1
|
Desmurget C, Perilleux A, Souquet J, Borth N, Douet J. Molecular biomarkers identification and applications in CHO bioprocessing. J Biotechnol 2024; 392:11-24. [PMID: 38852681 DOI: 10.1016/j.jbiotec.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Biomarkers are valuable tools in clinical research where they allow to predict susceptibility to diseases, or response to specific treatments. Likewise, biomarkers can be extremely useful in the biomanufacturing of therapeutic proteins. Indeed, constraints such as short timelines and the need to find hyper-productive cells could benefit from a data-driven approach during cell line and process development. Many companies still rely on large screening capacities to develop productive cell lines, but as they reach a limit of production, there is a need to go from empirical to rationale procedures. Similarly, during bioprocessing runs, substrate consumption and metabolism wastes are commonly monitored. None of them possess the ability to predict the culture behavior in the bioreactor. Big data driven approaches are being adapted to the study of industrial mammalian cell lines, enabled by the publication of Chinese hamster and CHO genome assemblies which allowed the use of next-generation sequencing with these cells, as well as continuous proteome and metabolome annotation. However, if these different -omics technologies contributed to the characterization of CHO cells, there is a significant effort remaining to apply this knowledge to biomanufacturing methods. The correlation of a complex phenotype such as high productivity or rapid growth to the presence or expression level of a specific biomarker could save time and effort in the screening of manufacturing cell lines or culture conditions. In this review we will first discuss the different biological molecules that can be identified and quantified in cells, their detection techniques, and associated challenges. We will then review how these markers are used during the different steps of cell line and bioprocess development, and the inherent limitations of this strategy.
Collapse
Affiliation(s)
- Caroline Desmurget
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Arnaud Perilleux
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Jonathan Souquet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Julien Douet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland.
| |
Collapse
|
2
|
Rives D, Peak C, Blenner MA. RNASeq highlights ATF6 pathway regulators for CHO cell engineering with different impacts of ATF6β and WFS1 knockdown on fed-batch production of IgG 1. Sci Rep 2024; 14:14141. [PMID: 38898154 PMCID: PMC11187196 DOI: 10.1038/s41598-024-64767-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
Secretion levels required of industrial Chinese hamster ovary (CHO) cell lines can challenge endoplasmic reticulum (ER) homeostasis, and ER stress caused by accumulation of misfolded proteins can be a bottleneck in biomanufacturing. The unfolded protein response (UPR) is initiated to restore homeostasis in response to ER stress, and optimization of the UPR can improve CHO cell production of therapeutic proteins. We compared the fed-batch growth, production characteristics, and transcriptomic response of an immunoglobulin G1 (IgG1) producer to its parental, non-producing host cell line. We conducted differential gene expression analysis using high throughput RNA sequencing (RNASeq) and quantitative polymerase chain reaction (qPCR) to study the ER stress response of each cell line during fed-batch culture. The UPR was activated in the IgG1 producer compared to the host cell line and our analysis of differential expression profiles indicated transient upregulation of ATF6α target mRNAs in the IgG1 producer, suggesting two upstream regulators of the ATF6 arm of the UPR, ATF6β and WFS1, are rational engineering targets. Although both ATF6β and WFS1 have been reported to negatively regulate ATF6α, this study shows knockdown of either target elicits different effects in an IgG1-producing CHO cell line. Stable knockdown of ATF6β decreased cell growth without decreasing titer; however, knockdown of WFS1 decreased titer without affecting growth. Relative expression measured by qPCR indicated no direct relationship between ATF6β and WFS1 expression, but upregulation of WFS1 in one pool was correlated with decreased growth and upregulation of ER chaperone mRNAs. While knockdown of WFS1 had negative impacts on UPR activation and product mRNA expression, knockdown of ATF6β improved the UPR specifically later in fed-batch leading to increased overall productivity.
Collapse
Affiliation(s)
- Dyllan Rives
- Department of Chemical & Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634-0909, USA
| | - Caroline Peak
- Department of Chemical & Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634-0909, USA
| | - Mark A Blenner
- Department of Chemical & Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634-0909, USA.
