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Nguyen M, Zimmer A. A reflection on the improvement of Chinese Hamster ovary cell-based bioprocesses through advances in proteomic techniques. Biotechnol Adv 2023; 65:108141. [PMID: 37001570 DOI: 10.1016/j.biotechadv.2023.108141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Chinese hamster ovary (CHO) cells are the preferred mammalian host for the large-scale production of recombinant proteins in the biopharmaceutical industry. Research endeavors have been directed to the optimization of CHO-based bioprocesses to increase protein quantity and quality, often in an empirical manner. To provide a rationale for those achievements, a myriad of CHO proteomic studies has arisen in recent decades. This review gives an overview of significant advances in LC-MS-based proteomics and sheds light on CHO proteomic studies, with a particular focus on CHO cells with superior bioprocessing phenotypes (growth, viability, titer, productivity and cQA), that have exploited novel proteomic or sub-omic techniques. These proteomic findings expand the current knowledge and understanding about the underlying protein clusters, protein regulatory networks and biological pathways governing such phenotypic changes. The proteomic studies, highlighted herein, will help in the targeted modulation of these cell factories to the desired needs.
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2
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Morrell BC, Perego MC, Maylem ERS, Zhang L, Schütz LF, Spicer LJ. Regulation of the transcription factor E2F1 mRNA in ovarian granulosa cells of cattle. J Anim Sci 2020; 98:5674948. [PMID: 31832639 DOI: 10.1093/jas/skz376] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022] Open
Abstract
The E2F family of transcription factors plays an important role in the control of the cell cycle, cell proliferation, and differentiation, and their role in ovarian function is just emerging. Although some evidence suggests a possible role of E2F1 in ovarian follicular development, what regulates its production in ovarian cells is unknown. Objectives of this study were to determine whether: (i) E2F1 gene expression in granulosa cells (GCs) and theca cells (TCs) change with follicular development and (ii) E2F1 mRNA abundance in TC and GC is hormonally regulated. Using real-time PCR, E2F1 mRNA abundance in GC was 5.5-fold greater (P < 0.05) in small (SM; 1 to 5 mm) than large (LG; >8 mm) follicles, but in TC, E2F1 expression did not differ among follicle sizes. SM-follicle GC had 2.1-fold greater (P < 0.05) E2F1 mRNA than TC. In SM-follicle GC, FGF9 induced a 7.6-fold increase in E2F1 mRNA abundance; however, FGF9 did not affect (P > 0.10) abundance of E2F1 mRNA in LG-follicle TC or GC. Follicle-stimulating hormone (FSH) had no effect (P > 0.10) on E2F1 gene expression in SM- or LG-follicle GC. SM-follicle GC were concomitantly treated with insulin-like growth factor 1 (30 ng/mL), FSH (30 ng/mL), and either 0 or 30 ng/mL of FGF9 with or without 50 µM of an E2F inhibitor (E2Fi; HLM0064741); FGF9 alone increased (P < 0.05) GC numbers, whereas E2Fi alone decreased (P < 0.05) GC numbers, and concomitant treatment of E2Fi with FGF9 blocked (P < 0.05) this stimulatory effect of FGF9. Estradiol production was inhibited (P < 0.05) by FGF9 alone and concomitant treatment of E2Fi with FGF9 attenuated (P < 0.05) this inhibitory effect of FGF9. SM-follicle GC treated with E2Fi decreased (P < 0.05) E2F1 mRNA abundance by 70%. Collectively, our studies show that GC E2F1 mRNA is developmentally and hormonally regulated in cattle. Inhibition of E2F1 reduced FGF9-induced GC proliferation and attenuated FGF9-inhibited estradiol production, indicating that E2F1 may be involved in follicular development in cattle.
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Affiliation(s)
- Breanne C Morrell
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK
| | - M Chiara Perego
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK
| | - Excel Rio S Maylem
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK
| | - Lingna Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK
| | - Luis F Schütz
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK
| | - Leon J Spicer
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK
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3
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Gutiérrez-González M, Latorre Y, Zúñiga R, Aguillón JC, Molina MC, Altamirano C. Transcription factor engineering in CHO cells for recombinant protein production. Crit Rev Biotechnol 2019; 39:665-679. [PMID: 31030575 DOI: 10.1080/07388551.2019.1605496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The continuous increase of approved biopharmaceutical products drives the development of more efficient recombinant protein expression systems. Chinese hamster ovary (CHO) cells are the mainstay for this purpose but have some drawbacks, such as low levels of expression. Several strategies have been applied to increase the productivity of CHO cells with different outcomes. Transcription factor (TF) engineering has emerged as an interesting and successful approach, as these proteins can act as master regulators; the expression and function of a TF can be controlled by small molecules, and it is possible to design tailored TFs and promoters with desired features. To date, the majority of studies have focused on the use of TFs with growth, metabolic, cell cycle or endoplasmic reticulum functions, although there is a trend to develop new, synthetic TFs. Moreover, new synthetic biological approaches are showing promising advances for the development of specific TFs, even with tailored ligand sensitivity. In this article, we summarize the strategies to increase recombinant protein expression by modulating and designing TFs and with advancements in synthetic biology. We also illustrate how this class of proteins can be used to develop more robust expression systems.
