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Nguyen L, Schmelzer B, Wilkinson S, Mattanovich D. From natural to synthetic: Promoter engineering in yeast expression systems. Biotechnol Adv 2024; 77:108446. [PMID: 39245291 DOI: 10.1016/j.biotechadv.2024.108446] [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: 07/12/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
Synthetic promoters are particularly relevant for application not only in yeast expression systems designed for high-level heterologous protein production but also in other applications such as metabolic engineering, cell biological research, and stage-specific gene expression control. By designing synthetic promoters, researcher can create customized expression systems tailored to specific needs, whether it is maximizing protein production or precisely controlling gene expression at different stages of a process. While recognizing the limitations of endogenous promoters, they also provide important information needed to design synthetic promoters. In this review, emphasis will be placed on some key approaches to identify endogenous, and to generate synthetic promoters in yeast expression systems. It shows the connection between endogenous and synthetic promoters, highlighting how their interplay contributes to promoter development. Furthermore, this review illustrates recent developments in biotechnological advancements and discusses how this field will evolve in order to develop custom-made promoters for diverse applications. This review offers detailed information, explores the transition from endogenous to synthetic promoters, and presents valuable perspectives on the next generation of promoter design strategies.
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Affiliation(s)
- Ly Nguyen
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria
| | - Bernhard Schmelzer
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria
| | | | - Diethard Mattanovich
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
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2
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Shin SW, Min H, Kim J, Lee JS. A precise and sustainable doxycycline-inducible cell line development platform for reliable mammalian cell engineering with gain-of-function mutations. Metab Eng 2024; 86:12-28. [PMID: 39242074 DOI: 10.1016/j.ymben.2024.09.004] [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: 05/28/2024] [Revised: 08/20/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
For mammalian synthetic biology research, multiple orthogonal and tunable gene expression systems have been developed, among which the tetracycline (Tet)-inducible system is a key tool for gain-of-function mutations. Precise and long-lasting regulation of genetic circuits is necessary for the effective use of these systems in genetically engineered stable cell lines. However, current cell line development strategies, which depend on either random or site-specific integration along with antibiotic selection, are unpredictable and unsustainable, limiting their widespread use. To overcome these issues, we aimed to establish a Robust Overexpression via Site-specific integration of Effector (ROSE) system, a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated streamlined Tet-On3G-inducible master cell line (MCL) development platform. ROSE MCLs equipped with a landing pad facilitated the transcriptional regulation of various effector genes via recombinase-mediated cassette exchange. Long-term investigation revealed that the modular design of genetic payloads and integration sites significantly affected the induction capacity and stability, with ROSE MCLs exhibiting exceptional induction performance. To demonstrate the versatility of our platform, we explored its efficiency for the precise regulation of selection stringency, manufacturing of therapeutic antibodies with tunable expression levels and timing, and transcription factor engineering. Overall, this study demonstrated the effectiveness and reliability of the ROSE platform, highlighting its potential for various biological and biotechnological applications.
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Affiliation(s)
- Sung Wook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Honggi Min
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Jiwon Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea; Advanced College of Bio-convergence Engineering, Ajou University, Suwon, 16499, Republic of Korea.
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3
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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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4
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Liu HN, Wang XY, Zou Y, Wu WB, Lin Y, Ji BY, Wang TY. Synthetic enhancers including TFREs improve transgene expression in CHO cells. Heliyon 2024; 10:e26901. [PMID: 38468921 PMCID: PMC10926067 DOI: 10.1016/j.heliyon.2024.e26901] [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: 12/27/2023] [Revised: 02/12/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
The human cytomegalovirus major immediate early gene (CMV) promoter is currently the most preferred promoter for recombinant therapeutic proteins (RTPs) production in CHO cells. To enhance the production of RTPs, five synthetic enhancers including multiple transcription factor regulatory elements (TFREs) were evaluated to enhance recombinant protein level in transient and stably transfected CHO cells. Compared with the control, four elements can enhance the report genes expression under both two transfected states. Further, the function of these four enhancers on human serum albumin (HSA) were investigated. We found that the transient expression can increase by up to 1.5 times, and the stably expression can maximum increase by up to 2.14 times. The enhancement of transgene expression was caused by the boost of their corresponding mRNA levels. Transcriptomics analysis was performed and found that transcriptional activation and cell cycle regulation genes were involved. In conclusion, optimization of enhancers in the CMV promoter could increase the production yield of transgene in transfected CHO cells, which has significance for developing high-yield CHO cell expression system.