- Department of Chemical & Biomolecular Engineering, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| |
Collapse
|
3
|
Sulaj E, Schwaigerlehner L, Sandell FL, Dohm JC, Marzban G, Kunert R. Quantitative proteomics reveals cellular responses to individual mAb expression and tunicamycin in CHO cells. Appl Microbiol Biotechnol 2024; 108:381. [PMID: 38896138 PMCID: PMC11186912 DOI: 10.1007/s00253-024-13223-1] [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: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Chinese hamster ovary (CHO) cells are popular in the pharmaceutical industry for their ability to produce high concentrations of antibodies and their resemblance to human cells in terms of protein glycosylation patterns. Current data indicate the relevance of CHO cells in the biopharmaceutical industry, with a high number of product commendations and a significant market share for monoclonal antibodies. To enhance the production capabilities of CHO cells, a deep understanding of their cellular and molecular composition is crucial. Genome sequencing and proteomic analysis have provided valuable insights into the impact of the bioprocessing conditions, productivity, and product quality. In our investigation, we conducted a comparative analysis of proteomic profiles in high and low monoclonal antibody-producing cell lines and studied the impact of tunicamycin (TM)-induced endoplasmic reticulum (ER) stress. We examined the expression levels of different proteins including unfolded protein response (UPR) target genes by using label-free quantification techniques for protein abundance. Our results show the upregulation of proteins associated with protein folding mechanisms in low producer vs. high producer cell line suggesting a form of ER stress related to specific protein production. Further, Hspa9 and Dnaja3 are notable candidates activated by the mitochondria UPR and play important roles in protein folding processes in mitochondria. We identified significant upregulation of Nedd8 and Lgmn proteins in similar levels which may contribute to UPR stress. Interestingly, the downregulation of Hspa5/Bip and Pdia4 in response to tunicamycin treatment suggests a low-level UPR activation. KEY POINTS: • Proteome profiling of recombinant CHO cells under mild TM treatment. • Identified protein clusters are associated with the unfolded protein response (UPR). • The compared cell lines revealed noticeable disparities in protein expression levels.
Collapse
Affiliation(s)
- Eldi Sulaj
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Linda Schwaigerlehner
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Felix L Sandell
- Department of Biotechnology, Institute of Computational Biology (ICB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology (ICB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Gorji Marzban
- Department of Biotechnology, Institute of Bioprocess Science and Engineering (IBSE), BOKU University, Muthgasse 18, 1190, Vienna, Austria.
| | - Renate Kunert
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| |
Collapse
|
4
|
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell-Derived Cells. Mol Cell Proteomics 2022; 21:100278. [PMID: 35934186 PMCID: PMC9562429 DOI: 10.1016/j.mcpro.2022.100278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 01/18/2023] Open
Abstract
Most of the recombinant biotherapeutics employed today to combat severe illnesses, for example, various types of cancer or autoimmune diseases, are produced by Chinese hamster ovary (CHO) cells. To meet the growing demand of these pharmaceuticals, CHO cells are under constant development in order to enhance their stability and productivity. The last decades saw a shift from empirical cell line optimization toward rational cell engineering using a growing number of large omics datasets to alter cell physiology on various levels. Especially proteomics workflows reached new levels in proteome coverage and data quality because of advances in high-resolution mass spectrometry instrumentation. One type of workflow concentrates on spatial proteomics by usage of subcellular fractionation of organelles with subsequent shotgun mass spectrometry proteomics and machine learning algorithms to determine the subcellular localization of large portions of the cellular proteome at a certain time point. Here, we present the first subcellular spatial proteome of a CHO-K1 cell line producing high titers of recombinant antibody in comparison to the spatial proteome of an antibody-producing plasma cell-derived myeloma cell line. Both cell lines show colocalization of immunoglobulin G chains with chaperones and proteins associated in protein glycosylation within the endoplasmic reticulum compartment. However, we report differences in the localization of proteins associated to vesicle-mediated transport, transcription, and translation, which may affect antibody production in both cell lines. Furthermore, pairing subcellular localization data with protein expression data revealed elevated protein masses for organelles in the secretory pathway in plasma cell-derived MPC-11 (Merwin plasma cell tumor-11) cells. Our study highlights the potential of subcellular spatial proteomics combined with protein expression as potent workflow to identify characteristics of highly efficient recombinant protein-expressing cell lines. Data are available via ProteomeXchange with identifier PXD029115.