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Affiliation(s)
| | - Yesenia Latorre
- b Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso , Valparaíso , Chile
| | - Roberto Zúñiga
- a Centro de InmunoBiotecnología, Universidad de Chile , Santiago , Chile
| | | | | | - Claudia Altamirano
- b Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso , Valparaíso , Chile
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4
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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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5
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Kluge S, Benndorf D, Genzel Y, Scharfenberg K, Rapp E, Reichl U. Monitoring changes in proteome during stepwise adaptation of a MDCK cell line from adherence to growth in suspension. Vaccine 2015; 33:4269-80. [DOI: 10.1016/j.vaccine.2015.02.077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/30/2015] [Accepted: 02/16/2015] [Indexed: 11/16/2022]
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6
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Yin M, Wang X, Yao G, Lü M, Liang M, Sun Y, Sun F. Transactivation of micrornA-320 by microRNA-383 regulates granulosa cell functions by targeting E2F1 and SF-1 proteins. J Biol Chem 2014; 289:18239-57. [PMID: 24828505 DOI: 10.1074/jbc.m113.546044] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Our previous studies have shown that microRNA-320 (miR-320) is one of the most down-regulated microRNAs (miRNA) in mouse ovarian granulosa cells (GCs) after TGF-β1 treatment. However, the underlying mechanisms of miR-320 involved in GC function during follicular development remain unknown. In this study, we found that pregnant mare serum gonadotropin treatment resulted in the suppression of miR-320 expression in a time-dependent manner. miR-320 was mainly expressed in GCs and oocytes of mouse ovarian follicles in follicular development. Overexpression of miR-320 inhibited estradiol synthesis and proliferation of GCs through targeting E2F1 and SF-1. E2F1/SF-1 mediated miR-320-induced suppression of GC proliferation and of GC steroidogenesis. FSH down-regulated the expression of miR-320 and regulated the function of miR-320 in mouse GCs. miR-383 promoted the expression of miR-320 and enhanced miR-320-mediated suppression of GC proliferation. Injection of miR-320 into the ovaries of mice partially promoted the production of testosterone and progesterone but inhibited estradiol release in vivo. Moreover, the expression of miR-320 and miR-383 was up-regulated in the follicular fluid of polycystic ovarian syndrome patients, although the expression of E2F1 and SF-1 was down-regulated in GCs. These data demonstrated that miR-320 regulates the proliferation and steroid production by targeting E2F1 and SF-1 in the follicular development. Understanding the regulation of miRNA biogenesis and function in the follicular development will potentiate the usefulness of miRNA in the treatment of reproduction and some steroid-related disorders.
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Affiliation(s)
- Mianmian Yin
- From the Institute of Immunology and Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, the Hefei National Laboratory for Physical Sciences at Microscale, Hefei, Anhui 230027, and
| | - Xiaorong Wang
- From the Institute of Immunology and Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, the Hefei National Laboratory for Physical Sciences at Microscale, Hefei, Anhui 230027, and
| | - Guidong Yao
- the Reproductive Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Mingrong Lü
- From the Institute of Immunology and Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, the Hefei National Laboratory for Physical Sciences at Microscale, Hefei, Anhui 230027, and
| | - Meng Liang
- From the Institute of Immunology and Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, the Hefei National Laboratory for Physical Sciences at Microscale, Hefei, Anhui 230027, and
| | - Yingpu Sun
- the Reproductive Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Fei Sun
- From the Institute of Immunology and Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, the Hefei National Laboratory for Physical Sciences at Microscale, Hefei, Anhui 230027, and
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7
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Kluge S, Rourou S, Vester D, Majoul S, Benndorf D, Genzel Y, Rapp E, Kallel H, Reichl U. Proteome analysis of virus-host cell interaction: rabies virus replication in Vero cells in two different media. Appl Microbiol Biotechnol 2013; 97:5493-506. [PMID: 23674149 DOI: 10.1007/s00253-013-4939-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 01/08/2023]
Abstract
The use of Vero cells for rabies vaccine production was recommended from the WHO in 2005. A controlled production process is necessary to reduce the risk of contaminants in the product. One step towards this is to turn away from animal-derived components (e.g. serum, trypsin, bovine serum albumin) and face a production process in animal component-free medium. In this study, a proteomic approach was applied, using 2-D differential gel electrophoresis and mass spectrometry to compare rabies virus propagation in Vero cells under different cultivation conditions in microcarrier culture. Protein alterations were investigated for uninfected and infected Vero cells over a time span from 1 to 8 days post-infection in two different types of media (serum-free versus serum-containing media). For mock-infected cells, proteins involved in stress response, redox status, protease activity or glycolysis, and protein components in the endoplasmic reticulum were found to be differentially expressed comparing both cultivation media at all sampling points. For virus-infected cells, additionally changes in protein expression involved in general cell regulation and in calcium homeostasis were identified under both cultivation conditions. The fact that neither of these additional proteins was identified for cells during mock infection, but similar protein expression changes were found for both systems during virus propagation, indicates for a specific response of the Vero cell proteome on rabies virus infection.
