1
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Raab N, Zeh N, Kretz R, Weiß L, Stadermann A, Lindner B, Fischer S, Stoll D, Otte K. Nature as blueprint: Global phenotype engineering of CHO production cells based on a multi-omics comparison with plasma cells. Metab Eng 2024; 83:110-122. [PMID: 38561148 DOI: 10.1016/j.ymben.2024.03.007] [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: 02/03/2023] [Revised: 03/17/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Especially for the production of artificial, difficult to express molecules a further development of the CHO production cell line is required to keep pace with the continuously increasing demands. However, the identification of novel targets for cell line engineering to improve CHO cells is a time and cost intensive process. Since plasma cells are evolutionary optimized for a high antibody expression in mammals, we performed a comprehensive multi-omics comparison between CHO and plasma cells to exploit optimized cellular production traits. Comparing the transcriptome, proteome, miRNome, surfaceome and secretome of both cell lines identified key differences including 392 potential overexpression targets for CHO cell engineering categorized in 15 functional classes like transcription factors, protein processing or secretory pathway. In addition, 3 protein classes including 209 potential knock-down/out targets for CHO engineering were determined likely to affect aggregation or proteolysis. For production phenotype engineering, several of these novel targets were successfully applied to transient and transposase mediated overexpression or knock-down strategies to efficiently improve productivity of CHO cells. Thus, substantial improvement of CHO productivity was achieved by taking nature as a blueprint for cell line engineering.
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Affiliation(s)
- Nadja Raab
- Biberach University of Applied Sciences, Germany.
| | - Nikolas Zeh
- Biberach University of Applied Sciences, Germany; Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Robin Kretz
- Hochschule Albstadt Sigmaringen, Germany; NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Linus Weiß
- Biberach University of Applied Sciences, Germany
| | - Anna Stadermann
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Benjamin Lindner
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Simon Fischer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Dieter Stoll
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Kerstin Otte
- Biberach University of Applied Sciences, Germany
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2
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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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3
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Zhao Q, Chen Y, Qu L. Combined Transcriptomic and Proteomic Analyses Reveal the Different Responses to UVA and UVB Radiation in Human Keratinocytes. Photochem Photobiol 2023; 99:137-152. [PMID: 35638308 DOI: 10.1111/php.13658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/25/2022] [Indexed: 01/25/2023]
Abstract
Ultraviolet (UV) radiation from sunlight is a major risk factor for many cutaneous pathologies including skin aging and cancers. Despite decades of research, the different responses to UVA and UVB in human keratinocytes have not been systemically investigated. Here, we performed multi-omics to characterize the common and different changes in gene transcription and protein expression after exposure to UVB and UVA, respectively. Keratinocyte cells, treated with or without UV, were analyzed by TMT-labeled MS/MS spectra and RNA-sequencing. A common set of genes/proteins was found to be impacted by both UVA and UVB and the other differential genes/proteins showed wavelength specificity. The common set of genes/proteins were mainly involved in keratinization, lipid metabolic processes and stimulus response. The UVB specifically responsive genes/proteins were mainly related to RNA processing, gene silencing regulation and cytoskeleton organization. The UVA specifically responsive genes/proteins were mainly involved in vesicle-mediated transport and oxygen-containing compound response. Meanwhile, the hub differential genes/proteins in each set were identified by protein-protein interaction networks and cluster analysis. This work provided a global view of the similar and differential molecular mechanisms of UVB- and UVA-induced cell damage in keratinocytes, which would be beneficial for further studies in the prevention or treatment of UV-related pathologies.
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Affiliation(s)
- Qinqin Zhao
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China
| | - Yueyue Chen
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China.,Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
| | - Liping Qu
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China.,Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China.,Yunnan Botanee Bio-technology Group Co., Ltd., Kunming, China
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4
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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.
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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
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5
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Sinharoy P, McFarland KS, Majewska NI, Betenbaugh MJ, Handlogten MW. Redox as a bioprocess parameter: analytical redox quantification in biological therapeutic production. Curr Opin Biotechnol 2021; 71:49-54. [PMID: 34243034 DOI: 10.1016/j.copbio.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/10/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022]
Abstract
Engineered Chinese hamster ovary (CHO) cells are the most widely utilized cell line for protein-based therapeutics production at industrial scales. Process development strategies which improve production capacity and quality are often implemented without an understanding of underlying intracellular changes. Intracellular redox conditions drive reactions in pathways critical to biologics production, including bioenergetic and biosynthetic pathways, necessitating methods to quantify redox-related changes. Advances in methods for analytical redox quantification presented here, including bioreactor probes, redox-targeted proteomics, genetically encoded redox-sensitive fluorescent proteins, and biochemical assays, are creating new opportunities to characterize the effects of redox in biologics production. Implementing these methods will lead to enhanced media formulations, improved bioprocess strategies, and new cell line engineering targets and ultimately develop redox into an optimizable bioprocess parameter to improve the yield and quality of these lifesaving medicines.
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Affiliation(s)
- Pritam Sinharoy
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA
| | - Kevin S McFarland
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, USA
| | - Natalia I Majewska
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, USA
| | - Michael W Handlogten
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA.
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6
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Schmieder V, Novak N, Dhiman H, Nguyen LN, Serafimova E, Klanert G, Baumann M, Kildegaard HF, Borth N. A pooled CRISPR/AsCpf1 screen using paired gRNAs to induce genomic deletions in Chinese hamster ovary cells. ACTA ACUST UNITED AC 2021; 31:e00649. [PMID: 34277363 PMCID: PMC8261548 DOI: 10.1016/j.btre.2021.e00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022]
Abstract
• Development of a small-scale CRISPR/AsCpf1 screen in CHO. • Usage of paired gRNAs enables full deletion of coding or noncoding genomic regions. • Growth perturbing paired gRNAs identified. • Key points for considerations in future screens identified.