Collapse
|
5
|
Kumar S, Kumar A, Huhn S, DeVine L, Cole R, Du Z, Betenbaugh M. A Proteomics Approach to Decipher a Sticky CHO Situation. Biotechnol Bioeng 2022; 119:2064-2075. [PMID: 35470426 PMCID: PMC9546176 DOI: 10.1002/bit.28108] [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: 11/18/2021] [Revised: 04/03/2022] [Accepted: 04/14/2022] [Indexed: 11/08/2022]
Abstract
Chinese hamster ovary (CHO) cells serve as protein therapeutics workhorses, so it is useful to understand what intrinsic properties make certain host cell lines and clones preferable for scale up and production of target proteins. In this study, two CHO host cell lines (H1, H2), and their respective clones were evaluated using comparative TMT‐proteomics. The clones obtained from host H1 showed increased productivity (6.8 times higher) in comparison to clones from host H2. Based on fold‐change analyses, we observed differential regulation in pathways including cell adhesion, aggregation, and cellular metabolism among others. In particular, the cellular adhesion pathway was downregulated in H1, in which podoplanin, an antiadhesion molecule, was upregulated the most in host H1 and associated clones. Phenotypically, these cells were less likely to aggregate and adhere to surfaces. In addition, enzymes involved in cellular metabolism such as isocitrate dehydrogenase (IDH) and mitochondrial‐d‐lactate dehydrogenase (
d‐LDHm) were also found to be differentially regulated. IDH plays a key role in TCA cycle and isocitrate‐alpha‐ketoglutarate cycle while
d‐LDHm aids in the elimination of toxic metabolite methylglyoxal, involved in protein degradation. These findings will enhance our efforts towards understanding why certain CHO cell lines exhibit enhanced performance and perhaps provide future cell engineering targets.
Collapse
Affiliation(s)
- Swetha Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Amit Kumar
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Steven Huhn
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Lauren DeVine
- Mass Spectrometry and Proteomics Facility, Johns Hopkins Medical Institute, Baltimore, MD, USA
| | - Robert Cole
- Mass Spectrometry and Proteomics Facility, Johns Hopkins Medical Institute, Baltimore, MD, USA
| | - Zhimei Du
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Insights into the Impact of Rosmarinic Acid on CHO Cell Culture Improvement through Transcriptomics Analysis. Processes (Basel) 2022. [DOI: 10.3390/pr10030533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The use of antioxidants in Chinese hamster ovary (CHO) cell cultures to improve monoclonal antibody production has been a topic of great interest. Nevertheless, the antioxidants do not have consistent benefits of production improvement, which might be cell line specific and/or process specific. In this work, we investigated how treatment with the antioxidant rosmarinic acid (RA) improved cell growth and titer in CHO cell cultures using transcriptomics. In particular, transcriptomics analysis indicated that RA treatment modified gene expression and strongly affected the MAPK and PI3K/Akt signaling pathways, which regulate cell survival and cell death. Moreover, it was observed that these signaling pathways, which had been identified to be up-regulated on day 2 and day 6 by RA, were also up-regulated over time (from initial growth phase day 2 to slow growth or protein production phase day 6) in both conditions. In summary, this transcriptomics analysis provides insights into the role of the antioxidant RA in industrial cell culture processes. The current study also represents an example in the industry of how omics can be applied to gain an in-depth understanding of CHO cell biology and to identify critical pathways that can contribute to cell culture process improvement and cell line engineering.
Collapse
|
8
|
Bryan L, Henry M, Kelly RM, Frye CC, Osborne MD, Clynes M, Meleady P. Mapping the molecular basis for growth related phenotypes in industrial producer CHO cell lines using differential proteomic analysis. BMC Biotechnol 2021; 21:43. [PMID: 34301236 PMCID: PMC8305936 DOI: 10.1186/s12896-021-00704-8] [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: 03/24/2021] [Accepted: 06/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background The ability to achieve high peak viable cell density earlier in CHO cell culture and maintain an extended cell viability throughout the production process is highly desirable to increase recombinant protein yields, reduce host cell impurities for downstream processing and reduce the cost of goods. In this study we implemented label-free LC-MS/MS proteomic profiling of IgG4 producing CHO cell lines throughout the duration of the cell culture to identify differentially expressed (DE) proteins and intracellular pathways associated with the high peak viable cell density (VCD) and extended culture VCD phenotypes. Results We identified key pathways in DNA replication, mitotic cell cycle and evasion of p53 mediated apoptosis in high peak VCD clonally derived cell lines (CDCLs). ER to Golgi vesicle mediated transport was found to be highly expressed in extended culture VCD CDCLs while networks involving endocytosis and oxidative stress response were significantly downregulated. Conclusion This investigation highlights key pathways for targeted engineering to generate desirable CHO cell phenotypes for biotherapeutic production. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00704-8.