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Affiliation(s)
- Sabine Kluge
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
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8
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Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS. Inverse metabolic engineering: A strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 2012; 52:109-21. [PMID: 18629857 DOI: 10.1002/(sici)1097-0290(19961005)52:1<109::aid-bit11>3.0.co;2-j] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The classical method of metabolic engineering, identifying a rate-determining step in a pathway and alleviating the bottleneck by enzyme overexpression, has motivated much research but has enjoyed only limited practical success. Intervention of other limiting steps, of counterbalancing regulation, and of unknown coupled pathways often confounds this direct approach. Here the concept of inverse metabolic engineering is codified and its application is illustrated with several examples. Inverse metabolic engineering means the elucidation of a metabolic engineering strategy by: first, identifying, constructing, or calculating a desired phenotype; second, determining the genetic or the particular environmental factors conferring that phenotype; and third, endowing that phenotype on another strain or organism by directed genetic or environmental manipulation. This paradigm has been successfully applied in several contexts, including elimination of growth factor requirements in mammalian cell culture and increasing the energetic efficiency of microaerobic bacterial respiration. (c) 1996 John Wiley & Sons, Inc.
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Affiliation(s)
- J E Bailey
- Institute of Biotechnology, ETH Zürich, CH-8093 Zürich, Switzerland
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9
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Cruz HJ, Moreira JL, Stacey G, Dias EM, Hayes K, Looby D, Griffiths B, Carrondo MJ. Adaptation of BHK cells producing a recombinant protein to serum-free media and protein-free medium. Cytotechnology 2012; 26:59-64. [PMID: 22359007 DOI: 10.1023/a:1007951813755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this work a recombinant BHK21 clone producing a fusion protein with potential application in tumour target therapy was adapted to five different serum-free media (SFM) and to a protein-free medium (PFM). Only the PFM did not require a gradual adaptation to cell growth in the absence of serum. All tested SFM required a gradual adaptation (up to 35 days). For the majority of the SFM tested, cell specific productivity was not affected by the decrease in serum concentration during adaptation; however, cell growth was significantly affected by the serum decrease. Both cell growth and productivity were increased when PFM SMIF6 was used instead of the control medium. Long term measurements (approximately 100 days) of cell specific productivity for PFM and the two best SFM showed that productivity was maintained. This indicates the media capability to be used in long term production processes.
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Affiliation(s)
- H J Cruz
- IBET/ITQB -, Instituto de Biologia Experimental e Tecnológica/Instituto de Tecnologia Química e Biológica, Apartado 12, P-2780, Oeiras, Portugal
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10
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Fassnacht D, Rössing S, Franěk F, Al-Rubeai M, Pörtner R. Effect of bcl-2 expression on hybridoma cell growth in serum-supplemented, protein-free and diluted media. Cytotechnology 2012; 26:219-25. [PMID: 22358618 DOI: 10.1023/a:1007914619219] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two transfected hybridoma cell lines TB/C3-bcl2 (overexpressing the Bcl-2 protein) and TB/C3-pEF (control cell line), were compared in batch suspension cultures using a medium supplemented either with horse serum or with a protein-free, iron-rich supplement. The membrane intact index (percentage of cells with intact membranes determined by trypan blue staining) of the TB/C3-bcl2 cell line decreased much slower than that of the control cell line during the dying phase of the cultures. No significant difference in antibody, lactate and ammonia production as well as glucose and glutamine consumption was noted in the exponential phase of the experiments. Both cell lines were also compared in batch experiments using media diluted with saline to further investigate the effect of Bcl-2 under sub-optimal conditions. The Bcl-2 overexpressing cell line again exhibited a higher membrane intact index at increasing dilution steps.