Chinese hamster ovary (CHO) cells are the most widely used host for the expression of therapeutic proteins. Recently, significant progress has been made due to advances in genome sequence and annotation quality to unravel the black box CHO. Nevertheless, in many cases the link between genotype and phenotype in the context of suspension cultivated production cell lines is still not fully understood. While frameshift approaches targeting coding genes are frequently used, the non-coding regions of the genome have received less attention with respect to such functional annotation. Importantly, for non-coding regions frameshift knock-out strategies are not feasible. In this study, we developed a CRISPR-mediated screening approach that performs full deletions of genomic regions to enable the functional study of both the translated and untranslated genome. An in silico pipeline for the computational high-throughput design of paired guide RNAs (pgRNAs) directing CRISPR/AsCpf1 was established and used to generate a library tackling process-related genes and long non-coding RNAs. Next generation sequencing analysis of the plasmid library revealed a sufficient, but highly variable pgRNA composition. Recombinase-mediated cassette exchange was applied for pgRNA library integration rather than viral transduction to ensure single copy representation of pgRNAs per cell. After transient AsCpf1 expression, cells were cultivated over two sequential batches to identify pgRNAs which massively affected growth and survival. By comparing pgRNA abundance, depleted candidates were identified and individually validated to verify their effect.
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Key Words
- AsCpf1, Cpf1 from Acidaminococcus sp BV3L6
- CHO, Chinese hamster ovary
- CPM, counts per million reads mapped
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- CRISPR/AsCpf1
- Cas9, CRISPR-associated protein 9
- Chinese hamster ovary cells
- Cpf1, CRISPR-associated protein in Prevotella and Francisella
- DE, differentially expressed
- DOWN-TTS, downstream transcription termination site
- DR, differentially represented
- EV, empty vector
- EpoFc, Erythropoietin Fc fusion protein
- FACS, fluorescence activated cell sorting
- FC, fold change
- FDR, false discovery rate
- GS, glutamine synthetase
- Genetic screen
- NGS, next generation sequencing
- NTC, no template control
- PAM, protospacer adjacent motif
- PCA, principal component analysis
- Qp, specific productivity
- RMCE, recombinase-mediated cassette exchange
- TMM, trimmed mean of M values
- UP-TSS, upstream transcription start site
- VCD, viable cell density
- dCas9, deactivated Cas9
- gRNA, guide RNA
- genomic deletion
- lncRNA, long non-coding RNA
- ncGene, non-coding gene
- oligo, oligonucleotide
- paired gRNAs
- pgRNA, paired gRNA
- sgRNA, single guide RNA
- µ, growth rate
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Affiliation(s)
- Valerie Schmieder
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Neža Novak
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Heena Dhiman
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Ly Ngoc Nguyen
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Evgenija Serafimova
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Gerald Klanert
- acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Martina Baumann
- acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Kgs. Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
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7
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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8
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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.
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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
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9
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Dai Z, Huang H, Zhang Q, Bei J, Chen Z, Liu Q, Gao J, Zhang S, Liu J. Comparative Multi-Omics of Tender Shoots from a Novel Evergrowing Tea Cultivar Provide Insight into the Winter Adaptation Mechanism. PLANT & CELL PHYSIOLOGY 2021; 62:366-377. [PMID: 33399871 DOI: 10.1093/pcp/pcaa167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 12/14/2020] [Indexed: 05/15/2023]
Abstract
Tea (Camellia sinensis [L.] O. Kuntze) tree is a perennial plant in which winter dormancy is an important biological adaptation to environmental changes. We discovered and reported a novel tea tree cultivar that can generate tender shoots in winter several years ago, but the molecular mechanism for this unique phenotype remains unknown . Here, we conducted comparative transcriptomics, proteomics and metabolomics along with phytohormone quantitation between the winter and spring tender shoots to investigate the physiological basis and putative regulatory mechanisms of its evergrowing character during winter. Our multi-omics study has led to the following findings. Gibberellin (GA) levels and key enzymes for GA biosynthesis and the signal transduction pathway were increased in the winter shoots, causing the ABA/GA content ratio to decrease, which might play a key regulatory role in maintaining normal growth during winter. The abundance of proteins, genes and metabolites involved in energy metabolism was all increased in winter shoots, indicating that energy is critical for continuous growth under the relatively weak-light and low-temperature environment. Abiotic resistance-related proteins and free amino acids were also increased in abundance in the winter shoots, which possibly represents an adaptation response to winter conditions. These results allowed us to hypothesize a novel molecular mechanism of adaptation for this unique tender shoot evergrowing in winter.
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Affiliation(s)
- Zhangyan Dai
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
| | - Hualin Huang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qunjie Zhang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
| | - Jinlong Bei
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
| | - Zhongjian Chen
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
| | - Qinjian Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
| | - Jiadong Gao
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
| | | | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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10
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Lee Z, Raabe M, Hu WS. Epigenomic features revealed by ATAC-seq impact transgene expression in CHO cells. Biotechnol Bioeng 2021; 118:1851-1861. [PMID: 33521928 DOI: 10.1002/bit.27701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022]
Abstract
Different regions of a mammalian genome have different accessibilities to transcriptional machinery. The integration site of a transgene affects how actively it is transcribed. Highly accessible genomic regions called super-enhancers have been recently described as strong regulatory elements that shape cell identity. Super-enhancers have been identified in Chinese hamster ovary (CHO) cells using the Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq). Genes near super-enhancer regions had high transcript levels and were enriched for oncogenic signaling and proliferation functions, consistent with an immortalized phenotype. Inaccessible regions in the genome with low ATAC signal also had low transcriptional activity. Genes in inaccessible regions were enriched for remote tissue functions such as taste, smell, and neuronal activation. A lentiviral reporter integration assay showed integration into super-enhancer regions conferred higher reporter expression than insertion into inaccessible regions. Targeted integration of an IgG vector into the Plec super-enhancer region yielded clones that expressed the immunoglobulin light chain gene mostly in the top 20% of all transcripts with the majority in the top 5%. The results suggest the epigenomic landscape of CHO cells can guide the selection of integration sites in the development of cell lines for therapeutic protein production.
