1
|
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
|
2
|
Life at the periphery: what makes CHO cells survival talents. Appl Microbiol Biotechnol 2022; 106:6157-6167. [PMID: 36038753 PMCID: PMC9468092 DOI: 10.1007/s00253-022-12123-6] [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: 04/14/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022]
Abstract
Abstract
The production of biopharmaceuticals relies on robust cell systems that can produce recombinant proteins at high levels and grow and survive in the stressful bioprocess environment. Chinese hamster ovary cells (CHO) as the main production hosts offer a variety of advantages including robust growth and survival in a bioprocess environment. Cell surface proteins are of special interest for the understanding of how CHO cells react to their environment while maintaining growth and survival phenotypes, since they enable cellular reactions to external stimuli and potentially initiate signaling pathways. To provide deeper insight into functions of this special cell surface sub-proteome, pathway enrichment analysis of the determined CHO surfaceome was conducted. Enrichment of growth/ survival-pathways such as the phosphoinositide-3-kinase (PI3K)–protein kinase B (AKT), mitogen-activated protein kinase (MAPK), Janus kinase/signal transducers and activators of transcription (JAK-STAT), and RAP1 pathways were observed, offering novel insights into how cell surface receptors and ligand-mediated signaling enable the cells to grow and survive in a bioprocess environment. When supplementing surfaceome data with RNA expression data, several growth/survival receptors were shown to be co-expressed with their respective ligands and thus suggesting self-induction mechanisms, while other receptors or ligands were not detectable. As data about the presence of surface receptors and their associated expressed ligands may serve as base for future studies, further pathway characterization will enable the implementation of optimization strategies to further enhance cellular growth and survival behavior. Key points • PI3K/AKT, MAPK, JAK-STAT, and RAP1 pathway receptors are enriched on the CHO cell surface and downstream pathways present on mRNA level. • Detected pathways indicate strong CHO survival and growth phenotypes. • Potential self-induction of surface receptors and respective ligands. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12123-6.
Collapse
|
3
|
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]
|
4
|
Comparative systeomics to elucidate physiological differences between CHO and SP2/0 cell lines. Sci Rep 2022; 12:3280. [PMID: 35228567 PMCID: PMC8885639 DOI: 10.1038/s41598-022-06886-1] [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: 08/01/2021] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
Omics-based tools were coupled with bioinformatics for a systeomics analysis of two biopharma cell types: Chinese hamster ovary (M-CHO and CHO-K1) and SP2/0. Exponential and stationary phase samples revealed more than 10,000 transcripts and 6000 proteins across these two manufacturing cell lines. A statistical comparison of transcriptomics and proteomics data identified downregulated genes involved in protein folding, protein synthesis and protein metabolism, including PPIA-cyclophilin A, HSPD1, and EIF3K, in M-CHO compared to SP2/0 while cell cycle and actin cytoskeleton genes were reduced in SP2/0. KEGG pathway comparisons revealed glycerolipids, glycosphingolipids, ABC transporters, calcium signaling, cell adhesion, and secretion pathways depleted in M-CHO while retinol metabolism was upregulated. KEGG and IPA also indicated apoptosis, RNA degradation, and proteosomes enriched in CHO stationary phase. Alternatively, gene ontology analysis revealed an underrepresentation in ion and potassium channel activities, membrane proteins, and secretory granules including Stxbpt2, Syt1, Syt9, and Cma1 proteins in M-CHO. Additional enrichment strategies involving ultracentrifugation, biotinylation, and hydrazide chemistry identified over 4000 potential CHO membrane and secretory proteins, yet many secretory and membrane proteins were still depleted. This systeomics pipeline has revealed bottlenecks and potential opportunities for cell line engineering in CHO and SP2/0 to improve their production capabilities.
Collapse
|
5
|
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
|
6
|
Strasser L, Farrell A, Ho JTC, Scheffler K, Cook K, Pankert P, Mowlds P, Viner R, Karger BL, Bones J. Proteomic Profiling of IgG1 Producing CHO Cells Using LC/LC-SPS-MS 3: The Effects of Bioprocessing Conditions on Productivity and Product Quality. Front Bioeng Biotechnol 2021; 9:569045. [PMID: 33898396 PMCID: PMC8062983 DOI: 10.3389/fbioe.2021.569045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
The biopharmaceutical market is dominated by monoclonal antibodies, the majority of which are produced in Chinese hamster ovary (CHO) cell lines. Intense cell engineering, in combination with optimization of various process parameters results in increasing product titers. To enable further improvements in manufacturing processes, detailed information about how certain parameters affect cellular mechanisms in the production cells, and thereby also the expressed drug substance, is required. Therefore, in this study the effects of commonly applied changes in bioprocessing parameters on an anti-IL8 IgG1 producing CHO DP-12 cell line were investigated on the level of host cell proteome expression combined with product quality assessment of the expressed IgG1 monoclonal antibody. Applying shifts in temperature, pH and dissolved oxygen concentration, respectively, resulted in altered productivity and product quality. Furthermore, analysis of the cells using two-dimensional liquid chromatography-mass spectrometry employing tandem mass tag based isotopic quantitation and synchronous precursor selection-MS3 detection revealed substantial changes in the protein expression profiles of CHO cells. Pathway analysis indicated that applied bioprocessing conditions resulted in differential activation of oxidative phosphorylation. Additionally, activation of ERK5 and TNFR1 signaling suggested an affected cell cycle. Moreover, in-depth product characterization by means of charge variant analysis, peptide mapping, as well as structural and functional analysis, revealed posttranslational and structural changes in the expressed drug substance. Taken together, the present study allows the conclusion that, in anti-IL8 IgG1 producing CHO DP-12 cells, an improved energy metabolism achieved by lowering the cell culture pH is favorable when aiming towards high antibody production rates while maintaining product quality.