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Affiliation(s)
- D Fassnacht
- Technische Universität Hamburg-Harburg, Bioprozeß- und Bioverfahrenstechnik, Denickestrasse 15, D-21071, Hamburg, Germany
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11
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CHO cells in biotechnology for production of recombinant proteins: current state and further potential. Appl Microbiol Biotechnol 2011; 93:917-30. [PMID: 22159888 DOI: 10.1007/s00253-011-3758-5] [Citation(s) in RCA: 505] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 10/14/2022]
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12
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Fussenegger M, Moser S, Bailey JE. Regulated multicistronic expression technology for mammalian metabolic engineering. Cytotechnology 2011; 28:111-26. [PMID: 19003413 PMCID: PMC3449837 DOI: 10.1023/a:1008037916674] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Contemporary basic research is rapidly revealing increasingly complex molecular regulatory networks which are often interconnected via key signal integrators. These connections among regulatory and catalytic networks often frustrate bioengineers as promising metabolic engineering strategies are bypassed by compensatory metabolic responses or cause unexpected, undesired outcomes such as apoptosis, product protein degradation or inappropriate post- translational modification. Therefore, for metabolic engineering to achieve greater success in mammalian cell culture processes and to become important for future applications such as gene therapy and tissue engineering, this technology must be enhanced to allow simultaneous, in cases conditional, reshaping of metabolic pathways to access difficult-to-attain cell states. Recent advances in this new territory of multigene metabolic engineering are intimately linked to the development of multicistronic expression technology which allows the simultaneous, and in some cases, regulated expression of several genes in mammalian cells. Here we review recent achievements in multicistronic expression technology in view of multigene metabolic engineering.
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Affiliation(s)
- M Fussenegger
- Swiss Federal Institute of Technology, ETH Zurich, Institute of Biotechnology, CH-8093, Zurich, Switzerland
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13
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Chun BH, Bang WG, Park YK, Woo SK. Stable expression of recombinant human coagulation factor XIII in protein-free suspension culture of Chinese hamster ovary cells. Cytotechnology 2008; 37:179-87. [PMID: 19002921 DOI: 10.1023/a:1020555918441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The recombinant a and bsubunits for human coagulation factor XIII were transfected into Chinese hamster ovary (CHO) cells. CHO cells were amplified and selected with methotrexate in adherent cultures containing serum, and CHO 1-62 cells were later selected in protein-free medium. To develop a recombinant factor XIII production process in a suspension culture, we have investigated the growth characteristics of CHO cells and the maintenance of factor XIII expression in the culture medium. Suspension adaptation of CHO cells was performed in protein-free medium, GC-CHO-PI, by two methods, such as serum weaning and direct switching from serum containing media to protein-free media. Although the growth of CHO cells in suspension culture was affected initially by serum depletion, cell specific productivity of factor XIII showed only minor changes by the direct switching to protein-free medium during a suspension culture. As for the long-term stability of factor XIII, CHO 1-62 cells showed a stable expression of factor XIII in protein-free condition for 1000 h. These results indicate that the CHO 1-62cells can be adapted to express recombinant human factor XIII in a stable maimer in suspension culture using a protein-free medium. Our results demonstrate that enhanced cell growth in a continuous manner is achievable for factor XIII production in a protein-free medium when a perfusion bioreactor culture system with a spin filter is employed.
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Affiliation(s)
- B H Chun
- Korea Green Cross Corp, 227 Kugal-Ri, Keeheung-Eup, 449-900, Yongin, Korea
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14
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E2F-1 overexpression increases viable cell density in batch cultures of Chinese hamster ovary cells. J Biotechnol 2008; 138:103-6. [DOI: 10.1016/j.jbiotec.2008.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2008] [Revised: 08/04/2008] [Accepted: 08/11/2008] [Indexed: 12/17/2022]
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15
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Jaluria P, Konstantopoulos K, Betenbaugh M, Shiloach J. Egr1 and Gas6 facilitate the adaptation of HEK-293 cells to serum-free media by conferring enhanced viability and higher growth rates. Biotechnol Bioeng 2008; 99:1443-52. [PMID: 18023050 DOI: 10.1002/bit.21707] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Animal-derived serum is an essential media supplement for mammalian cells in cell culture. For a number of reasons including cost, regulatory concerns, lot inconsistency, potential contamination with adventitious agents, and down-stream processing it is desirable to eliminate the use of serum. Existing protocols designed to adapt cells to serum-free media (SFM) are time-consuming and provide little insight into how the cells adapt. To better understand the physiological responses associated with serum withdrawal and to expedite the adaptation process, a Human Embryonic Kidney-293 (HEK-293) cell line was propagated in 10% fetal bovine serum (FBS) and was progressively adapted to SFM and analyzed at specific serum levels by oligonucleotide microarrays. Of the differentially expressed genes two, early growth response 1 (egr1) and growth arrest specific 6 (gas6), were selected for further analysis based on their level of differential expression, overall expression patterns, and proposed functionalities. HEK-293 cells, propagated in 10% FBS were transfected with egr1 or gas6 and then adapted to SFM. Results indicated that higher expression of either gene moderately enhanced the ability of both cell lines to adapt to SFM. Egr1 appeared to have a greater impact on adaptability than gas6. Results also indicated that specific protein production was unaltered when the expression of egr1 was increased. Flow cytometric analysis revealed increased expression of egr1 was associated with an increase in the percentage of cells in the G2/M phases. These results indicate that enhanced expression of egr1 or gas6 facilitate adaptation to SFM by improving growth and viability.
