva Harreither
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Matthias Hackl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Pichler
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Smriti Shridhar
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Paweł P Łabaj
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marcel Scheideler
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Michael Karbiener
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - David P Kreil
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria. .,ACIB GmbH, Graz, Austria.
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Fischer S, Mathias S, Schaz S, Emmerling VV, Buck T, Kleemann M, Hackl M, Grillari J, Aschrafi A, Handrick R, Otte K. Enhanced protein production by microRNA-30 family in CHO cells is mediated by the modulation of the ubiquitin pathway. J Biotechnol 2015; 212:32-43. [PMID: 26256096 DOI: 10.1016/j.jbiotec.2015.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/31/2015] [Accepted: 08/04/2015] [Indexed: 12/20/2022]
Abstract
Functional genomics represent a valuable approach to improve culture performance of Chinese hamster ovary (CHO) cell lines for biopharmaceutical manufacturing. Recent advances in applied microRNA (miRNAs) research suggest that these small non-coding RNAs are critical for the regulation of cell phenotypes in CHO cells. However, the notion that individual miRNAs usually control the expression of hundreds of different genes makes miRNA target identification highly complex. We have recently reported that the entire miR-30 family enhances recombinant protein production in CHO cells. To better understand the pro-productive effects of this miRNA family, we set out to identify their downstream target genes in CHO cells. Computational target prediction combined with a comprehensive functional validation enabled the discovery of a set of twenty putative target genes for all productivity enhancing miR-30 family members. We demonstrate that all miR-30 isoforms contribute to the regulation of the ubiquitin pathway in CHO cells by directly targeting the ubiquitin E3 ligase S-phase kinase-associated protein 2 (Skp2). Finally, we provide several lines of evidence that miR-30-mediated modulation of the ubiquitin pathway may enhance recombinant protein expression in CHO cells. In summary, this study supports the importance of non-coding RNAs, especially of miRNAs, in the context of cell line engineering.
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Affiliation(s)
- Simon Fischer
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany; University of Ulm, Faculty of Medicine, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Sven Mathias
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany; University of Ulm, Faculty of Natural Sciences, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Simone Schaz
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany; University of Ulm, Faculty of Natural Sciences, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Verena Vanessa Emmerling
- University of Ulm, Faculty of Medicine, Albert-Einstein-Allee 11, 89081 Ulm, Germany; Rentschler Biotechnologie GmbH, Erwin-Rentschler-Straße 21, 88471 Laupheim, Germany.
| | - Theresa Buck
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
| | - Michael Kleemann
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
| | | | - Johannes Grillari
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; Evercyte GmbH, Muthgasse 18, 1190 Vienna, Austria.
| | - Armaz Aschrafi
- Department of Neuroinformatics, Donders Institute for Brain Function, Cognition and Behaviour, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
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49
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Fischer S, Paul AJ, Wagner A, Mathias S, Geiss M, Schandock F, Domnowski M, Zimmermann J, Handrick R, Hesse F, Otte K. miR-2861 as novel HDAC5 inhibitor in CHO cells enhances productivity while maintaining product quality. Biotechnol Bioeng 2015; 112:2142-53. [DOI: 10.1002/bit.25626] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/13/2015] [Accepted: 04/23/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Simon Fischer
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
- Faculty of Medicine; University of Ulm; Albert-Einstein-Allee 11; 89081 Ulm Germany
| | - Albert Jesuran Paul
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
| | - Andreas Wagner
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
- Faculty of Natural Sciences; University of Ulm; Ulm Germany
| | - Sven Mathias
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
- Faculty of Natural Sciences; University of Ulm; Ulm Germany
| | - Melanie Geiss
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
- Faculty of Natural Sciences; University of Ulm; Ulm Germany
| | - Franziska Schandock
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
- Faculty of Natural Sciences; University of Ulm; Ulm Germany
| | - Martin Domnowski
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
- Faculty of Natural Sciences; University of Ulm; Ulm Germany
| | - Jörg Zimmermann
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
- Faculty of Natural Sciences; University of Ulm; Ulm Germany
| | - René Handrick
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
| | - Friedemann Hesse
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology; University of Applied Sciences Biberach; Biberach Germany
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50
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Xiao S, Chen YC, Betenbaugh MJ, Martin SE, Shiloach J. MiRNA mimic screen for improved expression of functional neurotensin receptor from HEK293 cells. Biotechnol Bioeng 2015; 112:1632-43. [PMID: 25676429 DOI: 10.1002/bit.25567] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/23/2015] [Accepted: 02/05/2015] [Indexed: 01/17/2023]
Abstract
Obtaining adequate quantities of functional mammalian membrane proteins has been a bottleneck in their structural and functional studies because the expression of these proteins from mammalian cells is relatively low. To explore the possibility of enhancing expression of these proteins using miRNA, a stable T-REx-293 cell line expressing the neurotensin receptor type 1 (NTSR1), a hard-to-express G protein-coupled receptor (GPCR), was constructed. The cell line was then subjected to human miRNA mimic library screening. In parallel, an HEK293 cell line expressing luciferase was also screened with the same human miRNA mimic library. Five microRNA mimics: hsa-miR-22-5p, hsa-miR-18a-5p, hsa-miR-22-3p, hsa-miR-429, and hsa-miR-2110were identified from both screens. They led to 48% increase in the expression of functional NTSR1 and to 239% increase of luciferase expression. These miRNAs were also effective in enhancing the expression of secretedglypican-3 hFc-fusion protein from HEK293 cells.The results indicate that these molecules may have a wide role in enhancing the production of proteins with biomedical interest.
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Affiliation(s)
- Su Xiao
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.,Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Yu-Chi Chen
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850
| | - Michael J Betenbaugh
- Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Scott E Martin
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.
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