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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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Wang XY, Zhang WL, Zhang X, Fu YS, Wang HM, Sun QL, Li Q, Jia YL, Zhang JH, Wang TY. Combination of MAR and intron increase transgene expression of episomal vectors in CHO cells. Biotechnol J 2023; 18:e2200643. [PMID: 37551822 DOI: 10.1002/biot.202200643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/09/2023]
Abstract
Previous work has shown that the EF-1α promoter of episomal vectors maintains high-level transgene expression in stably transfected Chinese hamster ovary (CHO) cells. However, the transgene expression levels need to be further increased. Here, we first incorporated matrix attachment regions (MARs), ubiquitous chromatin opening element (UCOE), stabilizing anti repressor elements 40 (STAR 40) elements into episomal vector at different sites and orientations, and systemically assessed their effects on transgene expression in transfected CHO-K1 cells. Results showed that enhanced green fluorescent protein (eGFP) expression levels increased remarkably when MAR X-29 was inserted upstream of the promoter, followed by the insertion of MAR1 downstream of the poly A, and the orientation had no significant effect. Moreover, MAR X-29 combined with human cytomegalovirus intron (hCMVI) yielded the highest transgene expression levels (4.52-fold). Transgene expression levels were not exclusively dependent on transgene copy numbers and were not related to the mRNA expression level. In addition, vector with MAR X-29+hCMVI can induce herpes simplex virus thymidine kinase (HSV-TK) protein expression, and the HSV-TK protein showed a cell-killing effect and an obvious bystander effect on HCT116 cells. In conclusion, the combination of MAR X-29 and hCMV intron can achieve high efficiency transgene expression mediated by episomal vectors in CHO-K1 cells.
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Affiliation(s)
- Xiao-Yin Wang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Wei-Li Zhang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
- Center for Medical Genetics, Nanyang Second General Hospital, Nanyang, China
| | - Xi Zhang
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Yu-Shun Fu
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Hao-Min Wang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Qiu-Li Sun
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Qin Li
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Yan-Long Jia
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Jun-He Zhang
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
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Bartolo-Aguilar Y, Chávez-Cabrera C, Flores-Cotera LB, Badillo-Corona JA, Oliver-Salvador C, Marsch R. The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells. J Genet Eng Biotechnol 2022; 20:173. [PMID: 36580173 PMCID: PMC9800685 DOI: 10.1186/s43141-022-00455-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Low-temperature expression of recombinant proteins may be advantageous to support their proper folding and preserve bioactivity. The generation of expression vectors regulated under cold conditions can improve the expression of some target proteins that are difficult to express in different expression systems. The cspA encodes the major cold-shock protein from Escherichia coli (CspA). The promoter of cspA has been widely used to develop cold shock-inducible expression platforms in E. coli. Moreover, it is often necessary to employ expression systems other than bacteria, particularly when recombinant proteins require complex post-translational modifications. Currently, there are no commercial platforms available for expressing target genes by cold shock in eukaryotic cells. Consequently, genetic elements that respond to cold shock offer the possibility of developing novel cold-inducible expression platforms, particularly suitable for yeasts, and mammalian cells. CONCLUSIONS This review covers the importance of the cellular response to low temperatures and the prospective use of cold-sensitive promoters to direct the expression of recombinant proteins. This concept may contribute to renewing interest in applying white technologies to produce recombinant proteins that are difficult to express.
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Affiliation(s)
- Yaneth Bartolo-Aguilar
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
- Instituto Politécnico Nacional-Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto s/n, Colonia Barrio La Laguna Ticomán, 07340, Mexico City, Mexico
| | - Cipriano Chávez-Cabrera
- Colegio de Estudios Científicos y Tecnológicos del Estado de Michoacán, CECyTE Michoacán, Héroes de la Revolución S/N, Col. Centro, 61880, Churumuco de Morelos, Michoacán, Mexico.
