1
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Zhang YS, Gong JS, Jiang JY, Xu ZH, Shi JS. Engineering protein translocation and unfolded protein response enhanced human PH-20 secretion in Pichia pastoris. Appl Microbiol Biotechnol 2024; 108:54. [PMID: 38175240 DOI: 10.1007/s00253-023-12878-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/04/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
Hyaluronidases catalyze the degradation of hyaluronan (HA), which is finding rising applications in medicine, cosmetic, and food industries. Recombinant expression of hyaluronidases in microbial hosts has been given special attention as a sustainable way to substitute animal tissue-derived hyaluronidases. In this study, we focused on optimizing the secretion of hyaluronidase from Homo sapiens in Pichia pastoris by secretion pathway engineering. The recombinant hyaluronidase was first expressed under the control of a constitutive promoter PGCW14. Then, two endoplasmic reticulum-related secretory pathways were engineered to improve the secretion capability of the recombinant strain. Signal peptide optimization suggested redirecting the protein into co-translational translocation using the ost1-proα signal sequence improved the secretion level by 20%. Enhancing the co-translational translocation by overexpressing signal recognition particle components further enhanced the secretory capability by 48%. Then, activating the unfolded protein response by overexpressing a transcriptional factor ScHac1p led to a secreted hyaluronidase activity of 4.06 U/mL, which was 2.1-fold higher than the original strain. Finally, fed-batch fermentation elevated the production to 19.82 U/mL. The combined engineering strategy described here could be applied to enhance the secretion capability of other proteins in yeast hosts. KEY POINTS: • Improving protein secretion by enhancing co-translational translocation in P. pastoris was reported for the first time. • Overexpressing Hac1p homologous from different origins improved the rhPH-20 secretion. • A 4.9-fold increase in rhPH-20 secretion was achieved after fermentation optimization and fed-batch fermentation.
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Affiliation(s)
- Yue-Sheng Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Jia-Yu Jiang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, People's Republic of China.
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China.
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2
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Yang CH, Li HC, Lo SY. Enhancing recombinant antibody yield in Chinese hamster ovary cells. Tzu Chi Med J 2024; 36:240-250. [PMID: 38993821 PMCID: PMC11236083 DOI: 10.4103/tcmj.tcmj_315_23] [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: 12/17/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 07/13/2024] Open
Abstract
A range of recombinant monoclonal antibodies (rMAbs) have found application in treating diverse diseases, spanning various cancers and immune system disorders. Chinese hamster ovary (CHO) cells have emerged as the predominant choice for producing these rMAbs due to their robustness, ease of transfection, and capacity for posttranslational modifications akin to those in human cells. Transient transfection and/or stable expression could be conducted to express rMAbs in CHO cells. To bolster the yield of rMAbs in CHO cells, a multitude of approaches have been developed, encompassing vector optimization, medium formulation, cultivation parameters, and cell engineering. This review succinctly outlines these methodologies when also addressing challenges encountered in the production process, such as issues with aggregation and fucosylation.
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Affiliation(s)
- Chee-Hing Yang
- Department of Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hui-Chun Li
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical, Hualien, Taiwan
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3
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Szkodny AC, Lee KH. A systemic approach to identifying sequence frameworks that decrease mAb production in a transient Chinese hamster ovary cell expression system. Biotechnol Prog 2024:e3466. [PMID: 38607316 DOI: 10.1002/btpr.3466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/17/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Monoclonal antibodies (mAbs) are often engineered at the sequence level for improved clinical performance yet are rarely evaluated prior to candidate selection for their "developability" characteristics, namely expression, which can necessitate additional resource investments to improve the manufacturing processes for problematic mAbs. A strong relationship between primary sequence and expression has emerged, with slight differences in amino acid sequence resulting in titers differing by up to an order of magnitude. Previous work on these "difficult-to-express" (DTE) mAbs has shown that these phenotypes are driven by post-translational bottlenecks in antibody folding, assembly, and secretion processes. However, it has been difficult to translate these findings across cell lines and products. This work presents a systematic approach to study the impact of sequence variation on mAb expression at a larger scale and under more industrially relevant conditions. The analysis found 91 mutations that decreased transient expression of an IgG1κ in Chinese hamster ovary (CHO) cells and revealed that mutations at inaccessible residues, especially those leading to decreases in residue hydrophobicity, are not favorable for high expression. This workflow can be used to better understand sequence determinants of mAb expression to improve candidate selection procedures and reduce process development timelines.
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Affiliation(s)
- Alana C Szkodny
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
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4
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Zhang X, Wang Y, Yi D, Zhang C, Ning B, Fu Y, Jia Y, Wang T, Wang X. Synergistic promotion of transient transgene expression in CHO cells by PDI/XBP-1s co-transfection and mild hypothermia. Bioprocess Biosyst Eng 2024; 47:557-565. [PMID: 38416261 DOI: 10.1007/s00449-024-02987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
Transient gene expression system is an important tool for rapid production of recombinant proteins in Chinese hamster ovary (CHO) cells. However, their low productivity is the main hurdle to overcome. An effective approach through which to obtain high protein yield involves targeting transcriptional, post-transcriptional events (PTEs), and culture conditions. Here, we investigated the effects of protein disulfide isomerase (PDI) and spliced X-box binding protein 1 (XBP-1s) co-overexpression combined with mild hypothermia on the transient yields of recombinant proteins in CHO cells. The results showed that the gene of interest (GOI) and the PDI/XBP-1s helper vector at a co-transfection ratio of 10:1 could obviously increase transient expression level of recombinant protein in CHO cells. However, PDI/XBP-1s overexpression had no significance effect on the mRNA levels of the recombinant protein, suggesting that it targeted PTEs. Moreover, the increased production was due to the enhancing of cell specific productivity, not related to cell growth, viability, and cell cycle. In addition, combined PDI/XBP-1s co-overexpression and mild hypothermia could further improve Adalimumab expression, compared to the control/37 °C and PDI/XBP-1s/37 °C, the Adalimumab volume yield of PDI/XBP-1s/33 °C increased by 203% and 142%, respectively. Mild hypothermia resulted in 3.52- and 2.33-fold increase in the relative mRNA levels of PDI and XBP-1s, respectively. In conclusion, the combination of PDI/XBP-1s overexpression and culture temperature optimization can achieve higher transient expression of recombinant protein, which provides a synergetic strategy to improve transient production of recombinant protein in CHO cells.
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Affiliation(s)
- Xi Zhang
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Yaokun Wang
- The School of Medical Humanities, Xinxiang Medical University, Xinxiang, 453003, China
| | - Dandan Yi
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Chi Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Binhuan Ning
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Yushun Fu
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Yanlong Jia
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Tianyun Wang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China.
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, China.
| | - Xiaoyin Wang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China.
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, China.
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5
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Jerabek T, Burkhart M, Goetz S, Greck B, Menthe A, Neef R, Otte K. Inefficient transcription is a production bottleneck for artificial therapeutic BiTE® proteins. N Biotechnol 2024; 79:91-99. [PMID: 38154615 DOI: 10.1016/j.nbt.2023.12.008] [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: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/25/2023] [Indexed: 12/30/2023]
Abstract
Antibodies are potent biopharmaceuticals used to treat severe diseases, including cancers. During the past decade, more complex modalities have been developed including bispecific T-cell engager (BiTE®) molecules, e.g. by Amgen. However, non-natural and complex molecule formats often prove to be difficult-to-express (DTE), which is the case for BiTE® molecules. Due to the growing importance of multispecific modalities such as half-life extended (HLE) BiTE® and HLE dual-targeting bispecific T-cell engager (dBiTE) molecules, this artificial class of therapeutic proteins was investigated for molecular bottlenecks in stable production cell lines, by analyzing all relevant steps of recombinant protein production. As a result, drastically reduced intracellular BiTE® molecule-encoding mRNA levels were identified as a potential production bottleneck. Using in vitro transcription (IVT), the transcription rate of the BiTE® molecule-encoding mRNA was identified as the root cause for reduced amounts of intracellular mRNA. In an attempt to improve the transcription rate of a BiTE® molecule, it could be demonstrated that the artificial and special structure of the BiTE® molecule was not the rate limiting step for reduced IVT rate. However, modulation of the primary DNA sequence led to significant improvement of IVT rate. The analyses presented provide insight into the HLE BiTE® / HLE d(BiTE®) class of DTE proteins and perhaps into other classes of DTE proteins, and therefore may lead to identification of further production bottlenecks and optimization strategies to overcome manufacturability challenges associated with various complex therapeutics.
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Affiliation(s)
- Tobias Jerabek
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, 88400 Biberach an der Riss, Germany.
| | - Madina Burkhart
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, 88400 Biberach an der Riss, Germany
| | - Selina Goetz
- Process Development, Amgen Research (Munich) GmbH, Staffelseestraße 2, 81477 Munich, Germany
| | - Benedikt Greck
- Process Development, Amgen Research (Munich) GmbH, Staffelseestraße 2, 81477 Munich, Germany
| | - Anika Menthe
- Process Development, Amgen Research (Munich) GmbH, Staffelseestraße 2, 81477 Munich, Germany
| | - Ruediger Neef
- Process Development, Amgen Research (Munich) GmbH, Staffelseestraße 2, 81477 Munich, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, 88400 Biberach an der Riss, Germany
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6
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Kim SH, Park JH, Shin S, Shin S, Chun D, Kim YG, Yoo J, You WK, Lee JS, Lee GM. Genome-Wide CRISPR/Cas9 Screening Unveils a Novel Target ATF7IP-SETDB1 Complex for Enhancing Difficult-to-Express Protein Production. ACS Synth Biol 2024; 13:634-647. [PMID: 38240694 DOI: 10.1021/acssynbio.3c00646] [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] [Indexed: 02/17/2024]
Abstract
With the emerging novel biotherapeutics that are typically difficult-to-express (DTE), improvement is required for high-yield production. To identify novel targets that can enhance DTE protein production, we performed genome-wide fluorescence-activated cell sorting (FACS)-based clustered regularly interspaced short palindromic repeats (CRISPR) knockout screening in bispecific antibody (bsAb)-producing Chinese hamster ovary (CHO) cells. The screen identified the two highest-scoring genes, Atf7ip and Setdb1, which are the binding partners for H3K9me3-mediated transcriptional repression. The ATF7IP-SETDB1 complex knockout in bsAb-producing CHO cells suppressed cell growth but enhanced productivity by up to 2.7-fold. Decreased H3K9me3 levels and an increased transcriptional expression level of the transgene were also observed. Furthermore, perturbation of the ATF7IP-SETDB1 complex in monoclonal antibody (mAb)-producing CHO cells led to substantial improvements in mAb production, increasing the productivity by up to 3.9-fold without affecting the product quality. Taken together, the genome-wide FACS-based CRISPR screen identified promising targets associated with histone methylation, whose perturbation enhanced the productivity by unlocking the transgene expression.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Jong-Ho Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biotherapeutics Translational Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Sungwook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Seunghyeon Shin
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Dahyun Chun
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, UST, , Daejeon 34113, Republic of Korea
| | - Jiseon Yoo
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Weon-Kyoo You
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
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7
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Thalén NB, Barzadd MM, Lundqvist M, Rodhe J, Andersson M, Bidkhori G, Possner D, Su C, Nilsson J, Eisenhut P, Malm M, Karlsson A, Vestin J, Forsberg J, Nordling E, Mardinoglu A, Volk AL, Sandegren A, Rockberg J. Tuning of CHO secretional machinery improve activity of secreted therapeutic sulfatase 150-fold. Metab Eng 2024; 81:157-166. [PMID: 38081506 DOI: 10.1016/j.ymben.2023.12.003] [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: 12/11/2022] [Revised: 10/12/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
Rare diseases are, despite their name, collectively common and millions of people are affected daily of conditions where treatment often is unavailable. Sulfatases are a large family of activating enzymes related to several of these diseases. Heritable genetic variations in sulfatases may lead to impaired activity and a reduced macromolecular breakdown within the lysosome, with several severe and lethal conditions as a consequence. While therapeutic options are scarce, treatment for some sulfatase deficiencies by recombinant enzyme replacement are available. The recombinant production of such sulfatases suffers greatly from both low product activity and yield, further limiting accessibility for patient groups. To mitigate the low product activity, we have investigated cellular properties through computational evaluation of cultures with varying media conditions and comparison of two CHO clones with different levels of one active sulfatase variant. Transcriptome analysis identified 18 genes in secretory pathways correlating with increased sulfatase production. Experimental validation by upregulation of a set of three key genes improved the specific enzymatic activity at varying degree up to 150-fold in another sulfatase variant, broadcasting general production benefits. We also identified a correlation between product mRNA levels and sulfatase activity that generated an increase in sulfatase activity when expressed with a weaker promoter. Furthermore, we suggest that our proposed workflow for resolving bottlenecks in cellular machineries, to be useful for improvements of cell factories for other biologics as well.