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Affiliation(s)
- Pratik Jaluria
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Biotechnology Unit, Building 14A, Room 173, Bethesda, Maryland 20892, USA
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16
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Gupta P, Lee KH. Genomics and proteomics in process development: opportunities and challenges. Trends Biotechnol 2007; 25:324-30. [PMID: 17475353 DOI: 10.1016/j.tibtech.2007.04.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 03/19/2007] [Accepted: 04/19/2007] [Indexed: 02/05/2023]
Abstract
Global gene expression profiling by genomic and proteomic analyses has changed the face of drug discovery and biological research in the past few years. The benefit of these technologies in the area of process development for recombinant protein production has been increasingly realized. This review discusses the application of genome-wide expression profiling tools in the design and optimization of bioprocesses, with the emphasis on the effect on process development of mammalian cell culture. Despite the lack of genome sequence information for most of the relevant mammalian cell lines used, these technologies can be applied during various process development steps. Although there are only a few examples in the literature that present a major improvement in productivity based on genomics and proteomics, further advances in analytical tools and genome sequencing technologies will greatly increase our knowledge at the molecular level and will drive the design of future bioprocesses.
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Affiliation(s)
- Prateek Gupta
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853, USA
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17
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Kuystermans D, Krampe B, Swiderek H, Al-Rubeai M. Using cell engineering and omic tools for the improvement of cell culture processes. Cytotechnology 2007; 53:3-22. [PMID: 19003186 DOI: 10.1007/s10616-007-9055-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 01/25/2007] [Indexed: 12/26/2022] Open
Abstract
Significant strides have been made in mammalian cell based biopharmaceutical process and cell line development over the past years. With several established mammalian host cell lines and expression systems, optimization of selection systems to reduce development times and improvement of glycosylation patterns are only some of the advances being made to improve cell culture processes. In this article, the advances pertaining to cell line development and cell engineering strategies are discussed. An overview of the cell engineering strategies to enhance cellular characteristics by genetic manipulation are illustrated, focusing on the use of genomics and proteomics tools and their application in such endeavors. Included in this review are some of the early studies using the 'omic' technique to understand cellular mechanisms of product synthesis and secretion, apoptosis, cell proliferation and the influence of the physicochemical environment. The article highlights the significance of integrating genomics and proteomics data with the vast amounts of bioprocess data for improved analysis of the biological pathways involved. Further improvements of the techniques and methodologies used are needed but ultimately, the new cell engineering strategies should provide great insight into the regulatory networks within the cell in a bioprocess environment and how to manipulate them to increase overall productivity.
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Affiliation(s)
- Darrin Kuystermans
- School of Chemical and Bioprocess Engineering and Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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18
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Pascoe DE, Arnott D, Papoutsakis ET, Miller WM, Andersen DC. Proteome analysis of antibody-producing CHO cell lines with different metabolic profiles. Biotechnol Bioeng 2007; 98:391-410. [PMID: 17461427 DOI: 10.1002/bit.21460] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Two-dimensional gel electrophoresis and tandem mass spectrometry were used to identify proteins associated with a metabolic shift during fed-batch cultures of two recombinant antibody-producing CHO cell lines. The first cell line underwent a marked change in lactate metabolism during culture, initially producing lactate and then consuming it, while the second cell line produced lactate for a similar duration but did not later consume it. The first cell line displayed a declining specific antibody productivity during culture, correlating to the 2-D gel results and the intracellular antibody concentration determined by HPLC. Several statistical analysis methods were compared during this work, including a fixed fold-change criterion and t-tests using standard deviations determined in several ways from the raw data and mathematically transformed data. Application of a variance-stabilizing transformation enabled the use of a global empirical standard deviation in the t-tests. Most of the protein spots changing in each cell line did not change significantly in the other cell line. A substantial fraction of the changing proteins were glycolytic enzymes; others included proteins related to antibody production, protein processing, and cell structure. Enolase, pyruvate kinase, BiP/GRP78, and protein disulfide isomerase were found in spots that changed over time in both cell lines, and some protein changes differed from previous reports. These data provide a foundation for future investigation of metabolism in industrially relevant mammalian cell culture processes, and suggest that along with differences between cell types, the proteins expressed in cultures with low lactate concentrations may depend on how those conditions were generated.