| | - Luis Bernardo Flores-Cotera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
| | - Jesús Agustín Badillo-Corona
- Instituto Politécnico Nacional-Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto s/n, Colonia Barrio La Laguna Ticomán, 07340, Mexico City, Mexico
| | - Carmen Oliver-Salvador
- Instituto Politécnico Nacional-Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto s/n, Colonia Barrio La Laguna Ticomán, 07340, Mexico City, Mexico
| | - Rodolfo Marsch
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, 07360, Mexico City, Mexico
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Waghela IN, Mallory KL, Taylor JA, Schneider CG, Savransky T, Janse CJ, Lin PJC, Tam YK, Weissman D, Angov E. Exploring in vitro expression and immune potency in mice using mRNA encoding the Plasmodium falciparum malaria antigen, CelTOS. Front Immunol 2022; 13:1026052. [PMID: 36591298 PMCID: PMC9798330 DOI: 10.3389/fimmu.2022.1026052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
The secreted malarial protein, Cell-Traversal protein for Ookinetes and Sporozoites (CelTOS), is highly conserved among Plasmodium species, and plays a role in the invasion of mosquito midgut cells and hepatocytes in the vertebrate host. CelTOS was identified as a potential protective antigen based on a proteomic analysis, which showed that CelTOS stimulated significant effector T cells producing IFN-γ in peripheral blood mononuclear cells (PBMCs) from radiation attenuated sporozoite-immunized, malaria-naïve human subjects. In a rodent malaria model, recombinant full-length CelTOS protein/adjuvant combinations induced sterile protection, and in several studies, functional antibodies were produced that had hepatocyte invasion inhibition and transmission-blocking activities. Despite some encouraging results, vaccine approaches using CelTOS will require improvement before it can be considered as an effective vaccine candidate. Here, we report on the use of mRNA vaccine technology to induce humoral and cell-mediated immune responses using this antigen. Several pfceltos encoding mRNA transcripts were assessed for the impact on protein translation levels in vitro. Protein coding sequences included those to evaluate the effects of signal sequence, N-glycosylation on translation, and of nucleoside substitutions. Using in vitro transfection experiments as a pre-screen, we assessed the quality of the expressed CelTOS target relative to the homogeneity, cellular localization, and durability of expression levels. Optimized mRNA transcripts, which demonstrated highest protein expression levels in vitro were selected for encapsulation in lipid nanoparticles (LNP) and used to immunize mice to assess for both humoral and cellular cytokine responses. Our findings indicate that mRNA transcripts encoding pfceltos while potent for inducing antigen-specific cellular cytokine responses in mice, were less able to mount PfCelTOS-specific antibody responses using a two-dose regimen. An additional booster dose was needed to overcome low seroconversion rates in mice. With respect to antibody fine specificities, N-glycosylation site mutated immunogens yielded lower immune responses, particularly to the N-terminus of the molecule. While it remains unclear the impact on CelTOS antigen as immunogen, this study highlights the need to optimize antigen design for vaccine development.