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Affiliation(s)
- Niklas Berndt Thalén
- Dept. of Protein science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Mona Moradi Barzadd
- Dept. of Protein science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magnus Lundqvist
- Dept. of Protein science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | | | | | - Gholamreza Bidkhori
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, 171 65, Sweden; AIVIVO Ltd. Unit 25, Bio-innovation centre, Cambridge Science park, Cambridge, UK
| | | | - Chao Su
- SOBI AB, Tomtebodavägen 23A, Stockholm, Sweden
| | | | - Peter Eisenhut
- ACIB - Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria; BOKU - University of Natural Resources and Life Sciences, Department of Biotechnology, Vienna, 1190, Austria
| | - Magdalena Malm
- Dept. of Protein science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Alice Karlsson
- Dept. of Protein science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | | | | | | | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, 171 65, Sweden
| | - Anna-Luisa Volk
- Dept. of Protein science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | | | - Johan Rockberg
- Dept. of Protein science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden.
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8
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Kellner K, Lao NT, Barron N. CRISPR Deletion of miR-27 Impacts Recombinant Protein Production in CHO Cells. Methods Mol Biol 2024; 2810:285-300. [PMID: 38926286 DOI: 10.1007/978-1-0716-3878-1_18] [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] [Indexed: 06/28/2024]
Abstract
MicroRNAs represent an interesting group of regulatory molecules with the unique ability of a single miRNA able to regulate the expression of potentially hundreds of target genes. In that regard, their utility has been demonstrated as a strategy to improve the cellular phenotypes important in the biomanufacturing of recombinant proteins. Common approaches to stably deplete miRNAs are the use of sponge decoy transcripts or shRNA inhibitors, both of which require the introduction and expression of extra genetic material in the cell. As an alternative, we implemented the CRISPR/Cas9 system in our laboratory to generate CHO cells which lack the expression of a specific miRNA for the purpose of functional studies. To implement the system, miR-27a/b was chosen as it has been shown to be upregulated during hypothermic conditions and therefore may be involved in influencing CHO cell growth and recombinant protein productivity. In this chapter, we present a protocol for targeting miRNAs in CHO cells using CRISPR/Cas9 and the analysis of the resulting phenotype, using miR-27 as an example. We show that it is possible to target miRNAs in CHO cells and achieved ≥80% targeting efficiency. Indel analysis and TOPO-TA cloning combined with Sanger sequencing showed a range of different indels. Furthermore, it was possible to identify clones with no detectable expression of mature miR-27b. Depletion of miR-27b led to improved viability in late stages of batch and fed-batch cultures, making it a potentially interesting target to improve bioprocess performance of CHO cells.
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Affiliation(s)
- Kevin Kellner
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Nga T Lao
- National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Niall Barron
- National Institute for Bioprocessing Research and Training, Dublin, Ireland.
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland.
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9
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Park SY, Choi DH, Song J, Park U, Cho H, Hong BH, Silberberg YR, Lee DY. Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses. Biotechnol J 2023; 18:e2300126. [PMID: 37605365 DOI: 10.1002/biot.202300126] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023]
Abstract
Designing and selecting cell culture media along with their feeding are a key strategy to maximize culture performance in biopharmaceutical processes. However, the sensitivity of mammalian cells to their culture environment necessitates specific nutritional requirements for their growth and the production of high-quality proteins such as antibodies, depending on the cell lines and operational conditions employed. In this regard, previously we developed a data-driven and in-silico model-guided systematic framework to investigate the effect of growth media on Chinese hamster ovary (CHO) cell culture performance, allowing us to design and reformulate basal media. To expand our exploration for media development research, we evaluated two chemically defined feed media, A and B, using a monoclonal antibody-producing CHO-K1 cell line in ambr15 bioreactor runs. We observed a significant impact of the feed media on various aspects of cell culture, including growth, longevity, viability, productivity, and the production of toxic metabolites. Specifically, the concentrated feed A was inadequate in sustaining prolonged cell culture and achieving high titers when compared to feed B. Within our framework, we systematically investigated the major metabolic bottlenecks in the tricarboxylic acid cycle and relevant amino acid transferase reactions. This analysis identified target components that play a crucial role in alleviating bottlenecks and designing highly productive cell cultures, specifically the addition of glutamate to feed A and asparagine to feed B. Based on our findings, we reformulated the feeds by adjusting the amounts of the targeted amino acids and successfully validated the effectiveness of the strategy in promoting cell growth, life span, and/or titer.
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Affiliation(s)
- Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
| | - Dong-Hyuk Choi
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
| | - Jinsung Song
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
| | - Uiseon Park
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Hyeran Cho
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Bee Hak Hong
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Yaron R Silberberg
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
- Bitwinners Pte. Ltd., Singapore
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10
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Zhu X, Li M, Zhu R, Xin Y, Guo Z, Gu Z, Zhang L, Guo Z. Up Front Unfolded Protein Response Combined with Early Protein Secretion Pathway Engineering in Yarrowia lipolytica to Attenuate ER Stress Caused by Enzyme Overproduction. Int J Mol Sci 2023; 24:16426. [PMID: 38003616 PMCID: PMC10670989 DOI: 10.3390/ijms242216426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Engineering the yeast Yarrowia lipolytica as an efficient host to produce recombinant proteins remains a longstanding goal for applied biocatalysis. During the protein overproduction, the accumulation of unfolded and misfolded proteins causes ER stress and cell dysfunction in Y. lipolytica. In this study, we evaluated the effects of several potential ER chaperones and translocation components on relieving ER stress by debottlenecking the protein synthetic machinery during the production of the endogenous lipase 2 and the E. coli β-galactosidase. Our results showed that improving the activities of the non-dominant translocation pathway (SRP-independent) boosted the production of the two proteins. While the impact of ER chaperones is protein dependent, the nucleotide exchange factor Sls1p for protein folding catalyst Kar2p is recognized as a common contributor enhancing the secretion of the two enzymes. With the identified protein translocation components and ER chaperones, we then exemplified how these components can act synergistically with Hac1p to enhance recombinant protein production and relieve the ER stress on cell growth. Specifically, the yeast overexpressing Sls1p and cytosolic heat shock protein Ssa8p and Ssb1p yielded a two-fold increase in Lip2p secretion compared with the control, while co-overexpressing Ssa6p, Ssb1p, Sls1p and Hac1p resulted in a 90% increase in extracellular β-galp activity. More importantly, the cells sustained a maximum specific growth rate (μmax) of 0.38 h-1 and a biomass yield of 0.95 g-DCW/g-glucose, only slightly lower than that was obtained by the wild type strain. This work demonstrated engineering ER chaperones and translocation as useful strategies to facilitate the development of Y. lipolytica as an efficient protein-manufacturing platform.
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Affiliation(s)
- Xingyu Zhu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Moying Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Rui Zhu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zitao Guo
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Jingkou District, Zhenjiang 212013, China;
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongpeng Guo
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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11
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Baghini SS, Razeghian E, Malayer SK, Pecho RDC, Obaid M, Awfi ZS, Zainab HA, Shamsara M. Recent advances in the application of genetic and epigenetic modalities in the improvement of antibody-producing cell lines. Int Immunopharmacol 2023; 123:110724. [PMID: 37582312 DOI: 10.1016/j.intimp.2023.110724] [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: 01/31/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
There are numerous applications for recombinant antibodies (rAbs) in biological and toxicological research. Monoclonal antibodies are synthesized using genetic engineering and other related processes involved in the generation of rAbs. Because they can identify specific antigenic sites on practically any molecule, including medicines, hormones, microbial antigens, and cell receptors, rAbs are particularly useful in scientific research. The key benefits of rAbs are improved repeatability, control, and consistency, shorter manufacturing times than with hybridoma technology, an easier transition from one format of antibody to another, and an animal-free process. The engineering of the host cell has recently been developed method for enhancing the production efficiency and improving the quality of antibodies from mammalian cell lines. In this light, genetic engineering is mostly utilized to manage cellular chaperones, decrease cell death, increase cell viability, change the microRNAs (miRNAs) pattern in mammalian cells, and glycoengineered cell lines. Here, we shed light on how genetic engineering can be used therapeutically to produce antibodies at higher levels with greater potency and effectiveness.