Collapse
Affiliation(s)
- Lisa Strasser
- Characterization and Comparability Laboratory, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Amy Farrell
- Characterization and Comparability Laboratory, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Jenny T C Ho
- Thermo Fisher Scientific, Hemel Hempstead, United Kingdom
| | | | - Ken Cook
- Thermo Fisher Scientific, Hemel Hempstead, United Kingdom
| | | | - Peter Mowlds
- Thermo Fisher Scientific, Hemel Hempstead, United Kingdom
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, United States
| | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, United States
| | - Jonathan Bones
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| |
Collapse
|
7
|
Heffner K, Hizal DB, Majewska NI, Kumar S, Dhara VG, Zhu J, Bowen M, Hatton D, Yerganian G, Yerganian A, O'Meally R, Cole R, Betenbaugh M. Expanded Chinese hamster organ and cell line proteomics profiling reveals tissue-specific functionalities. Sci Rep 2020; 10:15841. [PMID: 32985598 PMCID: PMC7522264 DOI: 10.1038/s41598-020-72959-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are the predominant production vehicle for biotherapeutics. Quantitative proteomics data were obtained from two CHO cell lines (CHO-S and CHO DG44) and compared with seven Chinese hamster (Cricetulus griseus) tissues (brain, heart, kidney, liver, lung, ovary and spleen) by tandem mass tag (TMT) labeling followed by mass spectrometry, providing a comprehensive hamster tissue and cell line proteomics atlas. Of the 8470 unique proteins identified, high similarity was observed between CHO-S and CHO DG44 and included increases in proteins involved in DNA replication, cell cycle, RNA processing, and chromosome processing. Alternatively, gene ontology and pathway analysis in tissues indicated increased protein intensities related to important tissue functionalities. Proteins enriched in the brain included those involved in acidic amino acid metabolism, Golgi apparatus, and ion and phospholipid transport. The lung showed enrichment in proteins involved in BCAA catabolism, ROS metabolism, vesicle trafficking, and lipid synthesis while the ovary exhibited enrichments in extracellular matrix and adhesion proteins. The heart proteome included vasoconstriction, complement activation, and lipoprotein metabolism enrichments. These detailed comparisons of CHO cell lines and hamster tissues will enhance understanding of the relationship between proteins and tissue function and pinpoint potential pathways of biotechnological relevance for future cell engineering.
Collapse
Affiliation(s)
- Kelley Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.,AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Natalia I Majewska
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.,AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Swetha Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Venkata Gayatri Dhara
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jie Zhu
- AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Michael Bowen
- Allogene Therapeutics, Product and Process Development, South San Francisco, CA, USA
| | - Diane Hatton
- AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | | | | | - Robert O'Meally
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert Cole
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
8
|
Sim KH, Liu LCY, Tan HT, Tan K, Ng D, Zhang W, Yang Y, Tate S, Bi X. A comprehensive CHO SWATH-MS spectral library for robust quantitative profiling of 10,000 proteins. Sci Data 2020; 7:263. [PMID: 32782267 PMCID: PMC7419519 DOI: 10.1038/s41597-020-00594-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/06/2020] [Indexed: 01/08/2023] Open
Abstract
Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) is a data-independent acquisition (DIA) strategy that requires a specific spectral library to generate unbiased and consistent quantitative data matrices of all peptides. SWATH-MS is a promising approach for in-depth proteomic profiling of Chinese hamster Ovary (CHO) cell lines, improving mechanistic understanding of process optimization, and real-time monitoring of process parameters in biologics R&D and manufacturing. However, no spectral library for CHO cells is publicly available. Here we present a comprehensive CHO global spectral library to measure the abundance of more than 10,000 proteins consisting of 199,102 identified peptides from a CHO-K1 cell proteome. The robustness, accuracy and consistency of the spectral library were validated for high confidence in protein identification and reproducible quantification in different CHO-derived cell lines, instrumental setups and downstream processing samples. The availability of a comprehensive SWATH CHO global spectral library will facilitate detailed characterization of upstream and downstream processes, as well as quality by design (QbD) in biomanufacturing. The data have been deposited to ProteomeXchange (PXD016047).
Collapse
Affiliation(s)
- Kae Hwan Sim
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Lillian Chia-Yi Liu
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Hwee Tong Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Kelly Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Daniel Ng
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Wei Zhang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | | | - Xuezhi Bi
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore.
- Duke-NUS Medical School, Singapore, 169857, Singapore.
| |
Collapse
|
9
|
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]
|
10
|
|
11
|
Zhang Z, Burke M, Mirokhin YA, Tchekhovskoi DV, Markey SP, Yu W, Chaerkady R, Hess S, Stein SE. Reverse and Random Decoy Methods for False Discovery Rate Estimation in High Mass Accuracy Peptide Spectral Library Searches. J Proteome Res 2018; 17:846-857. [DOI: 10.1021/acs.jproteome.7b00614] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zheng Zhang
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Meghan Burke
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Yuri A. Mirokhin
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Dmitrii V. Tchekhovskoi
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Sanford P. Markey
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Wen Yu
- Research
Bioinformatics, MedImmune LLC, One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Raghothama Chaerkady
- Antibody
Discovery and Protein Engineering, Protein Sciences, MedImmune LLC, One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Sonja Hess
- Antibody
Discovery and Protein Engineering, Protein Sciences, MedImmune LLC, One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Stephen E. Stein
- Mass
Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| |
Collapse
|