Collapse
Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ronan M Kelly
- Eli Lilly and Company, LTC-North, 1200 Kentucky Avenue, Indianapolis, IN, 46225, USA
| | - Christopher C Frye
- Eli Lilly and Company, LTC-North, 1200 Kentucky Avenue, Indianapolis, IN, 46225, USA
| | | | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Klingler F, Mathias S, Schneider H, Buck T, Raab N, Zeh N, Shieh YW, Pfannstiel J, Otte K. Unveiling the CHO surfaceome: Identification of cell surface proteins reveals cell aggregation-relevant mechanisms. Biotechnol Bioeng 2021; 118:3015-3028. [PMID: 33951178 DOI: 10.1002/bit.27811] [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: 02/26/2021] [Revised: 04/07/2021] [Accepted: 04/25/2021] [Indexed: 01/12/2023]
Abstract
Chinese hamster ovary (CHO) suspension cells are the main production hosts for biopharmaceuticals. For the improvement of production processes, it is essential to understand the interaction between CHO cells and their microenvironment. While the cellular membrane is the crucial surface barrier between the inner and outer cell compartments, the subgroup of cell surface proteins (surfaceome) is of particular interest due to its potential to react to external factors and initiate cell communication and interaction pathways. Therefore, the CHO surfaceome was explored for the first time by enriching exposed N-glycosylated membrane proteins before tandem mass spectrometry (MS/MS) analyses, identifying a total of 449 surface proteins, including 34 proteins specific for production cells. Functional annotation and classification located most proteins to the cell surface belonging mainly to the protein classes of receptors, enzymes, and transporters. In addition, adhesion molecules as cadherins, integrins, Ig superfamily and extracellular matrix (ECM) proteins as collagens, laminins, thrombospondin, fibronectin, and tenascin were significantly enriched, which are involved in mechanisms for the formation of cell junctions, cell-cell and cell-ECM adhesion as focal adhesions. As cell adhesion and aggregation counteracts scalable production of biopharmaceuticals, experimental validation confirmed differential expression of integrin β1 (ITGB1) and β3, CD44, laminin, and fibronectin on the surface of aggregation-prone CHO production cells. The subsequent modulation of the central interaction protein ITGB1 by small interfering RNA knockdown substantially counteracted cell aggregation pointing toward novel engineering routes for aggregation reduction in biopharmaceutical production cells and exemplifying the potential of the surfaceome for specified engineering strategies.
Collapse
Affiliation(s)
- Florian Klingler
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Sven Mathias
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany.,Early Stage Bioprocess Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Helga Schneider
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Theresa Buck
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nadja Raab
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nikolas Zeh
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Yu-Wei Shieh
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Jens Pfannstiel
- Core Facility Mass Spectrometry, University of Hohenheim, Stuttgart, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| |
Collapse
|
11
|
Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021; 49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.
Collapse
Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| |
Collapse
|
12
|
Bhaskara V, Leal MT, Seigner J, Friedrich T, Kreidl E, Gadermaier E, Tesarz M, Rogalli A, Stangl L, Wallwitz J, Hammel K, Rothbauer M, Moll H, Ertl P, Hahn R, Himmler G, Bauer A, Casanova E. Efficient production of recombinant secretory IgA against Clostridium difficile toxins in CHO-K1 cells. J Biotechnol 2021; 331:1-13. [PMID: 33689865 DOI: 10.1016/j.jbiotec.2021.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/25/2021] [Accepted: 02/22/2021] [Indexed: 12/29/2022]
Abstract
Despite the essential role secretory IgAs play in the defense against pathogenic invasion and the proposed value of recombinant secretory IgAs as novel therapeutics, currently there are no IgA-based therapies in clinics. Secretory IgAs are complex molecules and the major bottleneck limiting their therapeutic potential is a reliable recombinant production system. In this report, we addressed this issue and established a fast and robust production method for secretory IgAs in CHO-K1 cells using BAC-based expression vectors. As a proof of principle, we produced IgAs against Clostridium difficile toxins TcdA and TcdB. Recombinant secretory IgAs produced using our expression system showed comparable titers to IgGs, widely used as therapeutic biologicals. Importantly, secretory IgAs produced using our method were functional and could efficiently neutralize Clostridium difficile toxins TcdA and TcdB. These results show that recombinant secretory IgAs can be efficiently produced, thus opening the possibility to use them as therapeutic agents in clinics.