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Affiliation(s)
- Zion Lee
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Marina Raabe
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
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11
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Bryan L, Henry M, Kelly RM, Lloyd M, Frye CC, Osborne MD, Clynes M, Meleady P. Global phosphoproteomic study of high/low specific productivity industrially relevant mAb producing recombinant CHO cell lines. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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12
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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
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13
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Weinguny M, Eisenhut P, Klanert G, Virgolini N, Marx N, Jonsson A, Ivansson D, Lövgren A, Borth N. Random epigenetic modulation of CHO cells by repeated knockdown of DNA methyltransferases increases population diversity and enables sorting of cells with higher production capacities. Biotechnol Bioeng 2020; 117:3435-3447. [PMID: 32662873 PMCID: PMC7818401 DOI: 10.1002/bit.27493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 07/12/2020] [Indexed: 12/15/2022]
Abstract
Chinese hamster ovary (CHO) cells produce a large share of today's biopharmaceuticals. Still, the generation of satisfactory producer cell lines is a tedious undertaking. Recently, it was found that CHO cells, when exposed to new environmental conditions, modify their epigenome, suggesting that cells adapt their gene expression pattern to handle new challenges. The major aim of the present study was to employ artificially induced, random changes in the DNA-methylation pattern of CHO cells to diversify cell populations and consequently increase the finding of cell lines with improved cellular characteristics. To achieve this, DNA methyltransferases and/or the ten-eleven translocation enzymes were downregulated by RNA interference over a time span of ∼16 days. Methylation analysis of the resulting cell pools revealed that the knockdown of DNA methyltransferases was highly effective in randomly demethylating the genome. The same approach, when applied to stable CHO producer cells resulted in (a) an increased productivity diversity in the cell population, and (b) a higher number of outliers within the population, which resulted in higher specific productivity and titer in the sorted cells. These findings suggest that epigenetics play a previously underestimated, but actually important role in defining the overall cellular behavior of production clones.
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Affiliation(s)
- Marcus Weinguny
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Peter Eisenhut
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Gerald Klanert
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria
| | | | - Nicolas Marx
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | | | | | | | - Nicole Borth
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
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14
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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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15
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A platform for context-specific genetic engineering of recombinant protein production by CHO cells. J Biotechnol 2020; 312:11-22. [DOI: 10.1016/j.jbiotec.2020.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/12/2019] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
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16
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Henry MN, MacDonald MA, Orellana CA, Gray PP, Gillard M, Baker K, Nielsen LK, Marcellin E, Mahler S, Martínez VS. Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production. Biotechnol Bioeng 2020; 117:1187-1203. [DOI: 10.1002/bit.27269] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/25/2019] [Accepted: 01/04/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Matthew N. Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Michael A. MacDonald
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
| | - Camila A. Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Peter P. Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Marianne Gillard
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Kym Baker
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
- Patheon Biologics—A Part of Thermo Fisher Scientific Brisbane Queensland Australia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
- Metabolomics Australia The University of Queensland Brisbane Queensland Australia
- The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kgs. Lyngby Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
- Metabolomics Australia The University of Queensland Brisbane Queensland Australia
| | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
| | - Verónica S. Martínez
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
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17
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Dhiman H, Gerstl MP, Ruckerbauer D, Hanscho M, Himmelbauer H, Clarke C, Barron N, Zanghellini J, Borth N. Genetic and Epigenetic Variation across Genes Involved in Energy Metabolism and Mitochondria of Chinese Hamster Ovary Cell Lines. Biotechnol J 2019; 14:e1800681. [DOI: 10.1002/biot.201800681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/14/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Heena Dhiman
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - Matthias P. Gerstl
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - David Ruckerbauer
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - Michael Hanscho
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
| | - Colin Clarke
- National Institute for Bioprocessing Research and TrainingBlackrock, Co Dublin Ireland
| | - Niall Barron
- National Institute for Bioprocessing Research and TrainingBlackrock, Co Dublin Ireland
- School of Chemical and Bioprocess EngineeringUniversity College DublinGlasnevin Whitehall Dublin Ireland
| | - Jürgen Zanghellini
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
- Austrian Biotech University of Applied SciencesKonrad Lorenz Strasse 10 3430 Tulln Austria
| | - Nicole Borth
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
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18
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19
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Tossolini I, López-Díaz FJ, Kratje R, Prieto CC. Characterization of cellular states of CHO-K1 suspension cell culture through cell cycle and RNA-sequencing profiling. J Biotechnol 2018; 286:56-67. [DOI: 10.1016/j.jbiotec.2018.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/06/2023]
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20
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Tamošaitis L, Smales CM. Meta-Analysis of Publicly Available Chinese Hamster Ovary (CHO) Cell Transcriptomic Datasets for Identifying Engineering Targets to Enhance Recombinant Protein Yields. Biotechnol J 2018; 13:e1800066. [DOI: 10.1002/biot.201800066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/23/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Linas Tamošaitis
- Industrial Biotechnology Centre and School of Biosciences; University of Kent; Canterbury Kent CT2 7NJ UK
| | - Christopher Mark Smales
- Industrial Biotechnology Centre and School of Biosciences; University of Kent; Canterbury Kent CT2 7NJ UK
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21
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Torkashvand F, Mahboudi F, Vossoughi M, Fatemi E, Moosavi Basri SM, Heydari A, Vaziri B. Quantitative Proteomic Analysis of Cellular Responses to a Designed Amino Acid Feed in a Monoclonal Antibody
Producing Chinese Hamster Ovary Cell Line. IRANIAN BIOMEDICAL JOURNAL 2018. [PMID: 29678103 PMCID: PMC6305810 DOI: 10.29252/.22.6.385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background: Chinese hamster ovary (CHO) cell line is considered as the most common cell line in the biopharmaceutical industry because of its capability in performing efficient post-translational modifications and producing the recombinant proteins, which are similar to natural human proteins. The optimization of the upstream process via different feed strategies has a great impact on the target molecule expression and yield. Methods: To determine and understand the molecular events beneath the feed effects on the CHO cell, a label-free quantitative proteomic analysis was applied. The proteome changes followed by the addition of a designed amino acid feed to the monoclonal antibody producing CHO cell line culture medium were investigated. Results: The glutathione synthesis, the negative regulation of the programmed cell death, proteasomal catabolic process, and the endosomal transport pathway were up-regulated in the group fed with a designed amino acid feed compared to the control group. Conclusion: Our findings could be helpful to identify new targets for metabolic engineering.