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Affiliation(s)
- Sadegh Shojaei Baghini
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Ehsan Razeghian
- Human Genetics Division, Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Setare Kakavand Malayer
- Department of Biology, Faculty of Biological Science, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Zinah Salem Awfi
- Department of Dental Industry Techniques, Al-Noor University College, Nineveh, Iraq.
| | - H A Zainab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq.
| | - Mehdi Shamsara
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
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12
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Maltais JS, Lord-Dufour S, Morasse A, Stuible M, Loignon M, Durocher Y. Repressing expression of difficult-to-express recombinant proteins during the selection process increases productivity of CHO stable pools. Biotechnol Bioeng 2023; 120:2840-2852. [PMID: 37232536 DOI: 10.1002/bit.28435] [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: 01/11/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
More than half of licensed therapeutic recombinant proteins (r-proteins) are manufactured using constitutively-expressing, stably-transfected Chinese hamster ovary (CHO) clones. While constitutive CHO expression systems have proven their efficacy for the manufacturing of monoclonal antibodies, many next-generation therapeutics such as cytokines and bispecific antibodies as well as biological targets such as ectodomains of transmembrane receptors remain intrinsically challenging to produce. Herein, we exploited a cumate-inducible CHO platform allowing reduced expression of various classes of r-proteins during selection of stable pools. Following stable pool generation, fed-batch productions showed that pools generated without cumate (OFF-pools) were significantly more productive than pools selected in the presence of cumate (ON-pools) for 8 out of the 10 r-proteins tested, including cytokines, G-protein coupled receptors (GPCRs), the HVEM membrane receptor ectodomain, the multifunctional protein High Mobility Group protein B1 (HMGB1), as well as monoclonal and bispecific T-cell engager antibodies. We showed that OFF-pools contain a significantly larger proportion of cells producing high levels of r-proteins and that these cells tend to proliferate faster when expression is turned off, suggesting that r-protein overexpression imposes a metabolic burden on the cells. Cell viability was lower and pool recovery was delayed during selection of ON-pools (mimicking constitutive expression), suggesting that high producers were likely lost or overgrown by faster-growing, low-producing cells. We also observed a correlation between the expression levels of the GPCRs with Binding immunoglobulin Protein, an endoplasmic reticulum (ER) stress marker. Taken together, these data suggest that using an inducible system to minimize r-protein expression during stable CHO pool selection reduces cellular stresses, including ER stress and metabolic burden, leading to pools with greater frequency of high-expressing cells, resulting in improved volumetric productivity.
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Affiliation(s)
- Jean-Sébastien Maltais
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, Canada
| | - Simon Lord-Dufour
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, Canada
| | - Audrey Morasse
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, Canada
| | - Matthew Stuible
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, Canada
| | - Martin Loignon
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, Canada
| | - Yves Durocher
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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13
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Billerhart M, Hunjadi M, Hawlin V, Grünwald-Gruber C, Maresch D, Mayrhofer P, Kunert R. Recombinant Human CD19 in CHO-K1 Cells: Glycosylation Patterns as a Quality Attribute of High Yield Processes. Int J Mol Sci 2023; 24:10891. [PMID: 37446069 PMCID: PMC10341778 DOI: 10.3390/ijms241310891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
CD19 is an essential protein in personalized CD19-targeting chimeric antigen receptor (CAR)-T cell-based cancer immunotherapies and CAR-T cell functionality evaluation. However, the recombinant expression of this "difficult to-express" (DTE) protein is challenging, and therefore, commercial access to the protein is limited. We have previously described the successful stable expression of our soluble CD19-AD2 fusion protein of the CD19 extracellular part fused with human serum albumin domain 2 (AD2) in CHO-K1 cells. The function, stability, and secretion rate of DTE proteins can be improved by culture conditions, such as reduced temperature and a shorter residence time. Moreover, glycosylation, as one of the most important post-translational modifications, represents a critical quality attribute potentially affecting CAR-T cell effector function and thus impacting therapy's success. In this study, we increased the production rate of CD19-AD2 by 3.5-fold through applying hypothermic culture conditions. We efficiently improved the purification of our his-tagged CD19-AD2 fusion protein via a Ni-NTA-based affinity column using a stepwise increase in the imidazole concentration. The binding affinity to commercially available anti-CD19 antibodies was evaluated via Bio-Layer Interferometry (BLI). Furthermore, we revealed glycosylation patterns via Electrospray Ionization Mass Spectrometry (ESI-MS), and five highly sialylated and multi-antennary N-glycosylation sites were identified. In summary, we optimized the CD19-AD2 production and purification process and were the first to characterize five highly complex N-glycosylation sites.
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Affiliation(s)
- Magdalena Billerhart
- Institute of Animal Cell Technology and Systems Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (M.B.); (M.H.)
| | - Monika Hunjadi
- Institute of Animal Cell Technology and Systems Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (M.B.); (M.H.)
| | - Vanessa Hawlin
- Institute of Animal Cell Technology and Systems Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (M.B.); (M.H.)
| | - Clemens Grünwald-Gruber
- BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (C.G.-G.)
| | - Daniel Maresch
- BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (C.G.-G.)
| | - Patrick Mayrhofer
- Institute of Animal Cell Technology and Systems Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (M.B.); (M.H.)
| | - Renate Kunert
- Institute of Animal Cell Technology and Systems Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (M.B.); (M.H.)
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14
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Chen N, Yang S, You D, Shen J, Ruan B, Wu M, Zhang J, Luo X, Tang H. Systematic genetic modifications of cell wall biosynthesis enhanced the secretion and surface-display of polysaccharide degrading enzymes in Saccharomyces cerevisiae. Metab Eng 2023; 77:273-282. [PMID: 37100192 DOI: 10.1016/j.ymben.2023.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/31/2023] [Accepted: 04/15/2023] [Indexed: 04/28/2023]
Abstract
Saccharomyces cerevisiae is a robust cell factory to secrete or surface-display cellulase and amylase for the conversion of agricultural residues into valuable chemicals. Engineering the secretory pathway is a well-known strategy for overproducing these enzymes. Although cell wall biosynthesis can be tightly linked to the secretory pathway by regulation of all involved processes, the effect of its modifications on protein production has not been extensively studied. In this study, we systematically studied the effect of engineering cell wall biosynthesis on the activity of cellulolytic enzyme β-glucosidase (BGL1) by comparing seventy-nine gene knockout S. cerevisiae strains and newly identified that inactivation of DFG5, YPK1, FYV5, CCW12 and KRE1 obviously improved BGL1 secretion and surface-display. Combinatorial modifications of these genes, particularly double deletion of FVY5 and CCW12, along with the use of rich medium, increased the activity of secreted and surface-displayed BGL1 by 6.13-fold and 7.99-fold, respectively. Additionally, we applied this strategy to improve the activity of the cellulolytic cellobiohydrolase and amylolytic α-amylase. Through proteomic analysis coupled with reverse engineering, we found that in addition to the secretory pathway, regulation of translation processes may also involve in improving enzyme activity by engineering cell wall biosynthesis. Our work provides new insight into the construction of a yeast cell factory for efficient production of polysaccharide degrading enzymes.
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Affiliation(s)
- Nanzhu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuo Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology, 3501 Daxue Road, Jinan, 250353, China
| | - Dawei You
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junfeng Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Banlai Ruan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Mei Wu
- Synceres Biosciences (Shenzhen) Co., Ltd, Nanshan Medical Device Industrial Park, Nanhai Avenue, Shenzhen, 518067, China
| | - Jianzhi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongting Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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15
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Wang JY(J, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A 2023; 120:e2214556120. [PMID: 36888664 PMCID: PMC10089191 DOI: 10.1073/pnas.2214556120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/03/2023] [Indexed: 03/09/2023] Open
Abstract
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
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Affiliation(s)
- Jing Yang (John) Wang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Alena Khmelinskaia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Transdisciplinary Research Area “Building Blocks of Matter and Fundamental Interactions”, University of Bonn, 53113Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53121Bonn, Germany
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Marcos C. Miranda
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Andrew J. Borst
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Susana V. Torres
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Chelsea Shu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA98195
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Carl Walkey
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sidney Chan
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA94720
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA94720
| | - Mengyu Wu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
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16
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Mullins DR, Galosy SS. Development of a novel capillary electrophoresis method for quantitative measurements of intracellular recombinant protein titer. J Biotechnol 2023; 365:54-61. [PMID: 36780953 DOI: 10.1016/j.jbiotec.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/12/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
The measurement of volumetric titer is an integral step in the assessment and selection of a production cell line and cell culture process. The production of monoclonal antibodies (mAbs), a major class of therapeutic proteins, in Chinese Hamster Ovary (CHO) cell lines is challenging due to the clone-to-clone variations in the intrinsic capability to secrete a biologically complex protein. The measurement of intracellular mAb concentration could be a valuable tool to determine the ratio of intracellular to secreted product and be part of the evaluation of potential mAb productive cell lines. High throughput automation is a valuable tool that is used in bioprocess development to reduce work intensive steps. When coupled with the Simple Western (Wes) platform, automated capillary electrophoresis is an efficient method to measure recombinant protein concentration. In this study, we demonstrate the utility of using the automated Wes to rapidly measure intracellular titer and then compare the intracellular titer, volumetric titer and specific productivity between high and low production CHO clones expressing a model human IgG1 mAb.
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Affiliation(s)
- David R Mullins
- Global Investigative Safety, GlaxoSmithKline (GSK), Collegeville, PA, USA.
| | - Sybille S Galosy
- Biopharm Microbial & Cell Culture Development, GlaxoSmithKline (GSK), King of Prussia, PA, USA
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17
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Bueno-Soler A, Palacios-Oliva J, Dorvignit-Pedroso D, Quintana-Cantillo A, Ramirez-Roque Y, Santo Tomas-Pompa J, Solazabal-Armstrong JA, Ruiz-Ramirez I, Mateo-de Acosta C, Boggiano-Ayo T, Lao-Gonzalez T. Production of an anti-TNFα antibody in murine myeloma cells by perfusion culture. Appl Microbiol Biotechnol 2022; 106:5007-5021. [PMID: 35835964 DOI: 10.1007/s00253-022-12052-4] [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: 10/14/2021] [Revised: 06/16/2022] [Accepted: 06/25/2022] [Indexed: 11/26/2022]
Abstract
Infliximab is a mouse/human chimeric IgG1 monoclonal antibody which recognizes the proinflammatory cytokine, tumor necrosis factor α (TNFα), and inhibits receptor interactions, thereby decreasing inflammation and autoimmune response in patients. This monoclonal antibody has been successfully used to treat rheumatoid arthritis, ankylosing spondylitis, and psoriatic arthritis. However, the high treatment cost limits patient access to this biotherapy. One alternative to this problem is the use of biosimilars. In this work, we describe the stable expression and physicochemical characterization of an anti-TNFα antibody. While infliximab is produced in recombinant murine SP2/0 cells, our anti-TNFα IgG antibody was expressed in recombinant murine NS0 myeloma cells. The best anti-TNFα antibody-expressing clone was selected from three clone candidates based on the stability of IgG expression levels, specific productivity as well as TNFα-binding activity compared to commercial infliximab. Our results indicate that the selected cell clone, culture medium, and fermentation mode allowed for the production of an anti-TNFα antibody with similar characteristics to the reference commercially available product. An optimization of the selected culture medium by metabolomics may increase the volumetric productivity of the process to satisfy the demand for this product. Further experiments should be performed to evaluate the biological properties of this anti-TNFα antibody. KEY POINTS: • An anti-TNFα antibody was produced in NS0 cells using perfusion culture. • A proprietary chemically defined culture medium was used to replace commercially available protein-free medium. • The purified anti-TNFα antibody was comparable to the reference marketed product.
