1
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Nguyen M, Zimmer A. A reflection on the improvement of Chinese Hamster ovary cell-based bioprocesses through advances in proteomic techniques. Biotechnol Adv 2023; 65:108141. [PMID: 37001570 DOI: 10.1016/j.biotechadv.2023.108141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Chinese hamster ovary (CHO) cells are the preferred mammalian host for the large-scale production of recombinant proteins in the biopharmaceutical industry. Research endeavors have been directed to the optimization of CHO-based bioprocesses to increase protein quantity and quality, often in an empirical manner. To provide a rationale for those achievements, a myriad of CHO proteomic studies has arisen in recent decades. This review gives an overview of significant advances in LC-MS-based proteomics and sheds light on CHO proteomic studies, with a particular focus on CHO cells with superior bioprocessing phenotypes (growth, viability, titer, productivity and cQA), that have exploited novel proteomic or sub-omic techniques. These proteomic findings expand the current knowledge and understanding about the underlying protein clusters, protein regulatory networks and biological pathways governing such phenotypic changes. The proteomic studies, highlighted herein, will help in the targeted modulation of these cell factories to the desired needs.
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2
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Effects and mechanisms of animal-free hydrolysates on recombination protein yields in CHO cells. Appl Microbiol Biotechnol 2022; 106:7387-7396. [PMID: 36229612 DOI: 10.1007/s00253-022-12229-x] [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: 08/02/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/02/2022]
Abstract
Chinese hamster ovary (CHO) cells are the commonly used cell lines for producing recombinant therapeutic proteins (RTPs) because they possess post-translational modifications similar to human cells. Culture media are necessary for cell growth, and their quality affects the yields and quality of RTPs. Due to safety concerns for the complex purification of RTPs, the development of serum-free media (SFM) is necessary for CHO cells. To meet the need for CHO cells with higher cell density and RTP productivity with consistent product quality in large-scale suspension cultures, the optimization of SFM through adding some enzymatic animal-free hydrolysates (AFHs) is preferred. The AFHs can improve cell culture performance and product yield of RTPs without affecting their quality. Here, the effect and mechanism of various AFHs in improving CHO cell culture performance and protein expression are reviewed. KEY POINTS: • AFHs that improve the recombinant protein yield of CHO cells are reviewed. • AFHs improve recombinant protein yield via influencing cell performance. • The AFHs do not affect the quality of recombinant protein in CHO cells. • AFHs can provide nutrients, block cell cycle, and reduce oxidative stress.
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3
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Safari F, Farajnia S, Behzad Behbahani A, Zarredar H, Barekati-Mowahed M, Dehghani H. Caspase-7 deficiency in Chinese hamster ovary cells reduces cell proliferation and viability. Biol Res 2020; 53:52. [PMID: 33187557 PMCID: PMC7666471 DOI: 10.1186/s40659-020-00319-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/04/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Chinese hamster ovary (CHO) cells are the most commonly used mammalian host cell in the commercial-scale production of biopharmaceutical proteins. Modification of genes involved in apoptosis may improve the productivity of CHO cells. Executive caspases, including caspases 3 and 7, play critical roles in apoptosis. The effects of the ablation of the caspase 7 gene on proliferation and viability of CHO cells remains unknown. In this study, we applied clustered regularly interspaced short palindromic repeat (CRISPR/Cas9) to target caspase 7 gene of CHO K1 cell via all in one and homology targeted integration strategies. Consequently, the effect of caspase 7 deficiency on cell proliferation, viability, and apoptosis was studied by MTT assay and flow cytometry. RESULTS Findings of gel electrophoresis, western blotting, and sequencing confirmed the caspase 7 gene silencing in CHO cells (CHO-KO). Proliferation assay revealed that caspase 7 deficiency in CHO cells resulted in the reduction of proliferation in various CHO-KO clones. Besides, the disruption of caspase 7 had negative effects on cell viability in exposure with NaBu which confirmed by MTT assay. Results of flow cytometry using Anexin V/PI demonstrated that Nabu treatment (11 mM) declined the percentage of live CHO-K1 and CHO-KO cells to 70.3% and 5.79%. These results verified that the CHO-K1 cells were more resistant to apoptosis than CHO-KO, however most of CHO-KO cells undergone early apoptosis (91.9%) which seems to be a fascinating finding. CONCLUSION These results reveal that caspase 7 may be involved in the cell cycle progression of CHO cells. Furthermore, it seems that targeting caspase 7 is not the ideal route as it had previously been imagined within the prevention of apoptosis but the relation between caspase 7 deficiency, cell cycle arrest, and the occurrence of early apoptosis will require more investigation.