Collapse
Affiliation(s)
- Venugopal Bhaskara
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria.
| | - Maria Trinidad Leal
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | - Jacqueline Seigner
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | - Theresa Friedrich
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | | | | | | | | | - Laura Stangl
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | | | - Katharina Hammel
- Department for Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry and Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, 1060 Vienna, Austria
| | - Herwig Moll
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry and Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, 1060 Vienna, Austria
| | - Rainer Hahn
- Department for Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | | | - Anton Bauer
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria; The Antibody Lab GmbH, 1210 Vienna, Austria.
| | - Emilio Casanova
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria.
| |
Collapse
|
13
|
Lhota G, Sissolak B, Striedner G, Sommeregger W, Vorauer-Uhl K. Quantification of glycated IgG in CHO supernatants: A practical approach. Biotechnol Prog 2021; 37:e3124. [PMID: 33428326 PMCID: PMC8365726 DOI: 10.1002/btpr.3124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/09/2020] [Accepted: 12/20/2020] [Indexed: 01/26/2023]
Abstract
Post-translational, nonenzymatic glycation of monoclonal antibodies (mAbs) in the presence of reducing sugars (in bioprocesses) is a widely known phenomenon, which affects protein heterogeneity and potentially has an impact on quality, safety, and efficacy of the end product. Quantification of individual glycation levels is compulsory for each mAb therapeutically applied in humans. We therefore propose an analytical method for monitoring glycation levels of mAb products during the bioprocess. This is a useful tool for process-design considerations, especially concerning glucose-feed strategies and temperature as major driving factors of protein glycation. In this study, boronate affinity chromatography (BAC) was optimized for determination of the glycation level of mAbs in supernatants. In fact, the complex matrix found in supernatants is an underlying obstacle to use BAC, but with a simple clean-up step, we found that the elution profile could be significantly improved so that qualitative and quantitative determination could be reached. Complementary analytical methods confirmed the performance quality, including the correctness and specificity of the results. For quantitative determination of mAb glycation in supernatants, we established a calibration procedure for the retained mAb peak, identified as glycated antibody monomers. For this approach, an available fully characterized mAb standard, Humira®, was successfully applied, and continuous monitoring of mAbs across three repetitive fed-batch processes was finally performed. With this practical, novel approach, an insight was obtained into glycation levels during bioprocessing, in conjunction with glucose levels and product titer over time, facilitating efficient process development and batch-consistency monitoring.
Collapse
Affiliation(s)
- Gabriele Lhota
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bernhard Sissolak
- Research and Development, Bilfinger Industrietechnik Salzburg GmbH, Salzburg, Austria
| | - Gerald Striedner
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Wolfgang Sommeregger
- Research and Development, Bilfinger Industrietechnik Salzburg GmbH, Salzburg, Austria
| | - Karola Vorauer-Uhl
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
14
|
Pérez-Rodriguez S, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis of Chinese hamster ovary cell homogenates. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
15
|
Huang Z, Xu J, Yongky A, Morris CS, Polanco AL, Reily M, Borys MC, Li ZJ, Yoon S. CHO cell productivity improvement by genome-scale modeling and pathway analysis: Application to feed supplements. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
16
|
Tang D, Sandoval W, Lam C, Haley B, Liu P, Xue D, Roy D, Patapoff T, Louie S, Snedecor B, Misaghi S. UBR E3 ligases and the PDIA3 protease control degradation of unfolded antibody heavy chain by ERAD. J Cell Biol 2020; 219:151862. [PMID: 32558906 PMCID: PMC7337499 DOI: 10.1083/jcb.201908087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 12/01/2022] Open
Abstract
Accumulation of unfolded antibody chains in the ER triggers ER stress that may lead to reduced productivity in therapeutic antibody manufacturing processes. We identified UBR4 and UBR5 as ubiquitin E3 ligases involved in HC ER-associated degradation. Knockdown of UBR4 and UBR5 resulted in intracellular accumulation, enhanced secretion, and reduced ubiquitination of HC. In concert with these E3 ligases, PDIA3 was shown to cleave ubiquitinated HC molecules to accelerate HC dislocation. Interestingly, UBR5, and to a lesser degree UBR4, were down-regulated as cellular demand for antibody expression increased in CHO cells during the production phase, or in plasma B cells. Reducing UBR4/UBR5 expression before the production phase increased antibody productivity in CHO cells, possibly by redirecting antibody molecules from degradation to secretion. Altogether we have characterized a novel proteolysis/proteasome-dependent pathway involved in degradation of unfolded antibody HC. Proteins characterized in this pathway may be novel targets for CHO cell engineering.