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Affiliation(s)
- Alexi Bueno-Soler
- Process Development Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba
| | - Julio Palacios-Oliva
- Process Development Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba
| | - Denise Dorvignit-Pedroso
- Immunobiology Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Yaima Ramirez-Roque
- Process Development Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba
| | | | | | - Ingrid Ruiz-Ramirez
- Quality Control Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba
| | - Cristina Mateo-de Acosta
- Immunobiology Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba
- CIMAB S. A, 11600, Playa, Havana, Cuba
| | - Tammy Boggiano-Ayo
- Process Development Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba
| | - Thailin Lao-Gonzalez
- Process Development Direction, Center of Molecular Immunology, 11600, Playa, Havana, Cuba.
- Animal Biotechnology Division, Center for Genetic Engineering and Biotechnology, 10600, Playa, Havana, Cuba.
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18
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Yu Y, Liu M, Choi VNT, Cheung YW, Tanner JA. Selection and characterization of DNA aptamers inhibiting a druggable target of osteoarthritis, ADAMTS-5. Biochimie 2022; 201:168-176. [PMID: 35700850 DOI: 10.1016/j.biochi.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/15/2023]
Abstract
There is a critical need for the development of more potent inhibitors for osteoarthritis (OA) therapy given the poor life quality of arthritis patients. Aggrecanase ADAMTS-5 (a disintegrin and metalloproteinase with thrombospondin motifs 5) is an established drug target identified for osteoarthritis. In this study, we evolved and characterized two new DNA aptamer inhibitors of ADAMTS-5, namely apt21 and apt25. The aptamers exhibited nanomolar binding affinity and high specificity against ADAMTS-5. KD values of apt21 and apt25 were determined by the Enzyme-linked Oligonucleotide Assay (ELONA) at 1.54 ± 0.16 nM and 1.79 ± 0.08 nM, respectively. Circular Dichroism (CD) analysis demonstrated that both aptamers formed monovalent cation dependent G-quadruplex structures. Calcium ions did not affect the binding of the aptamers to ADAMTS-5. The inhibitory effects of apt21 and apt25 on ADAMTS-5 were evaluated by the Förster Resonance Energy Transfer (FRET) assay, in which IC50 values of apt21 and apt25 were estimated at 52.76 ± 6.70 μM and 61.14 ± 9.67 μM, respectively. These two aptamers are the first DNA G-quadruplex aptamers demonstrated to inhibit ADAMTS-5 and could have value for OA therapy.
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Affiliation(s)
- Yuanyuan Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, PR China
| | - Mengping Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Vanessa N T Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, PR China.
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19
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Park JH, Lee HM, Jin EJ, Lee EJ, Kang YJ, Kim S, Yoo SS, Lee GM, Kim YG. Development of an in vitro screening system for synthetic signal peptide in mammalian cell-based protein production. Appl Microbiol Biotechnol 2022; 106:3571-3582. [PMID: 35581431 DOI: 10.1007/s00253-022-11955-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022]
Abstract
Optimizing appropriate signal peptides in mammalian cell-based protein production is crucial given that most recombinant proteins produced in mammalian cells are thought to be secreted proteins. Until now, most studies on signal peptide in mammalian cells have replaced native signal peptides with well-known heterologous signal peptides and bioinformatics-based signal peptides. In the present study, we successfully established an in vitro screening system for synthetic signal peptide in CHO cells by combining a degenerate codon-based oligonucleotides library, a site-specific integration system, and a FACS-based antibody detection assay. Three new signal peptides were screened using this new screening system, confirming to have structural properties as signal peptides by the SignalP web server, a neural network-based algorithm that quantifies the signal peptide-ness of amino acid sequences. The novel signal peptides selected in this study increased Fc-fusion protein production in CHO cells by increasing specific protein productivity, whereas they did not negatively affect cell growth. Particularly, the SP-#149 clone showed the highest qp, 0.73 ± 0.01 pg/cell/day from day 1 to day 4, representing a 1.47-fold increase over the native signal peptide in a serum-free suspension culture mode. In addition, replacing native signal peptide with the novel signal peptides did not significantly affect sialylated N-glycan formation, N-terminal cleavage pattern, and biological function of Fc-fusion protein produced in CHO cells. The overall results indicate the utility of a novel in vitro screening system for synthetic signal peptide for mammalian cell-based protein production. KEY POINTS: • An in vitro screening system for synthetic signal peptide in mammalian cells was established • This system combined a degenerate codon-based library, site-specific integration, and a FACS-based detection assay • The novel signal peptides selected in this study could increase Fc-fusion protein production in mammalian cells.
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Affiliation(s)
- Jong-Ho Park
- Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
| | - Hoon-Min Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Eun-Ju Jin
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Eun-Ji Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Yeon-Ju Kang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Sungkyun Kim
- Choong Ang Vaccine Laboratory Co., Ltd. (CAVAC), 1476-37 Yuseong-daero, Yuseong-gu, Daejeon, Korea
| | - Sung-Sick Yoo
- Choong Ang Vaccine Laboratory Co., Ltd. (CAVAC), 1476-37 Yuseong-daero, Yuseong-gu, Daejeon, Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, Korea.
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea.
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea.
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20
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The potential of emerging sub-omics technologies for CHO cell engineering. Biotechnol Adv 2022; 59:107978. [DOI: 10.1016/j.biotechadv.2022.107978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/25/2022] [Accepted: 05/07/2022] [Indexed: 11/23/2022]
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21
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Torres M, Hussain H, Dickson AJ. The secretory pathway - the key for unlocking the potential of Chinese hamster ovary cell factories for manufacturing therapeutic proteins. Crit Rev Biotechnol 2022; 43:628-645. [PMID: 35465810 DOI: 10.1080/07388551.2022.2047004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mammalian cell factories (in particular the CHO cell system) have been crucial in the rise of biopharmaceuticals. Mammalian cells have compartmentalized organelles where intricate networks of proteins manufacture highly sophisticated biopharmaceuticals in a specialized production pipeline - the secretory pathway. In the bioproduction context, the secretory pathway functioning is key for the effectiveness of cell factories to manufacture these life-changing medicines. This review describes the molecular components and events involved in the secretory pathway, and provides a comprehensive summary of the intracellular steps limiting the production of therapeutic proteins as well as the achievements in engineering CHO cell secretory machinery. We also consider antibody-producing plasma cells (so called "professional" secretory cells) to explore the mechanisms underpinning their unique secretory function/features. Such understandings offer the potential to further enhancement of the current CHO cell production platforms for manufacturing next generation of biopharmaceuticals.
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Affiliation(s)
- Mauro Torres
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Department of Chemical Engineering and Analytical Science, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| | - Hirra Hussain
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Department of Chemical Engineering and Analytical Science, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| | - Alan J Dickson
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Department of Chemical Engineering and Analytical Science, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
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22
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Malm M, Kuo CC, Barzadd MM, Mebrahtu A, Wistbacka N, Razavi R, Volk AL, Lundqvist M, Kotol D, Tegel H, Hober S, Edfors F, Gräslund T, Chotteau V, Field R, Varley PG, Roth RG, Lewis NE, Hatton D, Rockberg J. Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins. Metab Eng 2022; 72:171-187. [PMID: 35301123 PMCID: PMC9189052 DOI: 10.1016/j.ymben.2022.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 10/31/2022]
Abstract
Biologics represent the fastest growing group of therapeutics, but many advanced recombinant protein moieties remain difficult to produce. Here, we identify metabolic engineering targets limiting expression of recombinant human proteins through a systems biology analysis of the transcriptomes of CHO and HEK293 during recombinant expression. In an expression comparison of 24 difficult to express proteins, one third of the challenging human proteins displayed improved secretion upon host cell swapping from CHO to HEK293. Guided by a comprehensive transcriptomics comparison between cell lines, especially highlighting differences in secretory pathway utilization, a co-expression screening of 21 secretory pathway components validated ATF4, SRP9, JUN, PDIA3 and HSPA8 as productivity boosters in CHO. Moreover, more heavily glycosylated products benefitted more from the elevated activities of the N- and O-glycosyltransferases found in HEK293. Collectively, our results demonstrate the utilization of HEK293 for expression rescue of human proteins and suggest a methodology for identification of secretory pathway components for metabolic engineering of HEK293 and CHO.
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Affiliation(s)
- Magdalena Malm
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Chih-Chung Kuo
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA; The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, CA, 92093, USA
| | - Mona Moradi Barzadd
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Aman Mebrahtu
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Num Wistbacka
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Ronia Razavi
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Anna-Luisa Volk
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magnus Lundqvist
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - David Kotol
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, 171 65, Sweden
| | - Hanna Tegel
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Sophia Hober
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, 171 65, Sweden
| | - Torbjörn Gräslund
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Veronique Chotteau
- Dept. of Industrial Biotechnology, KTH - Royal Institute of Technology, Stockholm, SE-10691, Sweden
| | - Ray Field
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Paul G Varley
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Robert G Roth
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Nathan E Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA; The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, CA, 92093, USA.
| | - Diane Hatton
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Johan Rockberg
- Dept. of Protein Science, KTH - Royal Institute of Technology, Stockholm, SE-106 91, Sweden.