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Affiliation(s)
- Fatemeh Safari
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave., Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Abbas Behzad Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mazyar Barekati-Mowahed
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Hesam Dehghani
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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4
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Orellana CA, Martínez VS, MacDonald MA, Henry MN, Gillard M, Gray PP, Nielsen LK, Mahler S, Marcellin E. 'Omics driven discoveries of gene targets for apoptosis attenuation in CHO cells. Biotechnol Bioeng 2020; 118:481-490. [PMID: 32865815 DOI: 10.1002/bit.27548] [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: 10/28/2019] [Revised: 07/22/2020] [Accepted: 08/14/2020] [Indexed: 12/15/2022]
Abstract
Chinese hamster ovary (CHO) cells are widely used in biopharmaceutical production. Improvements to cell lines and bioprocesses are constantly being explored. One of the major limitations of CHO cell culture is that the cells undergo apoptosis, leading to rapid cell death, which impedes reaching high recombinant protein titres. While several genetic engineering strategies have been successfully employed to reduce apoptosis, there is still room to further enhance CHO cell lines performance. 'Omics analysis is a powerful tool to better understand different phenotypes and for the identification of gene targets for engineering. Here, we present a comprehensive review of previous CHO 'omics studies that revealed changes in the expression of apoptosis-related genes. We highlight targets for genetic engineering that have reduced, or have the potential to reduce, apoptosis or to increase cell proliferation in CHO cells, with the final aim of increasing productivity.
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Affiliation(s)
- Camila A Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Verónica S Martínez
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Michael A MacDonald
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Matthew N Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Marianne Gillard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Peter P Gray
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Lars K Nielsen
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia.,Metabolomics Australia, The University of Queensland, Brisbane, Australia.,The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Esteban Marcellin
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia.,Metabolomics Australia, The University of Queensland, Brisbane, Australia
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5
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Thingholm TE, Rönnstrand L, Rosenberg PA. Why and how to investigate the role of protein phosphorylation in ZIP and ZnT zinc transporter activity and regulation. Cell Mol Life Sci 2020; 77:3085-3102. [PMID: 32076742 PMCID: PMC7391401 DOI: 10.1007/s00018-020-03473-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/13/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Zinc is required for the regulation of proliferation, metabolism, and cell signaling. It is an intracellular second messenger, and the cellular level of ionic, mobile zinc is strictly controlled by zinc transporters. In mammals, zinc homeostasis is primarily regulated by ZIP and ZnT zinc transporters. The importance of these transporters is underscored by the list of diseases resulting from changes in transporter expression and activity. However, despite numerous structural studies of the transporters revealing both zinc binding sites and motifs important for transporter function, the exact molecular mechanisms regulating ZIP and ZnT activities are still not clear. For example, protein phosphorylation was found to regulate ZIP7 activity resulting in the release of Zn2+ from intracellular stores leading to phosphorylation of tyrosine kinases and activation of signaling pathways. In addition, sequence analyses predict all 24 human zinc transporters to be phosphorylated suggesting that protein phosphorylation is important for regulation of transporter function. This review describes how zinc transporters are implicated in a number of important human diseases. It summarizes the current knowledge regarding ZIP and ZnT transporter structures and points to how protein phosphorylation seems to be important for the regulation of zinc transporter activity. The review addresses the need to investigate the role of protein phosphorylation in zinc transporter function and regulation, and argues for a pressing need to introduce quantitative phosphoproteomics to specifically target zinc transporters and proteins involved in zinc signaling. Finally, different quantitative phosphoproteomic strategies are suggested.