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Affiliation(s)
- Hui-Ning Liu
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, China
- SanQuan College of Xinxiang Medical University, Xinxiang 453003, China
| | - Xiao-Yin Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Ying Zou
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Wen-Bao Wu
- Shanghai Immunocan Biotech Co., LTD, Shanghai 200000, China
| | - Yan Lin
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, China
| | - Bo-Yu Ji
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, China
| | - Tian-Yun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Xinxiang Medical University, Xinxiang 453003, China
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Yoon C, Baek KE, Kim D, Lee GM. Mitigating transcriptional bottleneck using a constitutively active transcription factor, VP16-CREB, in mammalian cells. Metab Eng 2023; 80:33-44. [PMID: 37709006 DOI: 10.1016/j.ymben.2023.09.005] [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: 08/13/2022] [Revised: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
High-level expression of recombinant proteins in mammalian cells has long been an area of interest. Inefficient transcription machinery is often an obstacle in achieving high-level expression of recombinant proteins in mammalian cells. Synthetic promoters have been developed to improve the transcription efficiency, but have achieved limited success due to the limited availability of transcription factors (TFs). Here, we present a TF-engineering approach to mitigate the transcriptional bottlenecks of recombinant proteins. This includes: (i) identification of cAMP response element binding protein (CREB) as a candidate TF by searching for TFs enriched in the cytomegalovirus (CMV) promoter-driven high-producing recombinant Chinese hamster ovary (rCHO) cell lines via transcriptome analysis, (ii) confirmation of transcriptional limitation of active CREB in rCHO cell lines, and (iii) direct activation of the transgene promoter by expressing constitutively active CREB at non-cytotoxic levels in rCHO cell lines. With the expression of constitutively active VP16-CREB, the production of therapeutic proteins, such as monoclonal antibody and etanercept, in CMV promoter-driven rCHO cell lines was increased up to 3.9-fold. VP16-CREB was also used successfully with synthetic promoters containing cAMP response elements. Taken together, this strategy to introduce constitutively active TFs into cells is a useful means of overcoming the transcriptional limitations in recombinant mammalian cells.
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Affiliation(s)
- Chansik Yoon
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Kyoung Eun Baek
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Dongil Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea.
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Leitner K, Motheramgari K, Borth N, Marx N. Nanopore Cas9-targeted sequencing enables accurate and simultaneous identification of transgene integration sites, their structure and epigenetic status in recombinant Chinese hamster ovary cells. Biotechnol Bioeng 2023; 120:2403-2418. [PMID: 36938677 DOI: 10.1002/bit.28382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/27/2023] [Accepted: 03/12/2023] [Indexed: 03/21/2023]
Abstract
The integration of a transgene expression construct into the host genome is the initial step for the generation of recombinant cell lines used for biopharmaceutical production. The stability and level of recombinant gene expression in Chinese hamster ovary (CHO) can be correlated to the copy number, its integration site as well as the epigenetic context of the transgene vector. Also, undesired integration events, such as concatemers, truncated, and inverted vector repeats, are impacting the stability of recombinant cell lines. Thus, to characterize cell clones and to isolate the most promising candidates, it is crucial to obtain information on the site of integration, the structure of integrated sequence and the epigenetic status. Current sequencing techniques allow to gather this information separately but do not offer a comprehensive and simultaneous resolution. In this study, we present a fast and robust nanopore Cas9-targeted sequencing (nCats) pipeline to identify integration sites, the composition of the integrated sequence as well as its DNA methylation status in CHO cells that can be obtained simultaneously from the same sequencing run. A Cas9-enrichment step during library preparation enables targeted and directional nanopore sequencing with up to 724× median on-target coverage and up to 153 kb long reads. The data generated by nCats provides sensitive, detailed, and correct information on the transgene integration sites and the expression vector structure, which could only be partly produced by traditional Targeted Locus Amplification-seq data. Moreover, with nCats the DNA methylation status can be analyzed from the same raw data without prior DNA amplification.