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23
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Szkodny AC, Lee KH. Biopharmaceutical Manufacturing: Historical Perspectives and Future Directions. Annu Rev Chem Biomol Eng 2022; 13:141-165. [PMID: 35300518 DOI: 10.1146/annurev-chembioeng-092220-125832] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review describes key milestones related to the production of biopharmaceuticals-therapies manufactured using recombinant DNA technology. The market for biopharmaceuticals has grown significantly since the first biopharmaceutical approval in 1982, and the scientific maturity of the technologies used in their manufacturing processes has grown concomitantly. Early processes relied on established unit operations, with research focused on process scale-up and improved culture productivity. In the early 2000s, changes in regulatory frameworks and the introduction of Quality by Design emphasized the importance of developing manufacturing processes to deliver a desired product quality profile. As a result, companies adopted platform processes and focused on understanding the dynamic interplay between product quality and processing conditions. The consistent and reproducible manufacturing processes of today's biopharmaceutical industry have set high standards for product efficacy, quality, and safety, and as the industry continues to evolve in the coming decade, intensified processing capabilities for an expanded range of therapeutic modalities will likely become routine. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Alana C Szkodny
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA; ;
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA; ;
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24
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Barzadd MM, Lundqvist M, Harris C, Malm M, Volk AL, Thalén N, Chotteau V, Grassi L, Smith A, Abadi ML, Lambiase G, Gibson S, Hatton D, Rockberg J. Autophagy and intracellular product degradation genes identified by systems biology analysis reduce aggregation of bispecific antibody in CHO cells. N Biotechnol 2022; 68:68-76. [PMID: 35123066 DOI: 10.1016/j.nbt.2022.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 12/18/2022]
Abstract
Aggregation of therapeutic bispecific antibodies negatively affects the yield, shelf-life, efficacy and safety of these products. Pairs of stable Chinese hamster ovary (CHO) cell lines produced two difficult-to-express bispecific antibodies with different levels of aggregated product (10-75% aggregate) in a miniaturized bioreactor system. Here, transcriptome analysis was used to interpret the biological causes for the aggregation and to identify strategies to improve product yield and quality. Differential expression- and gene set analysis revealed upregulated proteasomal degradation, unfolded protein response and autophagy processes to be correlated with reduced protein aggregation. Fourteen candidate genes with the potential to reduce aggregation were co-expressed in the stable clones for validation. Of these, HSP90B1, DDIT3, AK1S1, and ATG16L1, were found to significantly lower aggregation in the stable producers and two (HSP90B1 and DNAJC3) increased titres of the anti-HER2 monoclonal antibody trastuzumab by 50% during transient expression. It is suggested that this approach could be of general use for defining aggregation bottlenecks in CHO cells.
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Affiliation(s)
- Mona Moradi Barzadd
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden.
| | - Magnus Lundqvist
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden.
| | - Claire Harris
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Magdalena Malm
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden
| | - Anna-Luisa Volk
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden
| | - Niklas Thalén
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden
| | - Veronique Chotteau
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Industrial Biotechnology, SE-106 91 Stockholm, Sweden
| | - Luigi Grassi
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andrew Smith
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Marina Leal Abadi
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Giulia Lambiase
- Analytical Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK and Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, UK
| | - Suzanne Gibson
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Diane Hatton
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Johan Rockberg
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden.
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25
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Cell-Free Protein Synthesis with Fungal Lysates for the Rapid Production of Unspecific Peroxygenases. Antioxidants (Basel) 2022; 11:antiox11020284. [PMID: 35204167 PMCID: PMC8868270 DOI: 10.3390/antiox11020284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Unspecific peroxygenases (UPOs, EC 1.11.2.1) are fungal biocatalysts that have attracted considerable interest for application in chemical syntheses due to their ability to selectively incorporate peroxide-oxygen into non-activated hydrocarbons. However, the number of available and characterized UPOs is limited, as it is difficult to produce these enzymes in homologous or hetero-logous expression systems. In the present study, we introduce a third approach for the expression of UPOs: cell-free protein synthesis using lysates from filamentous fungi. Biomass of Neurospora crassa and Aspergillus niger, respectively, was lysed by French press and tested for translational activity with a luciferase reporter enzyme. The upo1 gene from Cyclocybe (Agrocybe) aegerita (encoding the main peroxygenase, AaeUPO) was cell-free expressed with both lysates, reaching activities of up to 105 U L−1 within 24 h (measured with veratryl alcohol as substrate). The cell-free expressed enzyme (cfAaeUPO) was successfully tested in a substrate screening that included prototypical UPO substrates, as well as several pharmaceuticals. The determined activities and catalytic performance were comparable to that of the wild-type enzyme (wtAaeUPO). The results presented here suggest that cell-free expression could become a valuable tool to gain easier access to the immense pool of putative UPO genes and to expand the spectrum of these sought-after biocatalysts.
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26
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Chakrabarti L, Chaerkady R, Wang J, Weng SHS, Wang C, Qian C, Cazares L, Hess S, Amaya P, Zhu J, Hatton D. Mitochondrial membrane potential-enriched CHO host: a novel and powerful tool for improving biomanufacturing capability. MAbs 2022; 14:2020081. [PMID: 35030984 PMCID: PMC8765075 DOI: 10.1080/19420862.2021.2020081] [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] [Indexed: 11/17/2022] Open
Abstract
With the aim of increasing protein productivity of Chinese hamster ovary (CHO) cells, we sought to generate new CHO hosts with favorable biomanufacturing phenotypes and improved functionality. Here, we present an innovative approach of enriching the CHO host cells with a high mitochondrial membrane potential (MMP). Stable transfectant pools and clonal cell lines expressing difficult-to-express bispecific molecules generated from the MMP-enriched host outperformed the parental host by displaying (1) improved fed-batch productivity; (2) enhanced long-term cell viability of pools; (3) more favorable lactate metabolism; and (4) improved cell cloning efficiency during monoclonal cell line generation. Proteomic analysis together with Western blot validation were used to investigate the underlying mechanisms by which high MMP influenced production performance. The MMP-enriched host exhibited multifaceted protection against mitochondrial dysfunction and endoplasmic reticulum stress. Our findings indicate that the MMP-enriched host achieved an overall “fitter” phenotype that contributes to the significant improvement in biomanufacturing capability.
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Affiliation(s)
- Lina Chakrabarti
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Junmin Wang
- Dynamic Omics, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Chunlei Wang
- Analytical Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Chen Qian
- Analytical Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Lisa Cazares
- Dynamic Omics, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Sonja Hess
- Dynamic Omics, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Peter Amaya
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jie Zhu
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Diane Hatton
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge, UK
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27
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Altamura R, Doshi J, Benenson Y. Rational design and construction of multi-copy biomanufacturing islands in mammalian cells. Nucleic Acids Res 2022; 50:561-578. [PMID: 34893882 PMCID: PMC8754653 DOI: 10.1093/nar/gkab1214] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/21/2021] [Accepted: 11/26/2021] [Indexed: 11/14/2022] Open
Abstract
Cell line development is a critical step in the establishment of a biopharmaceutical manufacturing process. Current protocols rely on random transgene integration and amplification. Due to considerable variability in transgene integration profiles, this workflow results in laborious screening campaigns before stable producers can be identified. Alternative approaches for transgene dosage increase and integration are therefore highly desirable. In this study, we present a novel strategy for the rapid design, construction, and genomic integration of engineered multiple-copy gene constructs consisting of up to 10 gene expression cassettes. Key to this strategy is the diversification, at the sequence level, of the individual gene cassettes without altering their protein products. We show a computational workflow for coding and regulatory sequence diversification and optimization followed by experimental assembly of up to nine gene copies and a sentinel reporter on a contiguous scaffold. Transient transfections in CHO cells indicates that protein expression increases with the gene copy number on the scaffold. Further, we stably integrate these cassettes into a pre-validated genomic locus. Altogether, our findings point to the feasibility of engineering a fully mapped multi-copy recombinant protein 'production island' in a mammalian cell line with greatly reduced screening effort, improved stability, and predictable product titers.
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Affiliation(s)
- Raffaele Altamura
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Jiten Doshi
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Yaakov Benenson
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland
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28
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Zagoskin AA, Zakharova MV, Nagornykh MO. Structural Elements of DNA and RNA Eukaryotic Expression Vectors for In Vitro and In Vivo Genome Editor Delivery. Mol Biol 2022; 56:950-962. [PMCID: PMC9735121 DOI: 10.1134/s0026893322060218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 12/14/2022]
Abstract
Gene editing with programmable nucleases opens new perspectives in important practice areas, such as healthcare and agriculture. The most challenging problem for the safe and effective therapeutic use of gene editing technologies is the proper delivery and expression of gene editors in cells and tissues of different organisms. Virus-based and nonviral systems can be used for the successful delivery of gene editors. Here we have reviewed structural elements of nonviral DNA- and RNA-based expression vectors for gene editing and delivery methods in vitro and in vivo.
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Affiliation(s)
- A. A. Zagoskin
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - M. V. Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - M. O. Nagornykh
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia ,Sirius University of Science and Technology, Sirius, 354349 Sochi, Russia
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29
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Zhang HY, Fan ZL, Wang TY. Advances of Glycometabolism Engineering in Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2021; 9:774175. [PMID: 34926421 PMCID: PMC8675083 DOI: 10.3389/fbioe.2021.774175] [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: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/03/2022] Open
Abstract
As the most widely used mammalian cell line, Chinese hamster ovary (CHO) cells can express various recombinant proteins with a post translational modification pattern similar to that of the proteins from human cells. During industrial production, cells need large amounts of ATP to support growth and protein expression, and since glycometabolism is the main source of ATP for cells, protein production partly depends on the efficiency of glycometabolism. And efficient glycometabolism allows less glucose uptake by cells, reducing production costs, and providing a better mammalian production platform for recombinant protein expression. In the present study, a series of progresses on the comprehensive optimization in CHO cells by glycometabolism strategy were reviewed, including carbohydrate intake, pyruvate metabolism and mitochondrial metabolism. We analyzed the effects of gene regulation in the upstream and downstream of the glucose metabolism pathway on cell’s growth and protein expression. And we also pointed out the latest metabolic studies that are potentially applicable on CHO cells. In the end, we elaborated the application of metabolic models in the study of CHO cell metabolism.
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Affiliation(s)
- Huan-Yu Zhang
- Department of Biochemistry and Molecular Biology, 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
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
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30
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Hussain H, Patel T, Ozanne AMS, Vito D, Ellis M, Hinchliffe M, Humphreys DP, Stephens PE, Sweeney B, White J, Dickson AJ, Smales CM. A comparative analysis of recombinant Fab and full-length antibody production in Chinese hamster ovary cells. Biotechnol Bioeng 2021; 118:4815-4828. [PMID: 34585737 DOI: 10.1002/bit.27944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/31/2021] [Accepted: 09/12/2021] [Indexed: 01/05/2023]
Abstract
Monoclonal antibodies are the leading class of biopharmaceuticals in terms of numbers approved for therapeutic purposes. Antigen-binding fragments (Fab) are also used as biotherapeutics and used widely in research applications. The dominant expression systems for full-length antibodies are mammalian cell-based, whereas for Fab molecules the preference has been an expression in bacterial systems. However, advances in CHO and downstream technologies make mammalian systems an equally viable option for small- and large-scale Fab production. Using a panel of full-length IgG antibodies and their corresponding Fab pair with different antigen specificities, we investigated the impact of the IgG and Fab molecule format on production from Chinese hamster ovary (CHO) cells and assessed the cellular capability to process and produce these formats. The full-length antibody format resulted in the recovery of fewer mini-pools posttransfection when compared to the corresponding Fab fragment format that could be interpreted as indicative of a greater overall burden on cells. Antibody-producing cell pools that did recover were subsequently able to achieve higher volumetric protein yields (mg/L) and specific productivity than the corresponding Fab pools. Importantly, when the actual molecules produced per cell of a given format was considered (as opposed to mass), CHO cells produced a greater number of Fab molecules per cell than obtained with the corresponding IgG, suggesting that cells were more efficient at making the smaller Fab molecule. Analysis of cell pools showed that gene copy number was not correlated to the subsequent protein production. The amount of mRNA correlated with secreted Fab production but not IgG, whereby posttranscriptional processes act to limit antibody production. In summary, we provide the first comparative description of how full-length IgG and Fab antibody formats impact on the outcomes of a cell line construction process and identify potential limitations in their production that could be targeted for engineering increases in the efficiency in the manufacture of these recombinant antibody formats.