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Affiliation(s)
- T E Thingholm
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, J.B. Winsløws Vej 25, 3, 5000, Odense C, Denmark.
| | - L Rönnstrand
- Division of Translational Cancer Research, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Lund Stem Cell Center, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - P A Rosenberg
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Neurology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
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6
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Debottlenecking protein secretion and reducing protein aggregation in the cellular host. Curr Opin Biotechnol 2018; 53:151-157. [DOI: 10.1016/j.copbio.2018.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 01/05/2023]
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7
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Label-free protein quantification of sodium butyrate treated CHO cells by ESI-UHR-TOF-MS. J Biotechnol 2017; 257:87-98. [DOI: 10.1016/j.jbiotec.2017.03.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 11/18/2022]
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8
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Avello V, Tapia B, Vergara M, Acevedo C, Berrios J, Reyes JG, Altamirano C. Impact of sodium butyrate and mild hypothermia on metabolic and physiological behaviour of CHO TF 70R cells. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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9
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Azarian B, Sajedin SM, Azimi A, Raigani M, Vaziri B, Davami F. Proteomics Profiling of Chimeric-Truncated Tissue Plasminogen activator Producing- Chinese Hamster Ovary Cells Cultivated in a Chemically Defined Medium Supplemented with Protein Hydrolysates. IRANIAN BIOMEDICAL JOURNAL 2017; 21:154-66. [PMID: 28187683 PMCID: PMC5392218 DOI: 10.18869/acadpub.ibj.21.3.154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Background Culture media enrichment through the addition of protein hydrolysates is beneficial for achieving higher protein expression. Methods In this study, designing the optimum mixture of four soy and casein-derived hydrolysates was successfully performed by design of experiment and specific productivity increased in all predicted combinations. Protein profile of recombinant CHO (rCHO) cells producing tissue plasminogen activator in a serum-free medium (SFM) supplemented with designed hydrolysate additives was compared to that of rCHO cells cultivated in SFM. Results Identification of differentially expressed proteins using two-dimensional gel electrophoresis coupled with MALDI-TOF/TOF revealed the role of energy metabolism related proteins and importance of prevention of oxidative stress by this special media enrichment strategy. Up-regulation of mitochondrial enzymes, pyruvate dehydrogenase E1 and Peroxiredoxin-III, as well as other proteins involved in metabolic pathways, and uridine monophosphate/cytidine monophosphate kinase indicated higher metabolic activity. Furthermore, along with antioxidant effect of peptones, proteins with antioxidant function such as ferritin and peroxiredoxin-III were up-regulated. Conclusion Understanding molecular mechanisms involved in enhancement of protein expression can provide new approaches for efficiently engineering rCHO cell. These results support the competence of proteomics studies in finding new insights to biochemical pathways for a knowledge-based optimization of media compositions.