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Affiliation(s)
- Ishita N. Waghela
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States,Parsons Corporation, Centreville, VA, United States
| | - Katherine L. Mallory
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States,Parsons Corporation, Centreville, VA, United States
| | - Justin A. Taylor
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States,The Geneva Foundation, Tacoma, WA, United States
| | - Cosette G. Schneider
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States,Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Tatyana Savransky
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States,General Dynamics Information Technology, Falls Church, VA, United States
| | - Chris J. Janse
- Parasitology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | | | - Ying K. Tam
- Acuitas Therapeutics Inc., Vancouver, BC, Canada
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Evelina Angov
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States,*Correspondence: Evelina Angov,
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5
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Mallory KL, Taylor JA, Zou X, Waghela IN, Schneider CG, Sibilo MQ, Punde NM, Perazzo LC, Savransky T, Sedegah M, Dutta S, Janse CJ, Pardi N, Lin PJC, Tam YK, Weissman D, Angov E. Messenger RNA expressing PfCSP induces functional, protective immune responses against malaria in mice. NPJ Vaccines 2021; 6:84. [PMID: 34145286 PMCID: PMC8213722 DOI: 10.1038/s41541-021-00345-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/24/2021] [Indexed: 02/05/2023] Open
Abstract
Human malaria affects the vast majority of the world's population with the Plasmodium falciparum species causing the highest rates of morbidity and mortality. With no licensed vaccine and leading candidates achieving suboptimal protection in the field, the need for an effective immunoprophylactic option continues to motivate the malaria research community to explore alternative technologies. Recent advances in the mRNA discipline have elevated the long-neglected platform to the forefront of infectious disease research. As the immunodominant coat protein of the invasive stage of the malaria parasite, circumsporozoite protein (PfCSP) was selected as the antigen of choice to assess the immunogenic and protective potential of an mRNA malaria vaccine. In mammalian cell transfection experiments, PfCSP mRNA was well expressed and cell associated. In the transition to an in vivo murine model, lipid nanoparticle (LNP) encapsulation was applied to protect and deliver the mRNA to the cell translation machinery and supply adjuvant activity. The immunogenic effect of an array of factors was explored, such as formulation, dose, number, and interval of immunizations. PfCSP mRNA-LNP achieved sterile protection against infection with two P. berghei PfCSP transgenic parasite strains, with mRNA dose and vaccination interval having a greater effect on outcome. This investigation serves as the assessment of pre-erythrocytic malaria, PfCSP mRNA vaccine candidate resulting in sterile protection, with numerous factors affecting protective efficacy, making it a compelling candidate for further investigation.
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Affiliation(s)
- Katherine L Mallory
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Parsons Corporation, Centreville, VA, USA
| | - Justin A Taylor
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Geneva Foundation, Tacoma, WA, USA
| | - Xiaoyan Zou
- Naval Medical Research Center, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ishita N Waghela
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Parsons Corporation, Centreville, VA, USA
| | - Cosette G Schneider
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Michael Q Sibilo
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Parsons Corporation, Centreville, VA, USA
| | - Neeraja M Punde
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Geneva Foundation, Tacoma, WA, USA
| | - Leah C Perazzo
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- General Dynamics Information Technology, Falls Church, VA, USA
| | - Tatyana Savransky
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
- General Dynamics Information Technology, Falls Church, VA, USA
| | | | - Sheetij Dutta
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Chris J Janse
- Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Ying K Tam
- Acuitas Therapeutics, Vancouver, BC, Canada
| | | | - Evelina Angov
- Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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6
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McGraw CE, Peng D, Sandoval NR. Synthetic biology approaches: the next tools for improved protein production from CHO cells. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2020.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Guo X, Wang C, Wang TY. Chromatin-modifying elements for recombinant protein production in mammalian cell systems. Crit Rev Biotechnol 2020; 40:1035-1043. [PMID: 32777953 DOI: 10.1080/07388551.2020.1805401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mammalian cells are the preferred choice system for the production of complex molecules, such as recombinant therapeutic proteins. Although the technology for increasing the yield of proteins has improved rapidly, the process of selecting, identifying as well as maintaining high-yield cell clones is still troublesome, time-consuming and usually uncertain. Optimization of expression vectors is one of the most effective methods for enhancing protein expression levels. Several commonly used chromatin-modifying elements, including the matrix attachment region, ubiquitous chromatin opening elements, insulators, stabilizing anti-repressor elements can be used to increase the expression level and stability of recombinant proteins. In this review, these chromatin-modifying elements used for the expression vector optimization in mammalian cells are summarized, and future strategies for the utilization of expression cassettes are also discussed.