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Affiliation(s)
- Hirra Hussain
- Faculty of Science and Engineering, Department of Chemical Engineering and Analytical Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.,CPI, Central Park, Darlington, UK
| | - Tulshi Patel
- Division of Natural Sciences, Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, UK.,Horizon Discovery Biosciences Limited, Cambridge, UK
| | - Angelica M S Ozanne
- Division of Natural Sciences, Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, UK
| | - Davide Vito
- Division of Natural Sciences, Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, UK.,Mestag Therapeutics Limited, Cambridge, UK
| | - Mark Ellis
- Protein Sciences, UCB Pharma, Berkshire, UK
| | | | | | | | - Bernie Sweeney
- Protein Sciences, UCB Pharma, Berkshire, UK.,Lonza Biologics, Berkshire, UK
| | | | - Alan J Dickson
- Faculty of Science and Engineering, Department of Chemical Engineering and Analytical Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Christopher M Smales
- Division of Natural Sciences, Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, UK.,National Institute for Bioprocessing Research and Training, Co Dublin, Ireland
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31
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Xiong K, la Cour Karottki KJ, Hefzi H, Li S, Grav LM, Li S, Spahn P, Lee JS, Ventina I, Lee GM, Lewis NE, Kildegaard HF, Pedersen LE. An optimized genome-wide, virus-free CRISPR screen for mammalian cells. CELL REPORTS METHODS 2021; 1:100062. [PMID: 34935002 PMCID: PMC8687118 DOI: 10.1016/j.crmeth.2021.100062] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/17/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022]
Abstract
Pooled CRISPR screens have been widely applied to mammalian and other organisms to elucidate the interplay between genes and phenotypes of interest. The most popular method for delivering the CRISPR components into mammalian cells is lentivirus based. However, because lentivirus is not always an option, virus-free protocols are starting to emerge. Here, we demonstrate an improved virus-free, genome-wide CRISPR screening platform for Chinese hamster ovary cells with 75,488 gRNAs targeting 15,028 genes. Each gRNA expression cassette in the library is precisely integrated into a genomic landing pad, resulting in a very high percentage of single gRNA insertions and minimal clonal variation. Using this platform, we perform a negative selection screen on cell proliferation that identifies 1,980 genes that affect proliferation and a positive selection screen on the toxic endoplasmic reticulum stress inducer, tunicamycin, that identifies 77 gene knockouts that improve survivability.
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Affiliation(s)
- Kai Xiong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | | | - Hooman Hefzi
- The Novo Nordisk Foundation Center for Biosustainability, University of California at San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
| | - Songyuan Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Shangzhong Li
- The Novo Nordisk Foundation Center for Biosustainability, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Philipp Spahn
- The Novo Nordisk Foundation Center for Biosustainability, University of California at San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Ildze Ventina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Nathan E. Lewis
- The Novo Nordisk Foundation Center for Biosustainability, University of California at San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
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32
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Selection of CHO host and recombinant cell pools by inhibition of the proteasome results in enhanced product yields and cell specific productivity. J Biotechnol 2021; 337:35-45. [PMID: 34171439 DOI: 10.1016/j.jbiotec.2021.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/14/2021] [Accepted: 06/19/2021] [Indexed: 11/23/2022]
Abstract
Chinese hamster ovary (CHO) cells are the leading mammalian cell expression platform for biotherapeutic recombinant molecules yet some proteins remain difficult to express (DTE) in this, and other, systems. In recombinant cell lines expressing DTE proteins, cellular processes to restore proteostasis can be triggered when the folding and modification capabilities are exceeded, including the unfolded protein response and ER-associated degradation (ERAD) and proteasomal degradation. We therefore investigated whether the proteasome activity of CHO cells was linked to their ability to produce recombinant proteins. We found cell lines with diverse monoclonal antibody (mAb) productivity show different susceptibilities to inhibitors of proteasome activity. Subsequently, we applied selective pressure using proteasome inhibitors on mAb producing cells to determine the impact on cell growth and recombinant protein production, and to apply proteasome selective pressure above that of a metabolic selection marker during recombinant cell pool construction. The presence of proteasome inhibitors during cell pool construction expressing two different model molecules, including a DTE Fc-fusion protein, resulted in the generation of cell pools with enhanced productivity. The increased productivities, and ability to select for higher producing cells, has potential to improve clonal selection during upstream processes of DTE proteins.
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33
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Zhou Q, Zhang Y, Lu X, Wang C, Pei X, Lu Y, Cao C, Xu C, Zhang B. Stable overexpression of mutated PTEN in Chinese hamster ovary cells enhances their performance and therapeutic antibody production. Biotechnol J 2021; 16:e2000623. [PMID: 34053183 DOI: 10.1002/biot.202000623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022]
Abstract
Chinese hamster ovary (CHO) cells with a high viable cell density (VCD), resilience to culture stress, and the capacity to continuously express recombinant proteins are highly desirable. Phosphatase and tension homology deleted on chromosome ten (PTEN) functions as a key negative regulator of the PI3K/Akt signaling pathway, mediating cell growth and survival. Its oncogenic mutant endows cells with an enhanced proliferation rate and resistance to death. In this study, the role of oncogenic PTEN C124S or G129E on the performance of CHO-K1 and CHO-IgG cells was investigated. Our results showed that CHO-K1 cells stably expressing PTEN C124S or G129E exhibited enhanced proliferation, reduced apoptosis rate, and increased transient expression of therapeutic antibodies compared to the control cells. Moreover, the stable overexpression of PTEN C124S or G129E endowed CHO-IgG cells with higher cell viability, VCD, and antibody titers (yield increased by approximately 0.77-fold) in the fed-batch culture process and enhanced their performance in response to the addition of sodium lactate. Moreover, the engineering of mutated PTEN in CHO-IgG cells did not alter antibody quality. Collectively, our data suggest that mutated PTEN is a potential target for improving the manufacture of therapeutic antibodies.
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Affiliation(s)
- Qin Zhou
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Yujie Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Xiaoxiang Lu
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Chang Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Xinxin Pei
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Yafang Lu
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing, P. R. China
| | - Changzhi Xu
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Buchang Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
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34
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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35
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Combe M, Sokolenko S. Quantifying the impact of cell culture media on CHO cell growth and protein production. Biotechnol Adv 2021; 50:107761. [PMID: 33945850 DOI: 10.1016/j.biotechadv.2021.107761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 10/21/2022]
Abstract
In recombinant protein production, cell culture media development and optimization is typically seen as a useful strategy to increase titer and cell density, reduce by-products, as well as improve product quality (with cell density and titer often serving as the primary reported outcome of media studies). However, despite the large number of media optimization studies, there have been few attempts to comprehensively assess the overall effectiveness of media additives. The aim of this review is therefore both to document published media optimization studies over the last twenty years (in the context of Chinese hamster ovary cell recombinant production) and quantitatively estimate the impact of this media optimization on cell culture performance. In considering 78 studies, we have identified 238 unique media components that have been supplemented over the last 20 years. Among these additives, trace elements stood out as having a positive impact on cell density while nucleotides show potential for increasing titer, with commercial supplements benefiting both. However, we also identified that the impact of specific additives is far more variable than often perceived. With relatively few media studies considering multiple cell lines or multiple basal media, teasing out consistent and general trends becomes a considerable challenge. By extracting cell density and titer values from all of the reviewed studies, we were able to build a mixed-effect model capable of estimating the relative impact of additives, cell line, product type, basal medium, cultivation method (flask or reactor), and feeding strategy (batch or fed-batch). Overall, additives only accounted for 3% of the variation in cell density and 1% of the variation in titer. Similarly, the impact of basal media was also relatively modest, at 10% for cell density and 0% for titer. Cell line, product type, and feeding strategy were all found to have more impact. These results emphasize the need for media studies to consider more factors to ensure that reported observations can be generalized and further developed.
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Affiliation(s)
- Michelle Combe
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington St., PO Box 15000, Halifax, NS B3H 4R2, Canada
| | - Stanislav Sokolenko
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington St., PO Box 15000, Halifax, NS B3H 4R2, Canada.
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36
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Schmitt MG, White RN, Barnard GC. Development of a high cell density transient CHO platform yielding mAb titers greater than 2 g/L in only 7 days. Biotechnol Prog 2021; 36:e3047. [PMID: 33411420 DOI: 10.1002/btpr.3047] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022]
Abstract
We developed a simple transient Chinese Hamster Ovary expression platform. Titers for a random panel of 20 clinical monoclonal antibodies (mAbs) ranged from 0.6 to 2.7 g/L after 7 days. Two factors were the key in obtaining these high titers. First, we utilized an extremely high starting cell density (20 million cells/ml), and then arrested further cell growth by employing mild hypothermic conditions (32°C). Second, we performed a 6-variable Design of Experiments to find optimal concentrations of plasmid DNA (coding DNA), boost DNA (DNA encoding the XBP1S transcription factor), transfection reagent (polyethylenimine [PEI]), and nutrient feed amounts. High coding DNA concentrations (12.5 mg/L) were found to be optimal. We therefore diluted expensive coding DNA with inexpensive inert filler DNA (herring sperm DNA). Reducing the coding DNA concentration by 70% from 12.5 to 3.75 mg/L did not meaningfully reduce mAb titers. Titers for the same panel of 20 clinical mAbs ranged from 0.7 to 2.2 g/L after reducing the coding DNA concentration to 3.75 mg/L. Finally, we found that titer and product quality attributes were similar for a clinical mAb (rituximab) expressed at very different scales (volumes ranging from 3 ml to 2 L).