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Affiliation(s)
- Fatemeh Torkashvand
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fereidoun Mahboudi
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Manouchehr Vossoughi
- Department of Chemical and Petroleum Engineering, Biochemical and Bioenvironmental Research Center Sharif University of Technology, Tehran, Iran
| | - Elnaz Fatemi
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Masoud Moosavi Basri
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Amir Heydari
- Department of Chemical Engineering, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Behrouz Vaziri
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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22
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Koczka K, Peters P, Ernst W, Himmelbauer H, Nika L, Grabherr R. Comparative transcriptome analysis of a Trichoplusia ni cell line reveals distinct host responses to intracellular and secreted protein products expressed by recombinant baculoviruses. J Biotechnol 2018; 270:61-69. [PMID: 29432775 DOI: 10.1016/j.jbiotec.2018.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 01/12/2018] [Accepted: 02/02/2018] [Indexed: 12/17/2022]
Abstract
The baculovirus insect cell expression system has become a firmly established production platform in biotechnology. Various complex proteins, multi-subunit particles including veterinary and human vaccines are manufactured with this system on a commercial scale. Apart from baculovirus infected Spodoptera frugiperda (Sf9) cells, the Trichoplusia ni (HighFive) cell line is alternatively used as host organism. In this study, we explored the protein production capabilities of Tnms42 insect cells, a new derivative of HighFive, which is free of latent nodavirus infection. As a model system, a cytosolic (mCherry) and a secreted (hemagglutinin) protein were overexpressed in Tnms42 cells. The response of the host cells was followed in a time course experiment over the infection cycle by comparative transcriptome analysis (RNA-seq). As expected, the baculovirus infection per se had a massive impact on the host cell transcriptome, which was observed by the huge total number of differentially expressed transcripts (>14,000). Despite this severe overall cellular reaction, a specific response could be clearly attributed to the overexpression of secreted hemagglutinin, revealing limits in the secretory capacity of the host cell. About 400 significantly regulated transcripts were identified and assigned to biochemical pathways and gene ontology (GO) categories, all related to protein processing, folding and response to unfolded protein. The identification of relevant target genes will serve to design specific virus engineering concepts for improving the yield of proteins that are dependent on the secretory pathway.
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Affiliation(s)
- Krisztina Koczka
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Philipp Peters
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Wolfgang Ernst
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Lisa Nika
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
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23
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Orellana CA, Marcellin E, Palfreyman RW, Munro TP, Gray PP, Nielsen LK. RNA-Seq Highlights High Clonal Variation in Monoclonal Antibody Producing CHO Cells. Biotechnol J 2018; 13:e1700231. [DOI: 10.1002/biot.201700231] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/12/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Camila A. Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland; Brisbane QLD 4072 Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland; Brisbane QLD 4072 Australia
- Metabolomics Australia (Queensland Node), The University of Queensland; Brisbane QLD 4072 Australia
| | - Robin W. Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland; Brisbane QLD 4072 Australia
| | - Trent P. Munro
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland; Brisbane QLD 4072 Australia
| | - Peter P. Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland; Brisbane QLD 4072 Australia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland; Brisbane QLD 4072 Australia
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; 2800 Kgs, Lyngby Denmark
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24
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Romanova N, Noll T. Engineered and Natural Promoters and Chromatin-Modifying Elements for Recombinant Protein Expression in CHO Cells. Biotechnol J 2017; 13:e1700232. [DOI: 10.1002/biot.201700232] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/07/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Nadiya Romanova
- Cell Culture Technology; Faculty of Technology; Bielefeld University; Germany
| | - Thomas Noll
- Cell Culture Technology; Faculty of Technology; Bielefeld University; Germany
- Bielefeld University; Center for Biotechnology (CeBiTec); Germany
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25
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Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN. Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome. FRONTIERS IN PLANT SCIENCE 2017; 8:1239. [PMID: 28775726 PMCID: PMC5517461 DOI: 10.3389/fpls.2017.01239] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/30/2017] [Indexed: 05/18/2023]
Abstract
Leaves of Arabidopsis thaliana transferred from low to high light increase their capacity for photosynthesis, a process of dynamic acclimation. A mutant, gpt2, lacking a chloroplast glucose-6-phosphate/phosphate translocator, is deficient in its ability to acclimate to increased light. Here, we have used a label-free proteomics approach, to perform relative quantitation of 1993 proteins from Arabidopsis wild type and gpt2 leaves exposed to increased light. Data are available via ProteomeXchange with identifier PXD006598. Acclimation to light is shown to involve increases in electron transport and carbon metabolism but no change in the abundance of photosynthetic reaction centers. The gpt2 mutant shows a similar increase in total protein content to wild type but differences in the extent of change of certain proteins, including in the relative abundance of the cytochrome b6f complex and plastocyanin, the thylakoid ATPase and selected Benson-Calvin cycle enzymes. Changes in leaf metabolite content as plants acclimate can be explained by changes in the abundance of enzymes involved in metabolism, which were reduced in gpt2 in some cases. Plants of gpt2 invest more in stress-related proteins, suggesting that their reduced ability to acclimate photosynthetic capacity results in increased stress.
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Affiliation(s)
- Matthew A. E. Miller
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
| | - Ronan O’Cualain
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Julian Selley
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - David Knight
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Mohd F. Karim
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
| | - Simon J. Hubbard
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Giles N. Johnson
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
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26
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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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27
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Dahodwala H, Sharfstein ST. The 'Omics Revolution in CHO Biology: Roadmap to Improved CHO Productivity. Methods Mol Biol 2017; 1603:153-168. [PMID: 28493129 DOI: 10.1007/978-1-4939-6972-2_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Increased understanding of Chinese hamster ovary (CHO) cell physiology has been ushered in upon availability of the parental CHO-K1 cell line genome. Free and openly accessible sequence information has complemented transcriptomic and proteomic studies. The previous decade has also seen an increase in sensitivity and accuracy of proteomic methods due to technology development. In this genomic era, high-throughput screening methods, sophisticated informatic tools, and models continually drive major innovations in cell line development and process engineering. This review describes the various achievements in 'omics techniques and their application to improve recombinant protein expression from CHO cell lines.
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Affiliation(s)
- Hussain Dahodwala
- Vaccine production program (VPP), VRC/NIAID/NIH, Gaithersburg, MD, 20878, USA
- SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY, 12203, USA
| | - Susan T Sharfstein
- Vaccine production program (VPP), VRC/NIAID/NIH, Gaithersburg, MD, 20878, USA.