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Affiliation(s)
- Xiao Guo
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China.,Perildicals Publishing House, Xinxiang Medical University, Xinxiang, China
| | - Chong Wang
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China.,Perildicals Publishing House, Xinxiang Medical University, Xinxiang, China
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8
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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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9
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Nguyen LN, Novak N, Baumann M, Koehn J, Borth N. Bioinformatic Identification of Chinese Hamster Ovary (CHO) Cold‐Shock Genes and Biological Evidence of their Cold‐Inducible Promoters. Biotechnol J 2019; 15:e1900359. [DOI: 10.1002/biot.201900359] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/02/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Ly Ngoc Nguyen
- Austrian Centre of Industrial Biotechnology Muthgasse 11 1190 Vienna Austria
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences Muthgasse 18 1190 Vienna Austria
| | - Neža Novak
- Austrian Centre of Industrial Biotechnology Muthgasse 11 1190 Vienna Austria
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences Muthgasse 18 1190 Vienna Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology Muthgasse 11 1190 Vienna Austria
| | - Jadranka Koehn
- Rentschler Biopharma Erwin‐Rentschler‐Strasse 21 88471 Laupheim Germany
| | - Nicole Borth
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences Muthgasse 18 1190 Vienna Austria
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10
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Gupta K, Parasnis M, Jain R, Dandekar P. Vector-related stratagems for enhanced monoclonal antibody production in mammalian cells. Biotechnol Adv 2019; 37:107415. [DOI: 10.1016/j.biotechadv.2019.107415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
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11
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Lee Y, Kim H, Kim E, Park S, Ryu KH, Lee EG. Rational design of transient gene expression process with lipoplexes for high-level therapeutic protein production in HEK293 cells. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.06.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Nguyen LN, Baumann M, Dhiman H, Marx N, Schmieder V, Hussein M, Eisenhut P, Hernandez I, Koehn J, Borth N. Novel Promoters Derived from Chinese Hamster Ovary Cells via In Silico and In Vitro Analysis. Biotechnol J 2019; 14:e1900125. [DOI: 10.1002/biot.201900125] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/14/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Ly N. Nguyen
- Department of BiotechnologyBOKU University of Natural Resources and Life SciencesMuthgasse 18 1190 Vienna Austria
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
| | - Martina Baumann
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
| | - Heena Dhiman
- Department of BiotechnologyBOKU University of Natural Resources and Life SciencesMuthgasse 18 1190 Vienna Austria
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
| | - Nicolas Marx
- Department of BiotechnologyBOKU University of Natural Resources and Life SciencesMuthgasse 18 1190 Vienna Austria
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
| | - Valerie Schmieder
- Department of BiotechnologyBOKU University of Natural Resources and Life SciencesMuthgasse 18 1190 Vienna Austria
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
| | - Mohamed Hussein
- Department of BiotechnologyBOKU University of Natural Resources and Life SciencesMuthgasse 18 1190 Vienna Austria
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
| | - Peter Eisenhut
- Department of BiotechnologyBOKU University of Natural Resources and Life SciencesMuthgasse 18 1190 Vienna Austria
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
| | | | | | - Nicole Borth
- Department of BiotechnologyBOKU University of Natural Resources and Life SciencesMuthgasse 18 1190 Vienna Austria
- Austrian Center of Industrial Biotechnology GmbH1190 Vienna Austria
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13
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Pristovšek N, Nallapareddy S, Grav LM, Hefzi H, Lewis NE, Rugbjerg P, Hansen HG, Lee GM, Andersen MR, Kildegaard HF. Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell Engineering. ACS Synth Biol 2019; 8:758-774. [PMID: 30807689 DOI: 10.1021/acssynbio.8b00453] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many branches of biology depend on stable and predictable recombinant gene expression, which has been achieved in recent years through targeted integration of the recombinant gene into defined integration sites. However, transcriptional levels of recombinant genes in characterized integration sites are controlled by multiple components of the integrated expression cassette. Lack of readily available tools has inhibited meaningful experimental investigation of the interplay between the integration site and the expression cassette components. Here we show in a systematic manner how multiple components contribute to final net expression of recombinant genes in a characterized integration site. We develop a CRISPR/Cas9-based toolbox for construction of mammalian cell lines with targeted integration of a landing pad, containing a recombinant gene under defined 5' proximal regulatory elements. Generated site-specific recombinant cell lines can be used in a streamlined recombinase-mediated cassette exchange for fast screening of different expression cassettes. Using the developed toolbox, we show that different 5' proximal regulatory elements generate distinct and robust recombinant gene expression patterns in defined integration sites of CHO cells with a wide range of transcriptional outputs. This approach facilitates the generation of user-defined and product-specific gene expression patterns for programmable mammalian cell engineering.