Collapse
Affiliation(s)
- Danming Tang
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Cynthia Lam
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA
| | - Peter Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Di Xue
- Department of Research Biology, Genentech Inc., South San Francisco, CA
| | - Deepankar Roy
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Tom Patapoff
- Department of Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA
| | - Salina Louie
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Brad Snedecor
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| |
Collapse
|
17
|
Identifying metabolic features and engineering targets for productivity improvement in CHO cells by integrated transcriptomics and genome-scale metabolic model. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
18
|
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]
|
19
|
Schelletter L, Albaum S, Walter S, Noll T, Hoffrogge R. Clonal variations in CHO IGF signaling investigated by SILAC-based phosphoproteomics and LFQ-MS. Appl Microbiol Biotechnol 2019; 103:8127-8143. [DOI: 10.1007/s00253-019-10020-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022]
|
20
|
Poulain A, Mullick A, Massie B, Durocher Y. Reducing recombinant protein expression during CHO pool selection enhances frequency of high-producing cells. J Biotechnol 2019; 296:32-41. [DOI: 10.1016/j.jbiotec.2019.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/19/2022]
|
21
|
Grav LM, Sergeeva D, Lee JS, Marin de Mas I, Lewis NE, Andersen MR, Nielsen LK, Lee GM, Kildegaard HF. Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation. ACS Synth Biol 2018; 7:2148-2159. [PMID: 30060646 DOI: 10.1021/acssynbio.8b00140] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mammalian cells are widely used to express genes for basic biology studies and biopharmaceuticals. Current methods for generation of engineered cell lines introduce high genomic and phenotypic diversity, which hamper studies of gene functions and discovery of novel cellular mechanisms. Here, we minimized clonal variation by integrating a landing pad for recombinase-mediated cassette exchange site-specifically into the genome of CHO cells using CRISPR and generated subclones expressing four different recombinant proteins. The subclones showed low clonal variation with high consistency in growth, transgene transcript levels and global transcriptional response to recombinant protein expression, enabling improved studies of the impact of transgenes on the host transcriptome. Little variation over time in subclone phenotypes and transcriptomes was observed when controlling environmental culture conditions. The platform enables robust comparative studies of genome engineered CHO cell lines and can be applied to other mammalian cells for diverse biological, biomedical and biotechnological applications.
Collapse
Affiliation(s)
- Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Daria Sergeeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jae Seong Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Igor Marin de Mas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustatainability, University of California, San Diego, La Jolla, California 92093, United States
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
22
|
Zamani L, Lundqvist M, Zhang Y, Aberg M, Edfors F, Bidkhori G, Lindahl A, Mie A, Mardinoglu A, Field R, Turner R, Rockberg J, Chotteau V. High Cell Density Perfusion Culture has a Maintained Exoproteome and Metabolome. Biotechnol J 2018; 13:e1800036. [DOI: 10.1002/biot.201800036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/03/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Leila Zamani
- Department Industrial Biotechnology; School of Engineering Sciences in Chemistry, Biotechnology, and Health; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Magnus Lundqvist
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; AdBIOPRO, Centre for Advanced Bioproduction by Continuous Processing; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Ye Zhang
- Department Industrial Biotechnology; School of Engineering Sciences in Chemistry, Biotechnology, and Health; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Magnus Aberg
- Department of Analytical Chemistry; Stockholm University; 106 91 Stockholm Sweden
| | - Fredrik Edfors
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Science for Life Laboratory; KTH-Royal Institute of Technology; 171 65 Stockholm Sweden
| | - Gholamreza Bidkhori
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Science for Life Laboratory; KTH-Royal Institute of Technology; 171 65 Stockholm Sweden
| | - Anna Lindahl
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; 171 65 Solna Sweden
| | - Axel Mie
- Department of Clinical Science and Education; Karolinska Institute; 118 83 Solna Sweden
| | - Adil Mardinoglu
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Science for Life Laboratory; KTH-Royal Institute of Technology; 171 65 Stockholm Sweden
| | - Raymond Field
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; 171 65 Solna Sweden
| | - Richard Turner