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28
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Lee N, Shin J, Park JH, Lee GM, Cho S, Cho BK. Targeted Gene Deletion Using DNA-Free RNA-Guided Cas9 Nuclease Accelerates Adaptation of CHO Cells to Suspension Culture. ACS Synth Biol 2016; 5:1211-1219. [PMID: 26854539 DOI: 10.1021/acssynbio.5b00249] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chinese hamster ovary (CHO) cells are the preferred host for the production of a wide array of biopharmaceuticals. Thus, efficient and rational CHO cell line engineering methods have been in high demand to improve quality and productivity. Here, we provide a novel genome engineering platform for increasing desirable phenotypes of CHO cells based upon the integrative protocol of high-throughput RNA sequencing and DNA-free RNA-guided Cas9 (CRISPR associated protein9) nuclease-based genome editing. For commercial production of therapeutic proteins, CHO cells have been adapted for suspension culture in serum-free media, which is highly beneficial with respect to productivity and economics. To engineer CHO cells for rapid adaptation to a suspension culture, we exploited strand-specific RNA-seq to identify genes differentially expressed according to their adaptation trajectory in serum-free media. More than 180 million sequencing reads were generated and mapped to the currently available 109,152 scaffolds of the CHO-K1 genome. We identified significantly downregulated genes according to the adaptation trajectory and then verified their effects using the genome editing method. Growth-based screening and targeted amplicon sequencing revealed that the functional deletions of Igfbp4 and AqpI gene accelerate suspension adaptation of CHO-K1 cells. The availability of this strand-specific transcriptome sequencing and DNA-free RNA-guided Cas9 nuclease mediated genome editing facilitates the rational design of the CHO cell genome for efficient production of high quality therapeutic proteins.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - JongOh Shin
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Jin Hyoung Park
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
- Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea
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29
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Feichtinger J, Hernández I, Fischer C, Hanscho M, Auer N, Hackl M, Jadhav V, Baumann M, Krempl PM, Schmidl C, Farlik M, Schuster M, Merkel A, Sommer A, Heath S, Rico D, Bock C, Thallinger GG, Borth N. Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time. Biotechnol Bioeng 2016; 113:2241-53. [PMID: 27072894 PMCID: PMC5006888 DOI: 10.1002/bit.25990] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/15/2016] [Accepted: 04/07/2016] [Indexed: 01/03/2023]
Abstract
The most striking characteristic of CHO cells is their adaptability, which enables efficient production of proteins as well as growth under a variety of culture conditions, but also results in genomic and phenotypic instability. To investigate the relative contribution of genomic and epigenetic modifications towards phenotype evolution, comprehensive genome and epigenome data are presented for six related CHO cell lines, both in response to perturbations (different culture conditions and media as well as selection of a specific phenotype with increased transient productivity) and in steady state (prolonged time in culture under constant conditions). Clear transitions were observed in DNA‐methylation patterns upon each perturbation, while few changes occurred over time under constant conditions. Only minor DNA‐methylation changes were observed between exponential and stationary growth phase; however, throughout a batch culture the histone modification pattern underwent continuous adaptation. Variation in genome sequence between the six cell lines on the level of SNPs, InDels, and structural variants is high, both upon perturbation and under constant conditions over time. The here presented comprehensive resource may open the door to improved control and manipulation of gene expression during industrial bioprocesses based on epigenetic mechanisms. Biotechnol. Bioeng. 2016;113: 2241–2253. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Julia Feichtinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Inmaculada Hernández
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Christoph Fischer
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Michael Hanscho
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Norbert Auer
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Matthias Hackl
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Martina Baumann
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Peter M Krempl
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | | | - Andreas Sommer
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Simon Heath
- Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Daniel Rico
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Gerhard G Thallinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria. .,University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria.
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30
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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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31
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Jamnikar U, Nikolic P, Belic A, Blas M, Gaser D, Francky A, Laux H, Blejec A, Baebler S, Gruden K. Transcriptome study and identification of potential marker genes related to the stable expression of recombinant proteins in CHO clones. BMC Biotechnol 2015; 15:98. [PMID: 26499110 PMCID: PMC4812793 DOI: 10.1186/s12896-015-0218-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chinese hamster ovary (CHO) cells have become the host of choice for the production of recombinant proteins, due to their capacity for correct protein folding, assembly, and posttranslational modifications. The most widely used system for recombinant proteins is the gene amplification procedure that uses the CHO-Dhfr expression system. However, CHO cells are known to have a very unstable karyotype. This is due to chromosome rearrangements that can arise from translocations and homologous recombination, especially when cells with the CHO-Dhfr expression system are treated with methotrexate hydrate. The present method used in the industry for testing clones for their long-term stability of recombinant protein production is empirical, and it involves their cultivation over extended periods of time prior to the selection of the most suitable clone for further bioprocess development. The aim of the present study was the identification of marker genes that can predict stable expression of recombinant genes in particular clones early in the development stage. RESULTS The transcriptome profiles of CHO clones with stable and unstable recombinant protein production were investigated over 10-weeks of cultivation, using a DNA microarray. We identified 14 genes that were differentially expressed between the stable and unstable clones already at 2 weeks from the beginning of the cultivation. Their expression was validated by reverse-transcription quantitative real-time PCR (RT-qPCR). Furthermore, the k-nearest neighbour algorithm approach shows that the combination of the gene expression patterns of only five of these 14 genes is sufficient to predict stable recombinant protein production in clones in the early phases of cell-line development. CONCLUSIONS The exact molecular mechanisms that cause unstable recombinant protein production are not fully understood. However, the expression profiles of some genes in clones with stable and unstable recombinant protein production allow prediction of such instability early in the cell-line development stage. We have thus developed a proof-of-concept for a novel approach to eliminate unstable clones in the CHO-Dhfr expression system, which saves time and labour-intensive work in cell-line development.
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Affiliation(s)
- Uros Jamnikar
- Sandoz Biopharmaceuticals, Kolodvorska 27, SI-1234, Menges, Slovenia.
| | - Petra Nikolic
- Jozef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia.
| | - Ales Belic
- Sandoz Biopharmaceuticals, Kolodvorska 27, SI-1234, Menges, Slovenia.
| | - Marjanca Blas
- Sandoz Biopharmaceuticals, Kolodvorska 27, SI-1234, Menges, Slovenia.
| | - Dominik Gaser
- Sandoz Biopharmaceuticals, Kolodvorska 27, SI-1234, Menges, Slovenia.
| | - Andrej Francky
- Sandoz Biopharmaceuticals, Kolodvorska 27, SI-1234, Menges, Slovenia.
| | - Holger Laux
- Novartis Pharma AG, WKL-681.1.08, 4002, Basel, Switzerland.
| | - Andrej Blejec
- National Institute of Biology, Vecna pot 111, SI-1000, Ljubljana, Slovenia.
| | - Spela Baebler
- National Institute of Biology, Vecna pot 111, SI-1000, Ljubljana, Slovenia.
| | - Kristina Gruden
- National Institute of Biology, Vecna pot 111, SI-1000, Ljubljana, Slovenia.