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Affiliation(s)
- Nuša Pristovšek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Saranya Nallapareddy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Hooman Hefzi
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, California 92093, United States
| | - Nathan E. Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, California 92093, United States
| | - Peter Rugbjerg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Henning Gram Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
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Johari YB, Brown AJ, Alves CS, Zhou Y, Wright CM, Estes SD, Kshirsagar R, James DC. CHO genome mining for synthetic promoter design. J Biotechnol 2019; 294:1-13. [PMID: 30703471 DOI: 10.1016/j.jbiotec.2019.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 01/01/2023]
Abstract
Synthetic promoters are an attractive alternative for use in mammalian hosts such as CHO cells as they can be designed de novo with user-defined functionalities. In this study, we describe and validate a method for bioprocess-directed design of synthetic promoters utilizing CHO genomic sequence information. We designed promoters with two objective features, (i) constitutive high-level recombinant gene transcription, and (ii) upregulated transcription under mild hypothermia or late-stage culture. CHO genes varying in transcriptional activity were selected based on a comparative analysis of RNA-Seq transcript levels in normal and biphasic cultures in combination with estimates of mRNA half-life from published genome scale datasets. Discrete transcription factor regulatory elements (TFREs) upstream of these genes were informatically identified and functionally screened in vitro to identify a subset of TFREs with the potential to support high activity recombinant gene transcription during biphasic cell culture processes. Two libraries of heterotypic synthetic promoters with varying TFRE combinations were then designed in silico that exhibited a maximal 2.5-fold increase in transcriptional strength over the CMV-IE promoter after transient transfection into host CHO-K1 cells. A subset of synthetic promoters was then used to create stable transfectant pools using CHO-K1 cells under glutamine synthetase selection. Whilst not achieving the maximal 2.5-fold increase in productivity over stable pools harboring the CMV promoter, all stably transfected cells utilizing synthetic promoters exhibited increased reporter production - up to 1.6-fold that of cells employing CMV, both in the presence or absence of intron A immediately downstream of the promoter. The increased productivity of stably transfected cells harboring synthetic promoters was maintained during fed-batch culture, with or without a transition to mild hypothermia at the onset of stationary phase. Our data exemplify that it is important to consider both host cell and intended bioprocess contexts as design criteria in the de novo construction of synthetic genetic parts for mammalian cell engineering.
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Affiliation(s)
- Yusuf B Johari
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
| | - Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
| | | | - Yizhou Zhou
- Cell Culture Development, Biogen Inc., Cambridge, MA 02142, USA
| | | | - Scott D Estes
- Cell Culture Development, Biogen Inc., Cambridge, MA 02142, USA
| | | | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK.
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15
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Hamaker NK, Lee KH. Site-specific Integration Ushers in a New Era of Precise CHO Cell Line Engineering. Curr Opin Chem Eng 2018; 22:152-160. [PMID: 31086757 DOI: 10.1016/j.coche.2018.09.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chinese hamster ovary (CHO) cells are widely used for the production of therapeutic proteins. Customarily, CHO production cell lines are established through random integration, which requires laborious screening of many clones to isolate suitable producers. In contrast, site-specific integration (SSI) accelerates cell line development by targeting integration of transgenes to pre-validated genomic loci capable of supporting high and stable expression. To date, a relatively small number of these so called 'hot spots' have been identified, mainly through empirical methods. Nevertheless, nuclease-mediated and recombinase-mediated SSI have revolutionized cell line engineering by enabling rational and reproducible transgene targeting.