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Affiliation(s)
- Klaus Leitner
- Austrian Center of Industrial Biotechnology GmbH, Vienna, Austria
| | | | - Nicole Borth
- Austrian Center of Industrial Biotechnology GmbH, Vienna, Austria
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicolas Marx
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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Novak N, Baumann M, Friss A, Cairns V, DeMaria C, Borth N. LncRNA analysis of mAb producing CHO clones reveals marker and engineering potential. Metab Eng 2023; 78:26-40. [PMID: 37196898 DOI: 10.1016/j.ymben.2023.05.003] [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: 04/27/2022] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a potential new cell line engineering tool for improvement of yield and stability of CHO cells. In this study, we performed RNA sequencing of mAb producer CHO clones to study the lncRNA and protein coding transcriptome in relation to productivity. First, a robust linear model was used to identify genes correlating to productivity. To unravel specific patterns in expression of these genes, we employed weighted gene coexpression analysis (WGCNA) to find coexpressed modules, looking both for lncRNAs and coding genes. There was little overlap in the genes associated with productivity between the two products studied, possibly due to the difference in absolute range of productivity between the two mAbs. Therefore, we focused on the product with higher productivity and stronger candidate lncRNAs. To evaluate their potential as engineering targets, these candidate lncRNAs were transiently overexpressed or deleted by stable CRISPR Cas9 knock out both in a high and a low productivity subclone. We found that the thus achieved expression level of the identified lncRNAs, as confirmed by qPCR, does correlate well to productivity, so that they represent good markers that may be used for early clone selection. Additionally, we found that the deletion of one tested lncRNA region decreased viable cell density (VCD), prolonged culture time and increased cell size, final titer and specific productivity per cell. These results demonstrate the feasibility and usefulness of engineering lncRNA expression in production cell lines.
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Affiliation(s)
- Neža Novak
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Martina Baumann
- ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Amy Friss
- Sanofi Biopharmaceutics Development, Framingham, MA, USA
| | - Victor Cairns
- Sanofi Biopharmaceutics Development, Framingham, MA, USA
| | | | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria.
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Srila W, Baumann M, Riedl M, Rangnoi K, Borth N, Yamabhai M. Glutamine synthetase (GS) knockout (KO) using CRISPR/Cpf1 diversely enhances selection efficiency of CHO cells expressing therapeutic antibodies. Sci Rep 2023; 13:10473. [PMID: 37380701 DOI: 10.1038/s41598-023-37288-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
The glutamine synthetase (GS)-based Chinese hamster ovary (CHO) selection system is an attractive approach to efficiently identify suitable clones in the cell line generation process for biologics manufacture, for which GS-knockout (GS-KO) CHO cell lines are commonly used. Since genome analysis indicated that there are two GS genes in CHO cells, deleting only 1 GS gene could potentially result in the activation of other GS genes, consequently reducing the selection efficiency. Therefore, in this study, both GS genes identified on chromosome 5 (GS5) and 1 (GS1) of CHO-S and CHO-K1, were deleted using CRISPR/Cpf1. Both single and double GS-KO CHO-S and K1 showed robust glutamine-dependent growth. Next, the engineered CHO cells were tested for their efficiency of selection of stable producers of two therapeutic antibodies. Analysis of pool cultures and subclones after a single round of 25 µM methionine sulfoxinime (MSX) selection indicated that for CHO-K1 the double GS5,1-KO was more efficient as in the case of a single GS5-KO the GS1 gene was upregulated. In CHO-S, on the other hand, with an autologously lower level of expression of both variants of GS, a single GS5-KO was more robust and already enabled selection of high producers. In conclusion, CRISPR/Cpf1 can be efficiently used to knock out GS genes from CHO cells. The study also indicates that for the generation of host cell lines for efficient selection, the initial characterisation of expression levels of the target gene as well as the identification of potential escape mechanisms is important.
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Affiliation(s)
- Witsanu Srila
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Markus Riedl
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Kuntalee Rangnoi
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria.