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Affiliation(s)
- Deborah E Pascoe
- Bioprocess Development, Genentech, Inc., One DNA Way, South San Francisco, California 94080, USA
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Schröder M, Matischak K, Friedl P. Serum- and protein-free media formulations for the Chinese hamster ovary cell line DUKXB11. J Biotechnol 2004; 108:279-92. [PMID: 15006429 DOI: 10.1016/j.jbiotec.2003.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2003] [Revised: 12/01/2003] [Accepted: 12/08/2003] [Indexed: 11/25/2022]
Abstract
The production of therapeutic proteins in mammalian cell lines is of outstanding importance. The maintenance of most mammalian cell lines in culture requires the addition of serum to the culture medium. The elimination of serum from mammalian cell culture is desirable since serum is expensive and a source of contaminants, e.g. viruses, mycoplasma or prions. Here we describe the composition of serum- and protein-free media for the Chinese hamster ovary (CHO) cell line DUKXB11. The serum-free formulation supports excellent growth of CHO DUKXB11 cells at low (23cells/cm2) and high (2 x 10(4) cells/cm2) seeding densities characterized by a generation time of 10-12h, and, after addition of 0.2% pluronic F-68, the growth of a recombinant suspension cell line derived from DUKXB11. In addition, this formulation also allowed us to adapt recombinant cell lines expressing various amounts of human antithrombin ATIII (ATIII) to serum-free conditions. Secretion of ATIII was readily observed in the serum-free medium. Minor changes to the serum-free formulation resulted in a protein free formulation that supported growth of CHO DUKXB11 cells, growth of recombinant CHO cells expressing ATIII, and production of ATIII.
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Affiliation(s)
- Martin Schröder
- Institut für Biochemie, Technische Universität Darmstadt, Petersenstr. 22, D-64287 Darmstadt, Germany.
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Affiliation(s)
- Martin Fussenegger
- Institute of Biotechnology, Swiss Federal Institute of Technology, ETH Zurich, Switzerland.
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Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 2002; 79:568-79. [PMID: 12209828 DOI: 10.1002/bit.10441] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The classical method of metabolic engineering, identifying a rate-determining step in a pathway and alleviating the bottleneck by enzyme overexpression, has motivated much research but has enjoyed only limited practical success. Intervention of other limiting steps, of counter-balancing regulation, and of unknown coupled pathways often confounds this direct approach. Here the concept of inverse metabolic engineering is codified and its application is illustrated with several examples. Inverse metabolic engineering means the elucidation of a metabolic engineering strategy by: first, identifying, constructing, or calculating a desired phenotype; second, determining the genetic or the particular environmental factors conferring that phenotype; and third, endowing that phenotype on another strain or organism by directed genetic or environmental manipulation. This paradigm has been successfully applied in several contexts, including elimination of growth factor requirements in mammalian cell culture and increasing the energetic efficiency of microaerobic bacterial respiration.
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Korke R, Rink A, Seow TK, Chung MCM, Beattie CW, Hu WS. Genomic and proteomic perspectives in cell culture engineering. J Biotechnol 2002; 94:73-92. [PMID: 11792453 DOI: 10.1016/s0168-1656(01)00420-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the last few years, the number of biologics produced by mammalian cells have been steadily increasing. The advances in cell culture engineering science have contributed significantly to this increase. A common path of product and process development has emerged in the last decade and the host cell lines frequently used have converged to only a few. Selection of cell clones, their adaptation to a desired growth environment, and improving their productivity has been key to developing a new process. However, the fundamental understanding of changes during the selection and adaptation process is still lacking. Some cells may undergo irreversible alteration at the genome level, some may exhibit changes in their gene expression pattern, while others may incur neither genetic reconstruction nor gene expression changes, but only modulation of various fluxes by changing nutrient/metabolite concentrations and enzyme activities. It is likely that the selection of cell clones and their adaptation to various culture conditions may involve alterations not only in cellular machinery directly related to the selected marker or adapted behavior, but also those which may or may not be essential for selection or adaptation. The genomic and proteomic research tools enable one to globally survey the alterations at mRNA and protein levels and to unveil their regulation. Undoubtedly, a better understanding of these cellular processes at the molecular level will lead to a better strategy for 'designing' producing cells. Herein the genomic and proteomic tools are briefly reviewed and their impact on cell culture engineering is discussed.