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32
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Harreither E, Hackl M, Pichler J, Shridhar S, Auer N, Łabaj PP, Scheideler M, Karbiener M, Grillari J, Kreil DP, Borth N. Microarray profiling of preselected CHO host cell subclones identifies gene expression patterns associated with increased production capacity. Biotechnol J 2015; 10:1625-38. [PMID: 26315449 DOI: 10.1002/biot.201400857] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 06/22/2015] [Accepted: 08/21/2015] [Indexed: 01/02/2023]
Abstract
Over the last three decades, product yields from CHO cells have increased dramatically, yet specific productivity (qP) remains a limiting factor. In a previous study, using repeated cell-sorting, we have established different host cell subclones that show superior transient qP over their respective parental cell lines (CHO-K1, CHO-S). The transcriptome of the resulting six cell lines in different biological states (untransfected, mock transfected, plasmid transfected) was first explored by hierarchical clustering and indicated that gene activity associated with increased qP did not stem from a certain cellular state but seemed to be inherent for a high qP host line. We then performed a novel gene regression analysis identifying drivers for an increase in qP. Genes significantly implicated were first systematically tested for enrichment of GO terms using a Bayesian approach incorporating the hierarchical structure of the GO term tree. Results indicated that specific cellular components such as nucleus, ER, and Golgi are relevant for cellular productivity. This was complemented by targeted GSA that tested functionally homogeneous, manually curated subsets of KEGG pathways known to be involved in transcription, translation, and protein processing. Significantly implicated pathways included mRNA surveillance, proteasome, protein processing in the ER and SNARE interactions in vesicular transport.
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Affiliation(s)
- Eva Harreither
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Matthias Hackl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Pichler
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Smriti Shridhar
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Paweł P Łabaj
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marcel Scheideler
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Michael Karbiener
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - David P Kreil
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria. .,ACIB GmbH, Graz, Austria.
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33
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Fomina-Yadlin D, Mujacic M, Maggiora K, Quesnell G, Saleem R, McGrew JT. Transcriptome analysis of a CHO cell line expressing a recombinant therapeutic protein treated with inducers of protein expression. J Biotechnol 2015; 212:106-15. [PMID: 26325199 DOI: 10.1016/j.jbiotec.2015.08.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/23/2015] [Accepted: 08/26/2015] [Indexed: 11/17/2022]
Abstract
The search for specific productivity (qP) determinants in Chinese hamster ovary (CHO) cells has been the focus of the biopharmaceutical cell line engineering efforts aimed at creating "super-producer" cell lines. In this study, we evaluated the impact of small-molecule inducers and temperature shift on recombinant protein production, and used transcriptomic analysis to define gene-phenotype correlations for qP in our biological system. Next-generation RNA Sequencing (RNA-Seq) analysis revealed that each individual inducer (caffeine, hexamethylene bisacetamide (HMBA) and sodium butyrate (NaBu)) or a combination treatment had a distinct impact on the gene expression program of the RANK-Fc cell line. Temperature shift to 31 °C impacted inducer action with respect to transcriptional changes and phenotypic cell line parameters. We showed that inducer treatment was able to increase expression level of the Fc- fusion mRNA and the selectable marker mRNA from 16% up to 45% of total mRNA in the cell. We further demonstrated that qP exhibited a strong positive linear correlation to transcript levels of both the RANK-Fc fusion protein and the dihydrofolate reductase (DHFR) selectable marker. In fact, these were 2 out of 7 transcripts with significant positive correlation to qP at both temperatures. Many more transcripts were anti- correlated to qP, and gene set enrichment analysis (GSEA) revealed that those were involved in cell cycle progression, transcription, mRNA processing, translation and protein folding. Therefore, we postulate that the transcript level of the recombinant protein is a major qP determinant in our biological system, while downregulation of routine activity within the cell is necessary to divert cellular resources towards recombinant protein production.
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Affiliation(s)
- Dina Fomina-Yadlin
- Drug Substance Development, Amgen Inc., Seattle, WA 98119, United States
| | - Mirna Mujacic
- Drug Substance Development, Amgen Inc., Seattle, WA 98119, United States
| | - Kathy Maggiora
- Drug Substance Development, Amgen Inc., Seattle, WA 98119, United States
| | - Garrett Quesnell
- Drug Substance Development, Amgen Inc., Seattle, WA 98119, United States
| | - Ramsey Saleem
- Drug Substance Development, Amgen Inc., Seattle, WA 98119, United States
| | - Jeffrey T McGrew
- Drug Substance Development, Amgen Inc., Seattle, WA 98119, United States.