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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Glinšek K, Bozovičar K, Bratkovič T. CRISPR Technologies in Chinese Hamster Ovary Cell Line Engineering. Int J Mol Sci 2023; 24:ijms24098144. [PMID: 37175850 PMCID: PMC10179654 DOI: 10.3390/ijms24098144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The Chinese hamster ovary (CHO) cell line is a well-established platform for the production of biopharmaceuticals due to its ability to express complex therapeutic proteins with human-like glycopatterns in high amounts. The advent of CRISPR technology has opened up new avenues for the engineering of CHO cell lines for improved protein production and enhanced product quality. This review summarizes recent advances in the application of CRISPR technology for CHO cell line engineering with a particular focus on glycosylation modulation, productivity enhancement, tackling adventitious agents, elimination of problematic host cell proteins, development of antibiotic-free selection systems, site-specific transgene integration, and CRISPR-mediated gene activation and repression. The review highlights the potential of CRISPR technology in CHO cell line genome editing and epigenetic engineering for the more efficient and cost-effective development of biopharmaceuticals while ensuring the safety and quality of the final product.
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Affiliation(s)
- Katja Glinšek
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Krištof Bozovičar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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Hussein MK, Papež M, Dhiman H, Baumann M, Galosy S, Borth N. In silico design of CMV promoter binding oligonucleotides and their impact on inhibition of gene expression in Chinese hamster ovary cells. J Biotechnol 2022; 359:185-193. [DOI: 10.1016/j.jbiotec.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 10/31/2022]
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Srila W, Baumann M, Borth N, Yamabhai M. Codon and signal peptide optimization for therapeutic antibody production from Chinese hamster ovary (CHO) cell. Biochem Biophys Res Commun 2022; 622:157-162. [PMID: 35863090 DOI: 10.1016/j.bbrc.2022.06.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/22/2022] [Indexed: 11/02/2022]
Affiliation(s)
- Witsanu Srila
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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12
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Li ZM, Fan ZL, Wang XY, Wang TY. Factors Affecting the Expression of Recombinant Protein and Improvement Strategies in Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2022; 10:880155. [PMID: 35860329 PMCID: PMC9289362 DOI: 10.3389/fbioe.2022.880155] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/01/2022] [Indexed: 01/20/2023] Open
Abstract
Recombinant therapeutic proteins (RTPs) are important parts of biopharmaceuticals. Chinese hamster ovary cells (CHO) have become the main cell hosts for the production of most RTPs approved for marketing because of their high-density suspension growth characteristics, and similar human post-translational modification patterns et al. In recent years, many studies have been performed on CHO cell expression systems, and the yields and quality of recombinant protein expression have been greatly improved. However, the expression levels of some proteins are still low or even difficult-to express in CHO cells. It is urgent further to increase the yields and to express successfully the “difficult-to express” protein in CHO cells. The process of recombinant protein expression of is a complex, involving multiple steps such as transcription, translation, folding processing and secretion. In addition, the inherent characteristics of molecular will also affect the production of protein. Here, we reviewed the factors affecting the expression of recombinant protein and improvement strategies in CHO cells.
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Affiliation(s)
- Zheng-Mei Li
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Zhen-Lin Fan
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Institutes of Health Central Plain, Xinxiang Medical University, Xinxiang, China
| | - Xiao-Yin Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Department of Biochemistry and Molecular Biology, 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, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Tian-Yun Wang,
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Spahn PN, Zhang X, Hu Q, Lu H, Hamaker NK, Hefzi H, Li S, Kuo CC, Huang Y, Lee JC, Davis AJ, Ly P, Lee KH, Lewis NE. Restoration of DNA repair mitigates genome instability and increases productivity of Chinese hamster ovary cells. Biotechnol Bioeng 2022; 119:963-982. [PMID: 34953085 PMCID: PMC8821244 DOI: 10.1002/bit.28016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/11/2022]
Abstract
Chinese hamster ovary (CHO) cells are the primary host for manufacturing of therapeutic proteins. However, productivity loss is a major problem and is associated with genome instability, as chromosomal aberrations reduce transgene copy number and decrease protein expression. We analyzed whole-genome sequencing data from 11 CHO cell lines and found deleterious single-nucleotide variants in DNA repair genes. Comparison with primary Chinese hamster cells confirmed DNA repair to be compromised in CHO. Correction of key DNA repair genes by single-nucleotide variant reversal or expression of intact complementary DNAs successfully improved DNA repair and mitigated karyotypic instability. Moreover, overexpression of intact copies of LIG4 and XRCC6 in a CHO cell line expressing secreted alkaline phosphatase mitigated transgene copy loss and improved protein titer retention. These results show that correction of DNA repair genes yields improvements in genome stability in CHO, and provide new opportunities for cell line development for sustainable protein expression.