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; 171 65 Solna Sweden
| | - Johan Rockberg
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; AdBIOPRO, Centre for Advanced Bioproduction by Continuous Processing; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Veronique Chotteau
- Department Industrial Biotechnology; School of Engineering Sciences in Chemistry, Biotechnology, and Health; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; AdBIOPRO, Centre for Advanced Bioproduction by Continuous Processing; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- Biopharmaceutical Development; MedImmune; CB21 6GH Cambridge United Kingdom
| |
Collapse
|
23
|
Reinhart D, Damjanovic L, Kaisermayer C, Sommeregger W, Gili A, Gasselhuber B, Castan A, Mayrhofer P, Grünwald-Gruber C, Kunert R. Bioprocessing of Recombinant CHO-K1, CHO-DG44, and CHO-S: CHO Expression Hosts Favor Either mAb Production or Biomass Synthesis. Biotechnol J 2018; 14:e1700686. [PMID: 29701329 DOI: 10.1002/biot.201700686] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/26/2018] [Indexed: 01/02/2023]
Abstract
Chinese hamster ovary (CHO) cells comprise a variety of lineages including CHO-DXB11, CHO-K1, CHO-DG44, and CHO-S. Despite all CHO cell lines sharing a common ancestor, extensive mutagenesis, and clonal selection has resulted in substantial genetic heterogeneity among them. Data from sequencing show that different genes are missing in individual CHO cell lines and each cell line harbors a unique set of mutations with relevance to the bioprocess. However, not much literature is available about the influence of genetic differences of CHO on the performance of bioprocess operations. In this study, the host cell-specific differences among three widely used CHO cell lines (CHO-K1, CHO-S, and CHO-DG44) and recombinantly expressed the same monoclonal antibody (mAb) in an isogenic format by using bacterial artificial chromosomes (BACs) as transfer vector in all cell lines is examined. Cell-specific growth and product formation are studied in batch, fed-batch, and semi-continuous perfusion cultures. Further, two different cell culture media are used to investigate their effects. The authors find CHO cell line-specific preferences for mAb production or biomass synthesis that are determined by the host cell line. Additionally, quality attributes of the expressed mAb are influenced by the host cell line and media.
Collapse
Affiliation(s)
- David Reinhart
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Lukas Damjanovic
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| | | | - Wolfgang Sommeregger
- Bilfinger Industrietechnik Salzburg GmbH, Urstein Nord 31, 5412 Puch bei Hallein, Austria
| | - Andreas Gili
- Polymun Scientific Immunbiologische Forschung GmbH, Donaustraße 99, 3400 Klosterneuburg, Austria
| | - Bernhard Gasselhuber
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Andreas Castan
- GE Healthcare Life Sciences AB, Björkgatan 30, 75184 Uppsala, Sweden
| | - Patrick Mayrhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Renate Kunert
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| |
Collapse
|
24
|
Clonal variation in productivity and proteolytic clipping of an Fc-fusion protein in CHO cells: Proteomic analysis suggests a role for defective protein folding and the UPR. J Biotechnol 2018; 281:21-30. [PMID: 29860056 DOI: 10.1016/j.jbiotec.2018.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 05/27/2018] [Accepted: 05/30/2018] [Indexed: 11/21/2022]
Abstract
Product degradation, such as clipping, is a common quality issue in the production of Fc-fusion proteins from Chinese hamster ovary (CHO) cells. Degradation of proteins is mainly due to the action of either intracellular or extracellular host cell proteases. This study was carried out to understand more fundamentally the intracellular events that may play a role in determining why cell lines from the same cell line development project can vary with regards to the extent of Fc-fusion protein clipping. The cell lines that displayed the highest levels of clipping also produced less product than the cell lines with a lower level of clipping. In this study we applied differential quantitative label-free LC-MS/MS proteomic analysis to group clonally-derived cell lines (CDCLs) based on the level of clipping of the Fc-fusion protein. The analysis was carried out over two times points in culture and clones were designated as either having 'high' or 'low' clipping phenotypes. We have identified 200 differentially expressed proteins using quantitative label-free LC-MS/MS analysis between the two experimental groups. Functional assessment of the resultant proteomic data using Gene Ontology analysis showed a significant enrichment of biological processes and molecular functions related to protein folding, response to unfolded protein and protein translation. The levels of several proteases were also increased. This study identified protein targets that could be modified using cell line engineering approaches to improve the quality of recombinant Fc-fusion protein production in the biopharmaceutical industry.