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Affiliation(s)
- Matthew G Schmitt
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Technology Center, Indianapolis, Indiana, USA
| | - Regina N White
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Technology Center, Indianapolis, Indiana, USA
| | - Gavin C Barnard
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Technology Center, Indianapolis, Indiana, USA
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37
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Lao-Gonzalez T, Bueno-Soler A, Duran-Hernandez A, Sosa-Aguiar K, Hinojosa-Puerta LE, Hernandez-Garcia T, de la Luz-Hernandez KR, Palacios-Oliva J, Boggiano-Ayo T. Screening and selection strategy for the establishment of biosimilar to trastuzumab-expressing CHO-K1 cell lines. AMB Express 2021; 11:1. [PMID: 33389203 PMCID: PMC7778674 DOI: 10.1186/s13568-020-01157-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/04/2020] [Indexed: 12/24/2022] Open
Abstract
The high prices of biopharmaceuticals or biologics used in the treatment of many diseases limit the access of patients to these novel therapies. One example is the monoclonal antibody trastuzumab, successfully used for breast cancer treatment. An economic alternative is the generation of biosimilars to these expensive biopharmaceuticals. Since antibody therapies may require large doses over a long period of time, robust platforms and strategies for cell line development are essential for the generation of recombinant cell lines with higher levels of expression. Here, we obtained trastuzumab-expressing CHO-K1 cells through a screening and selection strategy that combined the use of host cells pre-adapted to protein-free media and suspension culture and lentiviral vectors. The results demonstrated that the early screening strategy obtained recombinant CHO-K1 cell populations with higher enrichment of IgG-expressing cells. Moreover, the measurement of intracellular heavy chain polypeptide by flow cytometry was a useful metric to characterize the homogeneity of cell population, and our results suggest this could be used to predict the expression levels of monoclonal antibodies in early stages of cell line development. Additionally, we propose an approach using 25 cm2 T-flasks in suspension and shaking culture conditions as a screening tool to identify high producing cell lines. Finally, trastuzumab-expressing CHO-K1 clones were generated and characterized by batch culture, and preliminary results related to HER2-recognition capacity were successful. Further optimization of elements such as gene optimization, vector selection, type of amplification/selection system, cell culture media composition, in combination with this strategy will allow obtaining high producing clones.
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Affiliation(s)
- Thailin Lao-Gonzalez
- Process Development Direction, Center of Molecular Immunology, Playa, Havana, 11600 Cuba
- Animal Biotechnology Division, Center for Genetic Engineering and Biotechnology, Playa, Havana, 10600 Cuba
| | - Alexi Bueno-Soler
- Process Development Direction, Center of Molecular Immunology, Playa, Havana, 11600 Cuba
| | | | - Katya Sosa-Aguiar
- Immunotherapy Direction, Center of Molecular Immunology, Playa, 11600 Havana, Cuba
| | - Luis Eduardo Hinojosa-Puerta
- Process Development Direction, Center of Molecular Immunology, Playa, Havana, 11600 Cuba
- CIMAB S. A, Playa, 11600 Havana, Cuba
| | - Tays Hernandez-Garcia
- Process Development Direction, Center of Molecular Immunology, Playa, Havana, 11600 Cuba
| | | | - Julio Palacios-Oliva
- Process Development Direction, Center of Molecular Immunology, Playa, Havana, 11600 Cuba
| | - Tammy Boggiano-Ayo
- Process Development Direction, Center of Molecular Immunology, Playa, Havana, 11600 Cuba
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38
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Esposito D, Mehalko J, Drew M, Snead K, Wall V, Taylor T, Frank P, Denson JP, Hong M, Gulten G, Sadtler K, Messing S, Gillette W. Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays. Protein Expr Purif 2020; 174:105686. [PMID: 32504802 PMCID: PMC7271859 DOI: 10.1016/j.pep.2020.105686] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 11/23/2022]
Abstract
The SARS-CoV-2 spike trimer is the primary antigen for several serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Through this investigation, we developed a simplified and robust purification strategy that consistently yields 5 mg of protein per liter of expression culture for two commonly used forms of the SARS-CoV-2 spike protein. We show that these proteins form well-behaved stable trimers and are consistently functional in serology assays across multiple protein production lots.
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Affiliation(s)
- Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA.
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Min Hong
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Gulcin Gulten
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
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39
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Pérez-Rodriguez S, de Jesús Ramírez-Lira M, Wulff T, Voldbor BG, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Enrichment of microsomes from Chinese hamster ovary cells by subcellular fractionation for its use in proteomic analysis. PLoS One 2020; 15:e0237930. [PMID: 32841274 PMCID: PMC7447005 DOI: 10.1371/journal.pone.0237930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/06/2020] [Indexed: 11/19/2022] Open
Abstract
Chinese hamster ovary cells have been the workhorse for the production of recombinant proteins in mammalian cells. Since biochemical, cellular and omics studies are usually affected by the lack of suitable fractionation procedures to isolate compartments from these cells, differential and isopycnic centrifugation based techniques were characterized and developed specially for them. Enriched fractions in intact nuclei, mitochondria, peroxisomes, cis-Golgi, trans-Golgi and endoplasmic reticulum (ER) were obtained in differential centrifugation steps and subsequently separated in discontinuous sucrose gradients. Nuclei, mitochondria, cis-Golgi, peroxisomes and smooth ER fractions were obtained as defined bands in 30-60% gradients. Despite the low percentage represented by the microsomes of the total cell homogenate (1.7%), their separation in a novel sucrose gradient (10-60%) showed enough resolution and efficiency to quantitatively separate their components into enriched fractions in trans-Golgi, cis-Golgi and ER. The identity of these organelles belonging to the classical secretion pathway that came from 10-60% gradients was confirmed by proteomics. Data are available via ProteomeXchange with identifier PXD019778. Components from ER and plasma membrane were the most frequent contaminants in almost all obtained fractions. The improved sucrose gradient for microsomal samples proved being successful in obtaining enriched fractions of low abundance organelles, such as Golgi apparatus and ER components, for biochemical and molecular studies, and suitable for proteomic research, which makes it a useful tool for future studies of this and other mammalian cell lines.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - María de Jesús Ramírez-Lira
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bjørn Gunnar Voldbor
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Octavio T. Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
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Kuhn A, Le Fourn V, Fisch I, Mermod N. Genome-wide analysis of single nucleotide variants allows for robust and accurate assessment of clonal derivation in cell lines used to produce biologics. Biotechnol Bioeng 2020; 117:3628-3638. [PMID: 32779734 PMCID: PMC7818110 DOI: 10.1002/bit.27534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/22/2020] [Accepted: 07/29/2020] [Indexed: 11/11/2022]
Abstract
A clonally derived (or “monoclonal”) cell line is a cell population derived from a single progenitor cell. Clonally derived cell lines are required for many biotechnological applications. For instance, recombinant mammalian cells used to produce therapeutic proteins are expected by regulatory authorities to be clonally derived. Assurance of clonal derivation (or “clonality”) is usually obtained from the characterization of the procedure used for cell cloning, for instance by assessing the success rate of single‐cell sorting but not by assessing the cell line itself. We have developed a method to assess clonal derivation directly from the genetic makeup of cells. The genomic test of clonality is based on whole‐genome sequencing and statistical analysis of single nucleotide variants. This approach quantifies the clonal fractions present in nonclonal samples and it provides a measure of the probability that a cell line is derived from a single cell. Upon experimental validation of the test, we show that it is highly accurate and that it can robustly detect minor clonal fractions of as little as 1% of the cell population. Moreover, we find that it is applicable to various cell line development protocols. This approach can simplify development protocols and shorten timelines while ensuring clonal derivation with high confidence.
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Affiliation(s)
- Alexandre Kuhn
- Department of Fundamental Microbiology, Institute of Biotechnology, University of Lausanne, Switzerland.,Selexis SA, Geneva, Switzerland
| | | | | | - Nicolas Mermod
- Department of Fundamental Microbiology, Institute of Biotechnology, University of Lausanne, Switzerland
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41
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Bojar D, Fussenegger M. The Role of Protein Engineering in Biomedical Applications of Mammalian Synthetic Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903093. [PMID: 31588687 DOI: 10.1002/smll.201903093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Engineered proteins with enhanced or altered functionality, generated for example by mutation or domain fusion, are at the core of nearly all synthetic biology endeavors in the context of precision medicine, also known as personalized medicine. From designer receptors sensing elevated blood markers to effectors rerouting signaling pathways to synthetic transcription factors and the customized therapeutics they regulate, engineered proteins play a crucial role at every step of novel therapeutic approaches using synthetic biology. Here, recent developments in protein engineering aided by advances in directed evolution, de novo design, and machine learning are discussed. Building on clinical successes already achieved with chimeric antigen receptor (CAR-) T cells and other cell-based therapies, these developments are expected to further enhance the capabilities of mammalian synthetic biology in biomedical and other applications.
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Affiliation(s)
- Daniel Bojar
- ETH Zurich, Department of Biosystems Science and Engineering, Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
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42
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Esposito D, Mehalko J, Drew M, Snead K, Wall V, Taylor T, Frank P, Denson JP, Hong M, Gulten G, Sadtler K, Messing S, Gillette W. Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.27.120204. [PMID: 32511418 PMCID: PMC7265690 DOI: 10.1101/2020.05.27.120204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The SARS-CoV-2 spike trimer is the primary antigen for several serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Through this investigation, we developed a simplified and robust purification strategy that consistently yields 5 mg of protein per liter of expression culture for two commonly used forms of the SARS-CoV-2 spike protein. We show that these proteins form well-behaved stable trimers and are consistently functional in serology assays across multiple protein production lots.
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Affiliation(s)
- Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Min Hong
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Gulcin Gulten
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
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43
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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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44
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Torres M, Akhtar S, McKenzie EA, Dickson AJ. Temperature Down-Shift Modifies Expression of UPR-/ERAD-Related Genes and Enhances Production of a Chimeric Fusion Protein in CHO Cells. Biotechnol J 2020; 16:e2000081. [PMID: 32271992 DOI: 10.1002/biot.202000081] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Indexed: 02/05/2023]
Abstract
Low culture temperature enhances the cell-specific productivity of Chinese hamster ovary (CHO) cells expressing varied recombinant (r-) proteins, but the mechanisms remain unclear. Regulation of unfolded protein response (UPR) pathway genes, such as transcriptional regulatory factors and endoplasmic reticulum (ER)-resident proteins, appear to be involved in the improvements of r-protein production under low temperature conditions. The transcriptional regulation of UPR-specific targets is studied in response to decreased culture temperature in relation to production of a difficult-to-express protein. A clonally-derived CHO cell line expressing a chimeric fusion protein (human erythropoietin [hEPO] linked to a murine Fc region, hEPO-Fc) is evaluated in terms of growth, metabolism, r-protein production and UPR-/ER associated degradation (ERAD)-specific gene expression at standard (37 °C) and low (32 °C) temperature in batch and fed-batch systems. Low temperature decreased peak cell density, improved viability, generated cell cycle arrest in the G1 phase and enhanced hEPO-Fc expression in both batch and fed-batch cultures. A low culture temperature significantly upregulated genes encoding UPR-specific transcriptional activators (xbp1s, ddit3, and atf5) and ER-resident proteins (grp78, grp94, trib3, and ero1α), that are associated with folding and processing of proteins within the ER. Further, low culture temperature decreased expression of genes involved in ERAD (edem3, sels, herpud1, and syvn1) indicating a decreased potential for protein degradation.