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Affiliation(s)
- Bahareh Azarian
- Protein Chemistry Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyedeh Matin Sajedin
- Protein Chemistry Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Microbiology, Science and Research Branch, Islamic Azad University, Guilan, Iran
| | - Amin Azimi
- Protein Chemistry Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Mozhgan Raigani
- Eukaryotic Expression Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behrouz Vaziri
- Protein Chemistry Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Davami
- Protein Chemistry Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Eukaryotic Expression Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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10
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Zhang Z, Albanetti T, Linkous T, Larkin CJ, Schoner R, McGivney JB, Dovichi NJ. Comprehensive analysis of host cell impurities in monoclonal antibodies with improved sensitivity by capillary zone electrophoresis mass spectrometry. Electrophoresis 2016; 38:401-407. [DOI: 10.1002/elps.201600390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN USA
| | - Thomas Albanetti
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Travis Linkous
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Christopher J. Larkin
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Ronald Schoner
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - James B. McGivney
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN USA
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11
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Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE. Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow. Biotechnol Adv 2016; 34:621-633. [DOI: 10.1016/j.biotechadv.2016.02.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 02/21/2016] [Accepted: 02/28/2016] [Indexed: 01/01/2023]
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12
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Zhu G, Sun L, Albanetti T, Linkous T, Larkin C, Schoner R, McGivney JB, Dovichi NJ. Quantitative analysis of the supernatant from host and transfected CHO cells using iTRAQ 8-plex technique. Biotechnol Bioeng 2016; 113:2140-8. [DOI: 10.1002/bit.25991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/19/2016] [Accepted: 04/07/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame Indiana 46556
| | - Liangliang Sun
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame Indiana 46556
| | - Thomas Albanetti
- BioPharmaceutical Development MedImmune LLC; Gaithersburg Maryland
| | - Travis Linkous
- BioPharmaceutical Development MedImmune LLC; Gaithersburg Maryland
| | | | - Ronald Schoner
- BioPharmaceutical Development MedImmune LLC; Gaithersburg Maryland
| | | | - Norman J. Dovichi
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame Indiana 46556
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13
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Sommeregger W, Mayrhofer P, Steinfellner W, Reinhart D, Henry M, Clynes M, Meleady P, Kunert R. Proteomic differences in recombinant CHO cells producing two similar antibody fragments. Biotechnol Bioeng 2016; 113:1902-12. [PMID: 26913574 PMCID: PMC4985663 DOI: 10.1002/bit.25957] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/25/2015] [Accepted: 02/14/2016] [Indexed: 12/28/2022]
Abstract
Chinese hamster ovary (CHO) cells are the most commonly used mammalian hosts for the production of biopharmaceuticals. To overcome unfavorable features of CHO cells, a lot of effort is put into cell engineering to improve phenotype. “Omics” studies investigating elevated growth rate and specific productivities as well as extracellular stimulus have already revealed many interesting engineering targets. However, it remains largely unknown how physicochemical properties of the recombinant product itself influence the host cell. In this study, we used quantitative label‐free LC‐MS proteomic analyses to investigate product‐specific proteome differences in CHO cells producing two similar antibody fragments. We established recombinant CHO cells producing the two antibodies, 3D6 and 2F5, both as single‐chain Fv‐Fc homodimeric antibody fragments (scFv‐Fc). We applied three different vector strategies for transgene delivery (i.e., plasmid, bacterial artificial chromosome, recombinase‐mediated cassette exchange), selected two best performing clones from transgene variants and transgene delivery methods and investigated three consecutively passaged cell samples by label‐free proteomic analysis. LC‐MS‐MS profiles were compared in several sample combinations to gain insights into different aspects of proteomic changes caused by overexpression of two different heterologous proteins. This study suggests that not only the levels of specific product secretion but the product itself has a large impact on the proteome of the cell. Biotechnol. Bioeng. 2016;113: 1902–1912. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Wolfgang Sommeregger
- Vienna Institute of BioTechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 18, B, 5th Floor, 1190 Vienna, Austria.,Polymun Scientific GmbH, Klosterneuburg, Austria.,Bilfinger Industrietechnik Salzburg GmbH, Salzburg, Austria
| | - Patrick Mayrhofer
- Vienna Institute of BioTechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 18, B, 5th Floor, 1190 Vienna, Austria
| | - Willibald Steinfellner
- Vienna Institute of BioTechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 18, B, 5th Floor, 1190 Vienna, Austria
| | - David Reinhart
- Vienna Institute of BioTechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 18, B, 5th Floor, 1190 Vienna, Austria
| | - Michael Henry
- National Institute for Cellular Biotechnology (NICB), Dublin City University, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology (NICB), Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology (NICB), Dublin City University, Dublin 9, Ireland.
| | - Renate Kunert
- Vienna Institute of BioTechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 18, B, 5th Floor, 1190 Vienna, Austria.