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34
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35
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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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36
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Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T. The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells. J Biotechnol 2015; 199:38-46. [DOI: 10.1016/j.jbiotec.2015.02.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/09/2015] [Accepted: 02/11/2015] [Indexed: 12/14/2022]
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37
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Orellana CA, Marcellin E, Schulz BL, Nouwens AS, Gray PP, Nielsen LK. High-Antibody-Producing Chinese Hamster Ovary Cells Up-Regulate Intracellular Protein Transport and Glutathione Synthesis. J Proteome Res 2015; 14:609-18. [DOI: 10.1021/pr501027c] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Camila A. Orellana
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Esteban Marcellin
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Benjamin L. Schulz
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Amanda S. Nouwens
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter P. Gray
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Lars K. Nielsen
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
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38
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Vishwanathan N, Le H, Le T, Hu WS. Advancing biopharmaceutical process science through transcriptome analysis. Curr Opin Biotechnol 2014; 30:113-9. [DOI: 10.1016/j.copbio.2014.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/13/2014] [Accepted: 06/13/2014] [Indexed: 01/02/2023]
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39
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Qian Y, Xing Z, Lee S, Mackin NA, He A, Kayne PS, He Q, Qian NX, Li ZJ. Hypoxia influences protein transport and epigenetic repression of CHO cell cultures in shake flasks. Biotechnol J 2014; 9:1413-24. [DOI: 10.1002/biot.201400315] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 09/15/2014] [Accepted: 09/29/2014] [Indexed: 11/08/2022]
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40
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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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41
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Statistical methods for mining Chinese hamster ovary cell ‘omics data: from differential expression to integrated multilevel analysis of the biological system. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.50] [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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42
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Gene expression measurements normalized to cell number reveal large scale differences due to cell size changes, transcriptional amplification and transcriptional repression in CHO cells. J Biotechnol 2014; 189:58-69. [PMID: 25194670 DOI: 10.1016/j.jbiotec.2014.08.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/18/2014] [Accepted: 08/25/2014] [Indexed: 01/20/2023]
Abstract
Conventional approaches to differential gene expression comparisons assume equal cellular RNA content among experimental conditions. We demonstrate that this assumption should not be universally applied because total RNA yield from a set number of cells varies among experimental treatments of the same Chinese Hamster Ovary (CHO) cell line and among different CHO cell lines expressing recombinant proteins. Conventional normalization strategies mask these differences in cellular RNA content and, consequently, skew biological interpretation of differential expression results. On the contrary, normalization to synthetic spike-in RNA standards added proportional to cell numbers reveals these differences and allows detection of global transcriptional amplification/repression. We apply this normalization method to assess differential gene expression in cell lines of different sizes, as well as cells treated with a cell cycle inhibitor (CCI), an mTOR inhibitor (mTORI), or subjected to high osmolarity conditions. CCI treatment of CHO cells results in a cellular volume increase and global transcriptional amplification, while mTORI treatment causes global transcriptional repression without affecting cellular volume. Similarly to CCI treatment, high osmolarity increases cell size, total RNA content and antibody expression. Furthermore, we show the importance of spike-in normalization for studies involving multiple CHO cell lines and advocate normalization to spike-in controls prior to correlating gene expression to specific productivity (qP). Overall, our data support the need for cell number specific spike-in controls for all gene expression studies where cellular RNA content differs among experimental conditions.
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43
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Xia C, Wang YJ, Liang Y, Niu QK, Tan XY, Chu LC, Chen LQ, Zhang XQ, Ye D. The ARID-HMG DNA-binding protein AtHMGB15 is required for pollen tube growth in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:741-56. [PMID: 24923357 DOI: 10.1111/tpj.12582] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 05/25/2014] [Accepted: 05/28/2014] [Indexed: 05/22/2023]
Abstract
In flowering plants, male gametes (sperm cells) develop within male gametophytes (pollen grains) and are delivered to female gametes for double fertilization by pollen tubes. Therefore, pollen tube growth is crucial for reproduction. The mechanisms that control pollen tube growth remain poorly understood. In this study, we demonstrated that the ARID-HMG DNA-binding protein AtHMGB15 plays an important role in pollen tube growth. This protein is preferentially expressed in pollen grains and pollen tubes and is localized in the vegetative nuclei of the tricellular pollen grains and pollen tubes. Knocking down AtHMGB15 expression via a Ds insertion caused retarded pollen tube growth, leading to a significant reduction in the seed set. The athmgb15-1 mutation affected the expression of 1686 genes in mature pollen, including those involved in cell wall formation and modification, cell signaling and cellular transport during pollen tube growth. In addition, it was observed that AtHMGB15 binds to DNA in vitro and interacts with the transcription factors AGL66 and AGL104, which are required for pollen maturation and pollen tube growth. These results suggest that AtHMGB15 functions in pollen tube growth through the regulation of gene expression.
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Affiliation(s)
- Chuan Xia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China; Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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44
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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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Hernández Bort JA, Shanmukam V, Pabst M, Windwarder M, Neumann L, Alchalabi A, Krebiehl G, Koellensperger G, Hann S, Sonntag D, Altmann F, Heel C, Borth N. Reduced quenching and extraction time for mammalian cells using filtration and syringe extraction. J Biotechnol 2014; 182-183:97-103. [PMID: 24794799 PMCID: PMC4071440 DOI: 10.1016/j.jbiotec.2014.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 04/08/2014] [Accepted: 04/11/2014] [Indexed: 10/30/2022]
Abstract
In order to preserve the in vivo metabolite levels of cells, a quenching protocol must be quickly executed to avoid degradation of labile metabolites either chemically or biologically. In the case of mammalian cell cultures cultivated in complex media, a wash step previous to quenching is necessary to avoid contamination of the cell pellet with extracellular metabolites, which could distort the real intracellular concentration of metabolites. This is typically achieved either by one or multiple centrifugation/wash steps which delay the time until quenching (even harsh centrifugation requires several minutes for processing until the cells are quenched) or filtration. In this article, we describe and evaluate a two-step optimized protocol based on fast filtration by use of a vacuum pump for quenching and subsequent extraction of intracellular metabolites from CHO (Chinese hamster ovary) suspension cells, which uses commercially available components. The method allows transfer of washed cells into liquid nitrogen within 10-15s of sampling and recovers the entire extraction solution volume. It also has the advantage to remove residual filter filaments in the final sample, thus preventing damage to separation columns during subsequent MS analysis. Relative to other methods currently used in the literature, the resulting energy charge of intracellular adenosine nucleotides was increased to 0.94 compared to 0.90 with cold PBS quenching or 0.82 with cold methanol/AMBIC quenching.