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Affiliation(s)
- Rashmi Korke
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, USA
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Ureta T, Fernández WY, Centelles JJ, Cascante M. In vivo measurements of control coefficients for hexokinase and glucose-6-phosphate dehydrogenase in Xenopus laevis oocytes. FEBS Lett 2000; 475:145-9. [PMID: 10858506 DOI: 10.1016/s0014-5793(00)01646-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hexokinase and glucose-6-phosphate dehydrogenase activities were increased in Xenopus laevis oocytes by microinjection of commercial pure enzymes. The effect of increased fractional activities on glycogen synthesis or on the production of 14CO(2) (the oxidative portion of the pentose phosphate pathway) was investigated by microinjection of [1-(14)C]glucose and measurements of the radioactivity in glycogen and CO(2). Control coefficients calculated from the data show that hexokinase plays an important role in the control of glycogen synthesis (control coefficient=0.7) but its influence on the control of the pentose phosphate pathway is almost nil (control coefficient=-0.01). Glucose-6-phosphate dehydrogenase injections did not affect the production of 14CO(2) by the pentose phosphate pathway, indicating that other factors control the operation of this pathway. In addition, an almost null control of this enzyme on glycogen synthesis flux was observed.
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Affiliation(s)
- T Ureta
- Departmento de Biología, Universidad de Chile, Santiago.
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Kell DB, King RD. On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: the need for machine learning. Trends Biotechnol 2000; 18:93-8. [PMID: 10675895 DOI: 10.1016/s0167-7799(99)01407-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
At present, the assignment of function to novel genes uncovered by the systematic genome-sequencing programmes is a problem. Many studies anticipate that this can be achieved by analysing patterns of gene expression via the transcriptome, proteome and metabolome. Thus, functional genomics is, in part, an exercise in pattern classification. Because many genes have known functional classes, the problem of predicting their functional class is a supervised learning problem. However, most pattern classification methods that have been applied to the problem have been unsupervised clustering methods. Consequently, the best classification tools have not always been used. Furthermore, the present functional classes are suboptimal and new unsupervised clustering methods are needed to improve them. Better-structured functional classes will facilitate the prediction of biochemically testable functions.
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Affiliation(s)
- D B Kell
- Institute of Biological Sciences, University of Wales, Aberystwyth, UK SY23 3DD.
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25
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Abstract
A mathematical model of regulation of the G1-S transition of the mammalian cell cycle has been formulated to organize available experimental molecular-level information in a systematic quantitative framework and to evaluate the ability of this manifestation of current knowledge to calculate correctly experimentally observed phenotypes. This model includes nine components and includes cyclin-cdk complexes, a pocket protein (pRb), a transcription factor (E2F-1), and a cyclin-cdk complex inhibitor. Simulation of the model equations yields stable oscillatory solutions corresponding to cell proliferation and asymptotically stable solutions corresponding to cell cycle arrest (quiescence). Bifurcation analysis of the system suggests changes in the intracellular concentrations of either E2F or cyclin E can activate cell proliferation and that co-overexpression of these molecules can prevent cell proliferation. Further analysis suggests that the amount of inhibitor necessary to prevent cell proliferation is independent of the concentrations of cyclin E and E2F and depends only on the equilibrium ratio between the bound and unbound forms of the inhibitor to the complex.
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Mazur X, Eppenberger HM, Bailey JE, Fussenegger M. A novel autoregulated proliferation-controlled production process using recombinant CHO cells. Biotechnol Bioeng 1999. [DOI: 10.1002/(sici)1097-0290(19991020)65:2<144::aid-bit3>3.0.co;2-q] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zanghi JA, Fussenegger M, Bailey JE. Serum protects protein-free competent Chinese hamster ovary cells against apoptosis induced by nutrient deprivation in batch culture. Biotechnol Bioeng 1999; 64:108-19. [PMID: 10397845 DOI: 10.1002/(sici)1097-0290(19990705)64:1<108::aid-bit12>3.0.co;2-b] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of serum- and protein-free Chinese hamster ovary (CHO) cell cultures is a high priority for the production of biopharmaceuticals. Protein-free competent CHO cells lines have been previously constructed by two different methods-metabolic engineering with cell-cycle regulatory proteins and long-term selective adaptation. Apoptosis was present in both cell lines during protein-free, static-batch culture as a result of nutrient deprivation, and glucose deprivation alone was a potent inducer of apoptosis compared to the depletion of other nutrients such as amino acids. By adding back serum to the cultures during batch growth or nutrient deprivation, it was shown that unidentified survival factors in serum can greatly reduce apoptosis in protein-competent cell lines in all phases of the culture. Both observations contrast to previous reports for hybridoma cells, in which amino acids were the key determinants of apoptosis and serum had no additional antiapoptotic effect. Serum's protective effect against CHO cell death in batch culture was multifaceted and complex: (1) 10% FBS increased cell viability to >99% during exponential growth from roughly 75-90%, (2) 5-10% fetal bovine serum (FBS) reduced specific glucose consumption rates in both cell lines by 40%, thereby delaying the onset of apoptosis caused by glucose deprivation, and (3) 5% FBS reduced the specific cell death rate by 65% during a 3-d lactate-consumption phase characterized by substantial abortive proliferation, in which the cells both proliferated and died at a constant rate. The benefit of serum on cell production over the various phases of batch growth was combined into a single parameter by integrating the viable cell concentration vs. time profile (termed here as cumulative volumetric viable cell-time, VCTvol). Despite the ability of both cell lines to grow indefinitely without any exogenous growth factors, the addition of serum resulted in a 2. 3-fold increase in the VCTvol. Thus, it is clear that there is much room for improvement of protein-free CHO cell lines despite their adequate growth competence, and new strategies different from those successfully used for hybridomas may be necessary to combat CHO cell apoptosis.