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14
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Liu Z, Dai S, Bones J, Ray S, Cha S, Karger BL, Li JJ, Wilson L, Hinckle G, Rossomando A. A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells. Biotechnol Prog 2015; 31:1026-38. [PMID: 25857574 DOI: 10.1002/btpr.2090] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 03/11/2015] [Indexed: 12/12/2022]
Abstract
A goal in recombinant protein production using Chinese hamster ovary (CHO) cells is to achieve both high specific productivity and high cell density. Addition of glucose to the culture media is necessary to maintain both cell growth and viability. We varied the glucose concentration in the media from 5 to 16 g/L and found that although specific productivity of CHO-DG44 cells increased with the glucose level, the integrated viable cell density decreased. To examine the biological basis of these results, we conducted a discovery proteomic study of CHO-DG44 cells grown under batch conditions in normal (5 g/L) or high (15 g/L) glucose over 3, 6, and 9 days. Approximately 5,000 proteins were confidently identified against an mRNA-based CHO-DG44 specific proteome database, with 2,800 proteins quantified with at least two peptides. A self-organizing map algorithm was used to deconvolute temporal expression profiles of quantitated proteins. Functional analysis of altered proteins suggested that differences in growth between the two glucose levels resulted from changes in crosstalk between glucose metabolism, recombinant protein expression, and cell death, providing an overall picture of the responses to high glucose environment. The high glucose environment may enhance recombinant dihydrofolate reductase in CHO cells by up-regulating NCK1 and down-regulating PRKRA, and may lower integrated viable cell density by activating mitochondrial- and endoplasmic reticulum-mediated cell death pathways by up-regulating HtrA2 and calpains. These proteins are suggested as potential targets for bioengineering to enhance recombinant protein production.
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Affiliation(s)
- Zhenke Liu
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Shujia Dai
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Jonathan Bones
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Somak Ray
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Sangwon Cha
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Barry L Karger
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Jingyi Jessica Li
- Dept. of Statistics, University of California, Los Angeles, CA, 90095
| | - Lee Wilson
- Alnylam Pharmaceuticals, Cambridge, MA, 02142
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15
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Wingens M, Gätgens J, Schmidt A, Albaum SP, Büntemeyer H, Noll T, Hoffrogge R. 2D-DIGE screening of high-productive CHO cells under glucose limitation--basic changes in the proteome equipment and hints for epigenetic effects. J Biotechnol 2015; 201:86-97. [PMID: 25612871 DOI: 10.1016/j.jbiotec.2015.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 01/21/2023]
Abstract
CHO derivates (Chinese hamster ovary) belong to the most important mammalian cells for industrial recombinant protein production. Many efforts have been made to improve productivity and stability of CHO cells in bioreactor processes. Here, we followed up one barely understood phenomenon observed with process optimizations: a significantly increased cell-specific productivity in late phases of glucose-limited perfusion cultivations, when glucose (and lactate) reserves are exhausted. Our aim was to elucidate the cellular activities connected to the metabolic shift from glucose surplus to glucose limitation phase. With 2D-DIGE, we compared three stages in a perfusion culture of CHO cells: the initial growth with high glucose concentration and low lactate production, the second phase with glucose going to limitation and high lactate level, and finally the state of glucose limitation and also low lactate concentration but increased cell-specific productivity. With our proteomic approach we were able to demonstrate consequences of glucose limitation for the protein expression machinery which also could play a role for a higher recombinant protein production. Most interestingly, we detected epigenetic effects on the level of proteins involved in histone modification (HDAC1/-2, SET, RBBP7, DDX5). Together with shifts in the protein inventory of energy metabolism, cytoskeleton and protein expression, a picture emerges of basic changes in the cellular equipment under long-term glucose limitation of CHO cells.
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Affiliation(s)
- Marc Wingens
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Jochem Gätgens
- IBG-1: Biotechnology; Bioprocesses and Bioanalytics, Research Center Jülich, Germany
| | - Anica Schmidt
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Stefan P Albaum
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Heino Büntemeyer
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Thomas Noll
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Raimund Hoffrogge
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany.