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Affiliation(s)
| | - Vinoth Shanmukam
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Martin Pabst
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Windwarder
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Laura Neumann
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | | | - Gunda Koellensperger
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Hann
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Friedrich Altmann
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Nicole Borth
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
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Ghorbaniaghdam A, Chen J, Henry O, Jolicoeur M. Analyzing clonal variation of monoclonal antibody-producing CHO cell lines using an in silico metabolomic platform. PLoS One 2014; 9:e90832. [PMID: 24632968 PMCID: PMC3954614 DOI: 10.1371/journal.pone.0090832] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/04/2014] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibody producing Chinese hamster ovary (CHO) cells have been shown to undergo metabolic changes when engineered to produce high titers of recombinant proteins. In this work, we have studied the distinct metabolism of CHO cell clones harboring an efficient inducible expression system, based on the cumate gene switch, and displaying different expression levels, high and low productivities, compared to that of the parental cells from which they were derived. A kinetic model for CHO cell metabolism was further developed to include metabolic regulation. Model calibration was performed using intracellular and extracellular metabolite profiles obtained from shake flask batch cultures. Model simulations of intracellular fluxes and ratios known as biomarkers revealed significant changes correlated with clonal variation but not to the recombinant protein expression level. Metabolic flux distribution mostly differs in the reactions involving pyruvate metabolism, with an increased net flux of pyruvate into the tricarboxylic acid (TCA) cycle in the high-producer clone, either being induced or non-induced with cumate. More specifically, CHO cell metabolism in this clone was characterized by an efficient utilization of glucose and a high pyruvate dehydrogenase flux. Moreover, the high-producer clone shows a high rate of anaplerosis from pyruvate to oxaloacetate, through pyruvate carboxylase and from glutamate to α-ketoglutarate, through glutamate dehydrogenase, and a reduced rate of cataplerosis from malate to pyruvate, through malic enzyme. Indeed, the increase of flux through pyruvate carboxylase was not driven by an increased anabolic demand. It is in fact linked to an increase of the TCA cycle global flux, which allows better regulation of higher redox and more efficient metabolic states. To the best of our knowledge, this is the first time a dynamic in silico platform is proposed to analyze and compare the metabolomic behavior of different CHO clones.
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Affiliation(s)
- Atefeh Ghorbaniaghdam
- Canada Research Chair in Applied Metabolic Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Jingkui Chen
- Canada Research Chair in Applied Metabolic Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Olivier Henry
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Mario Jolicoeur
- Canada Research Chair in Applied Metabolic Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
- * E-mail:
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47
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Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). J Biotechnol 2014; 178:23-31. [PMID: 24613301 DOI: 10.1016/j.jbiotec.2014.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/07/2014] [Accepted: 02/25/2014] [Indexed: 11/24/2022]
Abstract
The increasing importance of Chinese hamster ovary (CHO) cells for the production of pharmaceutical proteins has awakened the demand to understand the cellular metabolism of these cells. However, satisfactory gene expression studies have yet been impractical due to insufficient coverage of sequences. In this work, previously determined sequence information of CHO cells and newly derived data from 454 and Illumina sequencing was used to establish the CHO41K microarray which contains 41,304 probes. Self-hybridisation was performed for replica determination and samples were run in triplicates to increase statistical power. For determination of technical variance, confidence intervals at an M-value of ±0.6 for 95% and at ±2.3 for 99% of the probes were calculated. Intra-microarray and slide to slide variance was not detectable. In a first application, this microarray enabled an in-depth look inside the cellular transcriptome of CHO cells cultured in the presence or absence of the growth supporting substance "insulin like growth factor 1" (IGF-1) analogue LongR(3). Its effect on the cells ranged from enhanced growth to delay of cell death as well as cytoskeletal installation. Suggesting that under supplementation, a minimised cellular effort in installation of a large cytoskeleton occurs, possibly in favour of promoting faster cell division.
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48
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Dynamics of unfolded protein response in recombinant CHO cells. Cytotechnology 2014; 67:237-54. [PMID: 24504562 DOI: 10.1007/s10616-013-9678-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 12/14/2013] [Indexed: 10/25/2022] Open
Abstract
Genes in the protein secretion pathway have been targeted to increase productivity of monoclonal antibodies in Chinese hamster ovary cells. The results have been highly variable depending on the cell type and the relative amount of recombinant and target proteins. This paper presents a comprehensive study encompassing major components of the protein processing pathway in the endoplasmic reticulum (ER) to elucidate its role in recombinant cells. mRNA profiles of all major ER chaperones and unfolded protein response (UPR) pathway genes are measured at a series of time points in a high-producing cell line under the dynamic environment of a batch culture. An initial increase in IgG heavy chain mRNA levels correlates with an increase in productivity. We observe a parallel increase in the expression levels of majority of chaperones. The chaperone levels continue to increase until the end of the batch culture. In contrast, calreticulin and ERO1-L alpha, two of the lowest expressed genes exhibit transient time profiles, with peak induction on day 3. In response to increased ER stress, both the GCN2/PKR-like ER kinase and inositol-requiring enzyme-1alpha (Ire1α) signalling branch of the UPR are upregulated. Interestingly, spliced X-Box binding protein 1 (XBP1s) transcription factor from Ire1α pathway is detected from the beginning of the batch culture. Comparison with the expression levels in a low producer, show much lower induction at the end of the exponential growth phase. Thus, the unfolded protein response strongly correlates with the magnitude and timing of stress in the course of the batch culture.
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49
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Lee SM, Kim YG, Lee EG, Lee GM. Digital mRNA profiling of N-glycosylation gene expression in recombinant Chinese hamster ovary cells treated with sodium butyrate. J Biotechnol 2014; 171:56-60. [DOI: 10.1016/j.jbiotec.2013.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/18/2022]
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50
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Nishimiya D. Proteins improving recombinant antibody production in mammalian cells. Appl Microbiol Biotechnol 2013; 98:1031-42. [PMID: 24327213 DOI: 10.1007/s00253-013-5427-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 12/13/2022]
Abstract
Mammalian cells have been successfully used for the industrial manufacture of antibodies due to their ability to synthesize antibodies correctly. Nascent polypeptides must be subjected to protein folding and assembly in the ER and the Golgi to be secreted as mature proteins. If these reactions do not proceed appropriately, unfolded or misfolded proteins are degraded by the ER-associated degradation (ERAD) pathway. The accumulation of unfolded proteins or intracellular antibody crystals accompanied by this failure triggers the unfolded protein response (UPR), which can considerably attenuate the levels of translation, folding, assembly, and secretion, resulting in reduction of antibody productivity. Accumulating studies by omics-based analysis of recombinant mammalian cells suggest that not only protein secretion processes including protein folding and assembly but also translation are likely to be the rate-limiting factors for increasing antibody production. Here, this review describes the mechanism of antibody folding and assembly and recent advantages which could improve recombinant antibody production in mammalian cells by utilizing proteins such as ER chaperones or UPR-related proteins.
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Affiliation(s)
- Daisuke Nishimiya
- New Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan,
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