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Affiliation(s)
- J A Zanghi
- Institute of Biotechnology, Swiss Federal Institute of Technology, ETH Hönggerberg, HPT, CH-8093 Zürich, Switzerland
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28
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Bailey JE. Lessons from metabolic engineering for functional genomics and drug discovery. Nat Biotechnol 1999; 17:616-8. [PMID: 10409335 DOI: 10.1038/10794] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- J E Bailey
- Institute of Biotechnology, ETH Zurich, Switzerland.
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29
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Champion KM, Arnott D, Henzel WJ, Hermes S, Weikert S, Stults J, Vanderlaan M, Krummen L. A two-dimensional protein map of Chinese hamster ovary cells. Electrophoresis 1999; 20:994-1000. [PMID: 10344277 DOI: 10.1002/(sici)1522-2683(19990101)20:4/5<994::aid-elps994>3.0.co;2-n] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Chinese hamster ovary (CHO) cells are used extensively for the expression of biopharmaceutical protein products. As part of our effort to better understand CHO cell physiology and protein expression changes caused by modified culture conditions, we have begun to map CHO cell polypeptides. A parental cell line reference map was established using two-dimensional gel electrophoresis with immobilized pH gradients (pH 3-10) in the first dimension and a linear acrylamide gradient (9-18%T) in the second dimension. The map is composed of over 1000 silver-stained protein spots. Protein identification is proceeding using a combination of immunostaining, NH2-terminal sequencing, and mass spectrometric analyses. Among the proteins so far identified are glucose-regulated protein 78 (GRP78), protein disulfide isomerase (PDI), galectin-1, and several heat-shock proteins. The goal is to generate a database which emphasizes those proteins most relevant to the use of CHO cells as a host for recombinant protein expression.
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Affiliation(s)
- K M Champion
- Department of Analytical Chemistry, Genentech, South San Francisco, CA 94080, USA.
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30
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Abstract
Metabolic engineering is a rapidly evolving field. The term typically refers to the genetic modification of cellular biochemistry to introduce new properties or modify existing ones. Recent progress in genetics, molecular biology, microbiology and chemistry are driving advances in this field. Many well-studied areas continue to yield exciting results and new problems and technologies are constantly being developed.
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Affiliation(s)
- J R Jacobsen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5025, USA
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31
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Regulated multicistronic expression technology for mammalian metabolic engineering. CURRENT APPLICATIONS OF CELL CULTURE ENGINEERING 1998. [DOI: 10.1007/978-94-011-4786-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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32
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Abstract
Mammalian cell culture continues to draw major research efforts. A great deal of progress has recently been made in cellular physiology, especially in factors adversely affecting cell growth or viability. Through molecular genetic manipulation, cells are more readily cultivated in a medium free of animal proteins. Achieving a high cell concentration and high viability continue to be common themes in engineering research. The need to implement a control policy for fed-batch and perfusion cultures has prompted increased efforts in process monitoring and control. Integrating these advances will be beneficial for ensuring product quality and process consistency.
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Affiliation(s)
- W S Hu
- Chemical Engineering and Materials Science Department, University of Minnesota, 421 Washington Avenue South East, Minneapolis, MN 55455, USA
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Lee KH, Harrington MG, Bailey JE. Two-dimensional electrophoresis of proteins as a tool in the metabolic engineering of cell cycle regulation. Biotechnol Bioeng 1996; 50:336-40. [DOI: 10.1002/(sici)1097-0290(19960505)50:3<336::aid-bit12>3.0.co;2-l] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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