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16
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Harnessing Chinese hamster ovary cell proteomics for biopharmaceutical processing. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.49] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Farrell A, McLoughlin N, Milne JJ, Marison IW, Bones J. Application of Multi-Omics Techniques for Bioprocess Design and Optimization in Chinese Hamster Ovary Cells. J Proteome Res 2014; 13:3144-59. [DOI: 10.1021/pr500219b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amy Farrell
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Niaobh McLoughlin
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - John J. Milne
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Ian W. Marison
- Laboratory
of Integrated Bioprocessing, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Jonathan Bones
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
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Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, Palsson BO, Zhang H, Betenbaugh M. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res 2012; 11:5265-76. [PMID: 22971049 DOI: 10.1021/pr300476w] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimensional liquid chromatography, and solid phase extraction of glycopeptides (SPEG). From the 120 different mass spectrometry analyses generating 682,097 MS/MS spectra, 93,548 unique peptide sequences were identified with at most 0.02 false discovery rate (FDR). A total of 6164 grouped proteins were identified from both glycoproteome and proteome analysis, representing an 8-fold increase in the number of proteins currently identified in the CHO proteome. Furthermore, this is the first proteomic study done using the CHO genome exclusively, which provides for more accurate identification of proteins. From this analysis, the CHO codon frequency was determined and found to be distinct from humans, which will facilitate expression of human proteins in CHO cells. Analysis of the combined proteomic and mRNA data sets indicated the enrichment of a number of pathways including protein processing and apoptosis but depletion of proteins involved in steroid hormone and glycosphingolipid metabolism. Five-hundred four of the detected proteins included N-acetylation modifications, and 1292 different proteins were observed to be N-glycosylated. This first large-scale proteomic analysis will enhance the knowledge base about CHO capabilities for recombinant expression and provide information useful in cell engineering efforts aimed at modifying CHO cellular functions.
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Affiliation(s)
- Deniz Baycin-Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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Kim JY, Kim YG, Lee GM. Differential in-gel electrophoresis (DIGE) analysis of CHO cells under hyperosmotic pressure: osmoprotective effect of glycine betaine addition. Biotechnol Bioeng 2012; 109:1395-403. [PMID: 22252946 DOI: 10.1002/bit.24442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 01/04/2012] [Accepted: 01/04/2012] [Indexed: 12/13/2022]
Abstract
The use of glycine betaine combined with hyperosmolality is known to be an efficient means for achieving high protein production in recombinant Chinese hamster ovary (rCHO) cells. In order to understand the intracellular events and identify the key factors in rCHO cells cultivated with glycine betaine under hyperosmotic conditions, two-dimensional differential in-gel electrophoresis (2D-DIGE) followed by mass spectrometric analysis was applied. Differentially expressed 19 protein spots were selected and 16 different kinds of proteins were successfully identified. The identified proteins were associated with cellular metabolism (PEPCK, GAPDH, and PK), cellular architecture (β-tubulin and β-actin), protein folding (GRP78 and OSP94), mRNA processing (Rbm34, ACF, and IPMK), and protein secretion (γ-COP). 2D-Western blot analysis of β-tubulin, GAPDH, Peroxidoxin-1, and GRP78 confirmed the proteomic findings. The proteins identified from this study, which are related to cell growth and antibody production, can be applied to cell engineering for maximizing the efficacy of the use of glycine betaine combined with hyperosmolality in rCHO cells.