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Affiliation(s)
- Nathaniel K Hamaker
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Kelvin H Lee
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
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16
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Wang W, Guo X, Li YM, Wang XY, Yang XJ, Wang YF, Wang TY. Enhanced transgene expression using cis-acting elements combined with the EF1 promoter in a mammalian expression system. Eur J Pharm Sci 2018; 123:539-545. [DOI: 10.1016/j.ejps.2018.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2018] [Accepted: 08/11/2018] [Indexed: 10/28/2022]
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17
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Xu DH, Wang XY, Jia YL, Wang TY, Tian ZW, Feng X, Zhang YN. SV40 intron, a potent strong intron element that effectively increases transgene expression in transfected Chinese hamster ovary cells. J Cell Mol Med 2018; 22:2231-2239. [PMID: 29441681 PMCID: PMC5867124 DOI: 10.1111/jcmm.13504] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/15/2017] [Indexed: 12/20/2022] Open
Abstract
Chinese hamster ovary (CHO) cells have become the most widely utilized mammalian cell line for the production of recombinant proteins. However, the product yield and transgene instability need to be further increased and solved. In this study, we investigated the effect of five different introns on transgene expression in CHO cells. hCMV intron A, adenovirus tripartite leader sequence intron, SV40 intron, Chinese hamster EF-1alpha gene intron 1 and intervening sequence intron were cloned downstream of the eGFP expression cassette in a eukaryotic vector, which was then transfected into CHO cells. qRT-PCR and flow cytometry were used to explore eGFP expression levels. And gene copy number was also detected by qPCR, respectively. Furthermore, the erythropoietin (EPO) protein was used to test the selected more strong intron. The results showed that SV40 intron exhibited the highest transgene expression level among the five compared intron elements under transient and stable transfections. In addition, the SV40 intron element can increase the ratio of positive colonies and decrease the coefficient of variation in transgene expression level. Moreover, the transgene expression level was not related to the gene copy number in stable transfected CHO cells. Also, the SV40 intron induced higher level of EPO expression than IVS intron in transfected CHO cell. In conclusion, SV40 intron is a potent strong intron element that increases transgene expression, which can readily be used to more efficient transgenic protein production in CHO cells.
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Affiliation(s)
- Dan-Hua Xu
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiao-Yin Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yan-Long Jia
- Pharmacy collage, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zheng-Wei Tian
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xin Feng
- Grade 2014, The Third Clinical Medical College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Yin-Na Zhang
- Grade 2014, The Third Clinical Medical College of Xinxiang Medical University, Xinxiang, Henan, China
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18
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Romanova N, Noll T. Engineered and Natural Promoters and Chromatin-Modifying Elements for Recombinant Protein Expression in CHO Cells. Biotechnol J 2017; 13:e1700232. [DOI: 10.1002/biot.201700232] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/07/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Nadiya Romanova
- Cell Culture Technology; Faculty of Technology; Bielefeld University; Germany
| | - Thomas Noll
- Cell Culture Technology; Faculty of Technology; Bielefeld University; Germany
- Bielefeld University; Center for Biotechnology (CeBiTec); Germany
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19
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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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20
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Identification of regulatory motifs in the CHO genome for stable monoclonal antibody production. Cytotechnology 2016; 69:451-460. [PMID: 27544513 DOI: 10.1007/s10616-016-0017-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/08/2016] [Indexed: 01/05/2023] Open
Abstract
Chinese hamster ovary (CHO) cell lines are widely used for therapeutic protein production. When a transgene is integrated into the genome of a CHO cell, the expression level is highly dependent on the site of integration because of positional effects such as gene silencing. To overcome negative positional effects and establish stable CHO cell lines with high productivity, several regulatory DNA elements are used in vector construction. Previously, we established the CHO DR1000L-4N cell line, a stable and high copy number Dhfr gene-amplified cell line. It was hypothesized that the chromosomal location of the exogenous gene-amplified region in the CHO DR1000L-4N genome contains regulatory motifs for stable protein production. Therefore, we isolated DNA regulatory motifs from the CHO DR1000L-4N cell line and determined whether these motifs act as an insulator. Our results suggest that stable expression of a transgene can be promoted by the CHO genome sequence, and it would be a powerful tool for therapeutic protein manufacturing.
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