Collapse
|
25
|
Sha S, Bhatia H, Yoon S. An RNA-seq based transcriptomic investigation into the productivity and growth variants with Chinese hamster ovary cells. J Biotechnol 2018; 271:37-46. [DOI: 10.1016/j.jbiotec.2018.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 01/26/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023]
|
26
|
Stolfa G, Smonskey MT, Boniface R, Hachmann AB, Gulde P, Joshi AD, Pierce AP, Jacobia SJ, Campbell A. CHO-Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction. Biotechnol J 2017; 13:e1700227. [PMID: 29072373 DOI: 10.1002/biot.201700227] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 01/07/2023]
Abstract
CHO cells are the most prevalent platform for modern bio-therapeutic production. Currently, there are several CHO cell lines used in bioproduction with distinct characteristics and unique genotypes and phenotypes. These differences limit advances in productivity and quality that can be achieved by the most common approaches to bioprocess optimization and cell line engineering. Incorporating omics-based approaches into current bioproduction processes will complement traditional methodologies to maximize gains from CHO engineering and bioprocess improvements. In order to highlight the utility of omics technologies in CHO bioproduction, the authors discuss current applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, lipidomics, fluxomics, glycomics, and multi-omics approaches and the potential they hold for the future of bioproduction. Multiple omics approaches are currently being used to improve CHO bioprocesses; however, the application of these technologies is still limited. As more CHO-omic datasets become available and integrated into systems models, the authors expect significant gains in product yield and quality. While individual omics technologies provide incremental improvements in bioproduction, the authors will likely see the most significant gains by applying multi-omics and systems biology approaches to individual CHO cell lines.
Collapse
Affiliation(s)
- Gino Stolfa
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Ryan Boniface
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Paul Gulde
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Atul D Joshi
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Anson P Pierce
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Scott J Jacobia
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Andrew Campbell
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| |
Collapse
|
27
|
Henry M, Power M, Kaushik P, Coleman O, Clynes M, Meleady P. Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift. J Proteome Res 2017; 16:2339-2358. [DOI: 10.1021/acs.jproteome.6b00868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Henry
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Power
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Prashant Kaushik
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Orla Coleman
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| |
Collapse
|
28
|
Luu LDW, Octavia S, Zhong L, Raftery M, Sintchenko V, Lan R. Characterisation of the Bordetella pertussis secretome under different media. J Proteomics 2017; 158:43-51. [PMID: 28242451 DOI: 10.1016/j.jprot.2017.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 01/07/2023]
Abstract
Our understanding of the Bordetella pertussis secretome remains limited including the role of different growth conditions in the secretome. In this study the secretome of L1423, a clinical isolate from the 2008-2012 Australian epidemic, cultured on Stainer-Scholte (SS) and Thalen-IJssel (THIJS) media for 12h was characterised using liquid chromatography-mass spectrometry (LC-MS/MS). In the supernatant, LC-MS/MS identified 260 proteins with 143 bioinformatically predicted to be secreted. Eighty percent of proteins were identified in both media. Proteins secreted were functionally associated with cell surface (41%), pathogenicity (16%) and transport (17%). The most abundant proteins identified were pathogenic proteins including toxins (PtxA and CyaA), adhesins (TcfA) and type III secretion (T3SS) proteins. There were 46 proteins found uniquely in THIJS including 8 virulence associated proteins. These included T3SS proteins, adhesins (FhaL and FhaS) and a putative toxin (BP1251). Nine proteins were found uniquely in SS and these were metabolic and transport-related proteins. None of the unique proteins detected in SS were known to be virulence associated. This study found that THIJS promotes secretion of virulence factors based on the number of unique virulence proteins found and may be a growth media of choice for the study of B. pertussis virulence and vaccine development. BIOLOGICAL SIGNIFICANCE Over the past two decades, the number of B. pertussis notifications has risen despite vaccination. There is a greater need to understand the biology behind B. pertussis infections. The secretome of B. pertussis in two different media was characterised using LC-MS/MS. The results showed that THIJS promotes secretion of importance virulence factors which may be important for the development of vaccines.
Collapse
Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ling Zhong
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark Raftery
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| |
Collapse
|
29
|
Hansen HG, Pristovšek N, Kildegaard HF, Lee GM. Improving the secretory capacity of Chinese hamster ovary cells by ectopic expression of effector genes: Lessons learned and future directions. Biotechnol Adv 2017; 35:64-76. [DOI: 10.1016/j.biotechadv.2016.11.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/12/2016] [Accepted: 11/28/2016] [Indexed: 12/12/2022]
|