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Affiliation(s)
- Jee Yon Kim
- Department of Biological Sciences, Graduate School of Nanoscience and Technology (WCU), KAIST, 373-1 Kusong-Dong, Yusong-Gu, Daejon 305-701, Korea
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CHO cells in biotechnology for production of recombinant proteins: current state and further potential. Appl Microbiol Biotechnol 2011; 93:917-30. [PMID: 22159888 DOI: 10.1007/s00253-011-3758-5] [Citation(s) in RCA: 506] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 10/14/2022]
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Baik JY, Ha TK, Kim YH, Lee GM. Proteomic understanding of intracellular responses of recombinant chinese hamster ovary cells adapted to grow in serum-free suspension culture. Biotechnol Prog 2011. [DOI: 10.1002/btpr.685] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Proteomic understanding of intracellular responses of recombinant Chinese hamster ovary cells cultivated in serum-free medium supplemented with hydrolysates. Appl Microbiol Biotechnol 2011; 89:1917-28. [PMID: 21286710 DOI: 10.1007/s00253-011-3106-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/30/2010] [Accepted: 01/06/2011] [Indexed: 12/11/2022]
Abstract
In order to understand the intracellular responses in recombinant CHO (rCHO) cells producing antibody in serum-free medium (SFM) supplemented with optimized hydrolysates mixtures, yielding the highest specific growth rate (μ, SFM#S1) or the highest specific antibody productivity (q(Ab,) SFM#S2), differentially expressed proteins in rCHO cells are measured by two-dimensional gel electrophoresis combined with nano-LC-ESI-Q-TOF tandem MS. The comparative proteomic analysis with basal SFM without hydrolysates revealed that the addition of hydrolysate mixtures significantly altered the profiles of CHO proteome. In SFM#S1, the expression of metabolism-related proteins, cytoskeleton-associated proteins, and proliferation-related proteins was up-regulated. On the other hand, the expression of anti-proliferative proteins and pro-apoptotic protein was down-regulated. In SFM#S2, the expression of various chaperone proteins and proliferation-linked proteins was altered. 2D-Western blot analysis of differentially expressed proteins confirmed the proteomic results. Taken together, identification of differentially expressed proteins in CHO cells by a proteomic approach can provide insights into understanding the effect of hydrolysates on intracellular events and clues to find candidate genes for cell engineering to maximize the protein production in rCHO cells.
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Lee JS, Park HJ, Kim YH, Lee GM. Protein reference mapping of dihydrofolate reductase-deficient CHO DG44 cell lines using 2-dimensional electrophoresis. Proteomics 2010; 10:2292-302. [DOI: 10.1002/pmic.200900430] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jin M, Szapiel N, Zhang J, Hickey J, Ghose S. Profiling of host cell proteins by two-dimensional difference gel electrophoresis (2D-DIGE): Implications for downstream process development. Biotechnol Bioeng 2010; 105:306-16. [DOI: 10.1002/bit.22532] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Baik JY, Lee GM. A DIGE approach for the assessment of differential expression of the CHO proteome under sodium butyrate addition: Effect of Bcl-xLoverexpression. Biotechnol Bioeng 2010; 105:358-67. [DOI: 10.1002/bit.22534] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Kim JY, Kim YG, Baik JY, Joo EJ, Kim YH, Lee GM. A proteomic approach for identifying cellular proteins interacting with erythropoietin in recombinant Chinese hamster ovary cells. Biotechnol Prog 2009; 26:246-51. [PMID: 19918894 DOI: 10.1002/btpr.323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Identification of the cellular proteins interacting with incompletely folded and unfolded forms of erythropoietin (EPO) in recombinant CHO (rCHO) cells leads to better insight into the possible genetic manipulation approaches for increasing EPO production. To do so, a pull-down assay was performed with dual-tagged (N-terminal GST- and C-terminal hexahistidine-tagged) EPO expressed in E. coli as bait proteins and cell lysates of rCHO cells (DG44) as prey proteins. Cellular proteins interacting with dual-tagged EPO were then resolved by two-dimensional gel electrophoresis (2DE) and identified by MALDI-TOF MS/MS. A total of 27 protein spots including glucose-regulated protein 78 (GRP78) were successfully identified. Western blot analysis of GRP78 confirmed the results of the MS analyses. Taken together, a pull-down assay followed by a proteomic approach is found to be an efficient means to identify cellular proteins interacting with foreign protein in rCHO cells.
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Affiliation(s)
- Jee Yon Kim
- Dept. of Biological Sciences, KAIST, 373-1, Kusong-Dong, Yusong-Gu, Daejon 305-701, Korea
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Wu SC. RNA interference technology to improve recombinant protein production in Chinese hamster ovary cells. Biotechnol Adv 2009; 27:417-22. [DOI: 10.1016/j.biotechadv.2009.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 03/07/2009] [Accepted: 03/08/2009] [Indexed: 12/28/2022]
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