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Affiliation(s)
- Philipp N. Spahn
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, San Diego, La Jolla, CA 92093
| | - Xiaolin Zhang
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711
| | - Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Huiming Lu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Nathaniel K. Hamaker
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711
| | - Hooman Hefzi
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Chih-Chung Kuo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Yingxiang Huang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
| | - Jamie C. Lee
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Anthony J. Davis
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kelvin H. Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, These authors jointly supervised this work: Kelvin H. Lee, , 302-831-0344, Nathan E. Lewis, , 858-997-5844
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, San Diego, La Jolla, CA 92093, Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, These authors jointly supervised this work: Kelvin H. Lee, , 302-831-0344, Nathan E. Lewis, , 858-997-5844
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14
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Screening of CHO-K1 endogenous promoters for expressing recombinant proteins in mammalian cell cultures. Plasmid 2022; 119-120:102620. [DOI: 10.1016/j.plasmid.2022.102620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/28/2022]
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15
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Tihanyi B, Nyitray L. Recent advances in CHO cell line development for recombinant protein production. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 38:25-34. [PMID: 34895638 DOI: 10.1016/j.ddtec.2021.02.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 12/20/2022]
Abstract
Recombinant proteins used in biomedical research, diagnostics and different therapies are mostly produced in Chinese hamster ovary cells in the pharmaceutical industry. These biotherapeutics, monoclonal antibodies in particular, have shown remarkable market growth in the past few decades. The increasing demand for high amounts of biologics requires continuous optimization and improvement of production technologies. Research aims at discovering better means and methods for reaching higher volumetric capacity, while maintaining stable product quality. An increasing number of complex novel protein therapeutics, such as viral antigens, vaccines, bi- and tri-specific monoclonal antibodies, are currently entering industrial production pipelines. These biomolecules are, in many cases, difficult to express and require tailored product-specific solutions to improve their transient or stable production. All these requirements boost the development of more efficient expression optimization systems and high-throughput screening platforms to facilitate the design of product-specific cell line engineering and production strategies. In this minireview, we provide an overview on recent advances in CHO cell line development, targeted genome manipulation techniques, selection systems and screening methods currently used in recombinant protein production.
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Affiliation(s)
- Borbála Tihanyi
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/C, 1117 Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/C, 1117 Budapest, Hungary.
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16
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Shamie I, Duttke SH, Karottki KJLC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform 2021; 3:lqab061. [PMID: 34268494 PMCID: PMC8276764 DOI: 10.1093/nargab/lqab061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene Mgat3, facilitate activating silent genes by CRISPRa. Together, we envision our revised annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.
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Affiliation(s)
- Isaac Shamie
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Sascha H Duttke
- Department of Medicine, University of California, San Diego 92093, USA
| | - Karen J la Cour Karottki
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Anders H Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Hooman Hefzi
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Kai Xiong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Shangzhong Li
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Samuel J Roth
- Department of Medicine, University of California, San Diego 92093, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Gyun Min Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | | | | | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
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17
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Marx N, Dhiman H, Schmieder V, Freire CM, Nguyen LN, Klanert G, Borth N. Enhanced targeted DNA methylation of the CMV and endogenous promoters with dCas9-DNMT3A3L entails distinct subsequent histone modification changes in CHO cells. Metab Eng 2021; 66:268-282. [PMID: 33965614 DOI: 10.1016/j.ymben.2021.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/02/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023]
Abstract
With the emergence of new CRISPR/dCas9 tools that enable site specific modulation of DNA methylation and histone modifications, more detailed investigations of the contribution of epigenetic regulation to the precise phenotype of cells in culture, including recombinant production subclones, is now possible. These also allow a wide range of applications in metabolic engineering once the impact of such epigenetic modifications on the chromatin state is available. In this study, enhanced DNA methylation tools were targeted to a recombinant viral promoter (CMV), an endogenous promoter that is silenced in its native state in CHO cells, but had been reactivated previously (β-galactoside α-2,6-sialyltransferase 1) and an active endogenous promoter (α-1,6-fucosyltransferase), respectively. Comparative ChIP-analysis of histone modifications revealed a general loss of active promoter histone marks and the acquisition of distinct repressive heterochromatin marks after targeted methylation. On the other hand, targeted demethylation resulted in autologous acquisition of active promoter histone marks and loss of repressive heterochromatin marks. These data suggest that DNA methylation directs the removal or deposition of specific histone marks associated with either active, poised or silenced chromatin. Moreover, we show that de novo methylation of the CMV promoter results in reduced transgene expression in CHO cells. Although targeted DNA methylation is not efficient, the transgene is repressed, thus offering an explanation for seemingly conflicting reports about the source of CMV promoter instability in CHO cells. Importantly, modulation of epigenetic marks enables to nudge the cell into a specific gene expression pattern or phenotype, which is stabilized in the cell by autologous addition of further epigenetic marks. Such engineering strategies have the added advantage of being reversible and potentially tunable to not only turn on or off a targeted gene, but also to achieve the setting of a desirable expression level.