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Affiliation(s)
- Mauro Torres
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, M1 7DN, UK
| | - Samia Akhtar
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, M1 7DN, UK
| | - Edward A McKenzie
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, M1 7DN, UK.,Protein Expression Facility, Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, M1 7DN, UK
| | - Alan J Dickson
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, M1 7DN, UK
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45
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Pourcel L, Buron F, Garcia F, Delaloix MS, Le Fourn V, Girod PA, Mermod N. Transient vitamin B5 starving improves mammalian cell homeostasis and protein production. Metab Eng 2020; 60:77-86. [PMID: 32247827 DOI: 10.1016/j.ymben.2020.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 01/23/2020] [Accepted: 03/22/2020] [Indexed: 12/13/2022]
Abstract
Maintaining a metabolic steady state is essential for an organism's fitness and survival when confronted with environmental stress, and metabolic imbalance can be reversed by exposing the organism to fasting. Here, we attempted to apply this physiological principle to mammalian cell cultures to improve cellular fitness and consequently their ability to express recombinant proteins. We showed that transient vitamin B5 deprivation, an essential cofactor of central cellular metabolism, can quickly and irreversibly affect mammalian cell growth and division. A selection method was designed that relies on mammalian cell dependence on vitamin B5 for energy production, using the co-expression of the B5 transporter SLC5A6 and a gene of interest. We demonstrated that vitamin B5 selection persistently activates peroxisome proliferator-activated receptors (PPAR), a family of transcription factors involved in energy homeostasis, thereby altering lipid metabolism, improving cell fitness and therapeutic protein production. Thus, stable PPAR activation may constitute a cellular memory of past deprivation state, providing increased resistance to further potential fasting events. In other words, our results imply that cultured cells, once exposed to metabolic starvation, may display an improved metabolic fitness as compared to non-exposed cells, allowing increased resistance to cellular stress.
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Affiliation(s)
- Lucille Pourcel
- Center for Biotechnology and Department of Fundamental Microbiology, University of Lausanne, UNIL-EPFL, Lausanne, Switzerland.
| | - Flavien Buron
- Center for Biotechnology and Department of Fundamental Microbiology, University of Lausanne, UNIL-EPFL, Lausanne, Switzerland
| | - Fanny Garcia
- Center for Biotechnology and Department of Fundamental Microbiology, University of Lausanne, UNIL-EPFL, Lausanne, Switzerland
| | - Margaux-Sarah Delaloix
- Center for Biotechnology and Department of Fundamental Microbiology, University of Lausanne, UNIL-EPFL, Lausanne, Switzerland
| | | | | | - Nicolas Mermod
- Center for Biotechnology and Department of Fundamental Microbiology, University of Lausanne, UNIL-EPFL, Lausanne, Switzerland
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46
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Berger A, Le Fourn V, Masternak J, Regamey A, Bodenmann I, Girod P, Mermod N. Overexpression of transcription factor Foxa1 and target genes remediate therapeutic protein production bottlenecks in Chinese hamster ovary cells. Biotechnol Bioeng 2020; 117:1101-1116. [PMID: 31956982 PMCID: PMC7079004 DOI: 10.1002/bit.27274] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/27/2019] [Accepted: 01/12/2020] [Indexed: 12/13/2022]
Abstract
Despite extensive research conducted to increase protein production from Chinese hamster ovary (CHO) cells, cellular bottlenecks often remain, hindering high yields. In this study, a transcriptomic analysis led to the identification of 32 genes that are consistently upregulated in high producer clones and thus might mediate high productivity. Candidate genes were associated with functions such as signaling, protein folding, cytoskeleton organization, and cell survival. We focused on two engineering targets, Erp27, which binds unfolded proteins and the Erp57 disulfide isomerase in the endoplasmic reticulum, and Foxa1, a pioneering transcription factor involved in organ development. Erp27 moderate overexpression increased production of an easy-to-express antibody, whereas Erp27 and Erp57 co-overexpression increased cell density, viability, and the yield of difficult-to-express proteins. Foxa1 overexpression increased cell density, cell viability, and easy- and difficult-to-express protein yields, whereas it decreased reactive oxygen species late in fed-batch cultures. Foxa1 overexpression upregulated two other candidate genes that increased the production of difficult- and/or easy-to-express proteins, namely Ca3, involved in protecting cells from oxidative stress, and Tagap, involved in signaling and cytoskeleton remodeling. Overall, several genes allowing to overcome CHO cell bottlenecks were identified, including Foxa1, which mediated multiple favorable metabolic changes that improve therapeutic protein yields.
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Affiliation(s)
- Audrey Berger
- Department of Fundamental Microbiology, Institute of BiotechnologyUniversity of LausanneLausanneSwitzerland
- Present address: Laboratory of Microsystems LMIS4Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | | | - Jacqueline Masternak
- Department of Fundamental Microbiology, Institute of BiotechnologyUniversity of LausanneLausanneSwitzerland
| | | | | | | | - Nicolas Mermod
- Department of Fundamental Microbiology, Institute of BiotechnologyUniversity of LausanneLausanneSwitzerland
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47
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Pourcel L, Buron F, Arib G, Le Fourn V, Regamey A, Bodenmann I, Girod P, Mermod N. Influence of cytoskeleton organization on recombinant protein expression by CHO cells. Biotechnol Bioeng 2020; 117:1117-1126. [PMID: 31956990 PMCID: PMC7079171 DOI: 10.1002/bit.27277] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/27/2019] [Accepted: 01/11/2020] [Indexed: 12/12/2022]
Abstract
In this study, we assessed the importance of cytoskeleton organization in the mammalian cells used to produce therapeutic proteins. Two cytoskeletal genes, Actin alpha cardiac muscle 1 (ACTC1) and a guanosine triphosphate GTPase-activating protein (TAGAP), were found to be upregulated in highly productive therapeutic protein-expressing Chinese hamster ovary (CHO) cells selected by the deprivation of vitamin B5. We report here that the overexpression of the ACTC1 protein was able to improve significantly recombinant therapeutic production, as well as to decrease the levels of toxic lactate metabolic by-products. ACTC1 overexpression was accompanied by altered as well as decreased polymerized actin, which was associated with high protein production by CHO cell cultured in suspension. We suggest that the depolymerization of actin and the possible modulation of integrin signaling, as well as changes in basal metabolism, may be driving the increase of protein secretion by CHO cells.
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Affiliation(s)
- Lucille Pourcel
- Department of Fundamental Microbiology, Institute of BiotechnologyUniversity of LausanneLausanneSwitzerland
| | - Flavien Buron
- Department of Fundamental Microbiology, Institute of BiotechnologyUniversity of LausanneLausanneSwitzerland
| | | | | | | | | | | | - Nicolas Mermod
- Department of Fundamental Microbiology, Institute of BiotechnologyUniversity of LausanneLausanneSwitzerland
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48
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Samy A, Kaneyoshi K, Omasa T. Improvement of Intracellular Traffic System by Overexpression of KDEL Receptor 1 in Antibody-Producing CHO Cells. Biotechnol J 2020; 15:e1900352. [PMID: 32073237 DOI: 10.1002/biot.201900352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/24/2020] [Indexed: 11/08/2022]
Abstract
The localization of soluble endoplasmic reticulum (ER) chaperones in the cell organelle is mediated by the C-terminal KDEL (lysine, aspartic acid, glutamic acid and leucine) motif. This motif is recognized by the KDEL receptor, a seven-transmembrane protein that cycles between the ER and cis-Golgi to capture missorted KDEL chaperones from post-ER compartments in a pH-dependent manner. The KDEL receptor's target chaperones have a substantial role in protein folding and assembly. In this study, the gene expression level of KDEL receptor 1 shows a moderate upregulation during either ER stress or growth of Chinese hamster ovary (CHO) cells in batch culture, while the ER chaperones show higher upregulation. This might indicate the possibility of saturation of the ER retention machinery or at least hindered retention during late stage batch culture in recombinant CHO cells. KDELR1 is overexpressed in a monoclonal antibody-producing CHO cell line to improve the intracellular chaperone retention rate in the ER. An increase in the specific productivity of IgG1 by 13.2% during the exponential phase, and 23.8% in the deceleration phase of batch culture is observed. This is the first study to focus on the ER retention system as a cell engineering target for enhancing recombinant protein production.
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Affiliation(s)
- Andrew Samy
- Graduate School of Engineering , Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kohei Kaneyoshi
- Graduate School of Engineering , Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Omasa
- Graduate School of Engineering , Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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49
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A platform for context-specific genetic engineering of recombinant protein production by CHO cells. J Biotechnol 2020; 312:11-22. [DOI: 10.1016/j.jbiotec.2020.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/12/2019] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
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50
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Amadi IM, Agrawal V, Christianson T, Bardliving C, Shamlou P, LeBowitz JH. Inhibition of endogenous miR-23a/miR-377 in CHO cells enhances difficult-to-express recombinant lysosomal sulfatase activity. Biotechnol Prog 2020; 36:e2974. [PMID: 31990124 DOI: 10.1002/btpr.2974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/11/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022]
Abstract
Difficult-to-express (DTE) recombinant proteins such as multi-specific proteins, DTE monoclonal antibodies, and lysosomal enzymes have seen difficulties in manufacturability using Chinese hamster ovary (CHO) cells or other mammalian cells as production platforms. CHO cells are preferably used for recombinant protein production for their ability to secrete human-like recombinant proteins with posttranslational modification, resistance to viral infection, and familiarity with drug regulators. However, despite huge progress made in engineering CHO cells for high volumetric productivity, DTE proteins like recombinant lysosomal sulfatase represent one of the poorly understood proteins. Furthermore, there is growing interest in the use of microRNA (miRNA) to engineer CHO cells expressing DTE proteins to improve cell performance of relevant bioprocess phenotypes. To our knowledge, no research has been done to improve CHO cell production of DTE recombinant lysosomal sulfatase using miRNA. We identified miR-23a and miR-377 as miRNAs predicted to target SUMF1, an activator of sulfatases, using in silico prediction tools. Transient inhibition of CHO endogenous miR-23a/miR-377 significantly enhanced recombinant sulfatase enzyme-specific activity by ~15-21% compared to scramble without affecting cell growth. Though inhibition of miR-23a/miR-377 had no significant effect on the mRNA and protein levels of SUMF1, overexpression of miR-23a/377 caused ~30% and ~27-29% significant reduction in endogenous SUMF1 protein and mRNA expression levels, respectively. In summary, our data demonstrate the importance of using miRNA to optimize the CHO cell line secreting DTE recombinant lysosomal sulfatase.
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Affiliation(s)
- Ifeanyi Michael Amadi
- BioMarin Pharmaceutical Inc., Novato, California.,Keck Graduate Institute, Claremont, California
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