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Affiliation(s)
- Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Heena Dhiman
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Valerie Schmieder
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | | | - Ly Ngoc Nguyen
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Gerald Klanert
- Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Nicole Borth
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria.
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18
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Lee Y, Kwak JM, Lee JS. Endogenous p21-Dependent Transgene Control for CHO Cell Engineering. ACS Synth Biol 2020; 9:1572-1580. [PMID: 32539343 DOI: 10.1021/acssynbio.9b00526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Numerous engineering efforts have been made in Chinese hamster ovary (CHO) cells for high level production of therapeutic proteins. However, the dynamic regulation of transgene expression is limited in current systems. Here, we investigated the effective regulation of transgene expression in CHO cells via targeted integration-based endogenous gene tagging with engineering target genes. Targeted integration of EGFP-human Bcl-2 into the p21 locus effectively reduced the apoptosis, compared with random populations in which Bcl-2 expression was driven by cytomegalovirus (CMV) promoter. Endogenous p21 and EGFP-human Bcl-2 displayed similar expression dynamics in batch cultures, and the antiapoptotic effect altered the expression pattern of endogenous p21 showing the mutual influences between expression of p21 and Bcl-2. We further demonstrated the inducible transgene expression by adding low concentrations of hydroxyurea. The present engineering strategy will provide a valuable CHO cell engineering tool that can be used to control dynamic transgene expression in accordance with cellular states.
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Affiliation(s)
- Youngsik Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jin Myeong Kwak
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
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19
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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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20
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Bydlinski N, Coats MT, Maresch D, Strasser R, Borth N. Transfection of glycoprotein encoding mRNA for swift evaluation of N-glycan engineering strategies. Biotechnol Prog 2020; 36:e2990. [PMID: 32134190 PMCID: PMC7507192 DOI: 10.1002/btpr.2990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 02/18/2020] [Accepted: 03/04/2020] [Indexed: 11/07/2022]
Abstract
N‐glycosylation is defined as a key quality attribute for the majority of complex biological therapeutics. Despite many N‐glycan engineering efforts, the demand to generate desired N‐glycan profiles that may vary for different proteins in a reproducible manner is still difficult to fulfill in many cases. Stable production of homogenous structures with a more demanding level of processing, for instance high degrees of branching and terminal sialylation, is particularly challenging. Among many other influential factors, the level of productivity can steer N‐glycosylation towards less mature N‐glycan structures. Recently, we introduced an mRNA transfection system capable of elucidating bottlenecks in the secretory pathway by stepwise increase of intracellular model protein mRNA load. Here, this system was applied to evaluate engineering strategies for enhanced N‐glycan processing. The tool proves to indeed be valuable for a quick assessment of engineering approaches on the cellular N‐glycosylation capacity at high productivity. The gene editing approaches tested include overexpression of key Golgi‐resident glycosyltransferases, partially coupled with multiple gene deletions. Changes in galactosylation, sialylation, and branching potential as well as N‐acetyllactosamine formation were evaluated.
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Affiliation(s)
- Nina Bydlinski
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael T Coats
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria
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21
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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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