Genomics and proteomics in process development: opportunities and challenges

Trends in Biotechnology - Tập 25 - Trang 324-330 - 2007
Prateek Gupta1, Kelvin H. Lee1
1School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853 USA

Tài liệu tham khảo

Walsh, 2006, Biopharmaceutical benchmarks 2006, Nat. Biotechnol., 24, 769, 10.1038/nbt0706-769 Lee, 2000, Genomic analysis, Curr. Opin. Biotechnol., 11, 171, 10.1016/S0958-1669(00)00077-X Dutt, 2000, Proteomic analysis, Curr. Opin. Biotechnol., 11, 176, 10.1016/S0958-1669(00)00078-1 Burbaum, 2002, Proteomics in drug discovery, Curr. Opin. Chem. Biol., 6, 427, 10.1016/S1367-5931(02)00337-X Butcher, 2004, Systems biology in drug discovery, Nat. Biotechnol., 22, 1253, 10.1038/nbt1017 Kramer, 2004, Functional genomics to new drug targets, Nat Rev Drug D iscov., 3, 965, 10.1038/nrd1552 Onyango, 2004, The role of emerging genomics and proteomics technologies in cancer drug target discovery, Curr. Cancer Drug Targets, 4, 111, 10.2174/1568009043481588 Wurm, 2004, Production of recombinant protein therapeutics in cultivated mammalian cells, Nat. Biotechnol., 22, 1393, 10.1038/nbt1026 Wlaschin, 2006, Toward genomic cell culture engineering, Cytotechnology, 50, 121, 10.1007/s10616-006-9004-9 Wlaschin, 2005, EST sequencing for gene discovery in Chinese hamster ovary cells, Biotechnol. Bioeng., 91, 592, 10.1002/bit.20511 Boone, 1971, Quality control studies on fetal bovine serum used in tissue culture, In Vitro, 7, 174, 10.1007/BF02617963 Zheng, 2006, Proteomic analysis for the assessment of different lots of fetal bovine serum as a raw material for cell culture. Part IV. Application of proteomics to the manufacture of biological drugs, Biotechnol. Prog., 22, 1294, 10.1021/bp060121o Allison, 2005, Development and optimization of cell culture media — genomic and proteomic approaches, BioProcess Int., 3, 2 Wong, 2006, Zinc as an insulin replacement in hybridoma cultures, Biotechnol. Bioeng., 93, 553, 10.1002/bit.20746 Wurm, 1994, Plasmid integration, amplification and cytogenetics in CHO cells: questions and comments, Biologicals, 22, 95, 10.1006/biol.1994.1015 Yoshikawa, 2000, Amplified gene location in chromosomal DNA affected recombinant protein production and stability of amplified genes, Biotechnol. Prog., 16, 710, 10.1021/bp000114e Barnes, 2004, Molecular definition of predictive indicators of stable protein expression in recombinant NS0 myeloma cells, Biotechnol. Bioeng., 85, 115, 10.1002/bit.10893 Jones, 2003, High level expression of recombinant IgG in the human cell line PER.C6, Biotechnol. Prog., 19, 163, 10.1021/bp025574h Barnes, 2007, Molecular analysis of successful cell line selection in transfected GS-NS0 myeloma cells, Biotechnol. Bioeng., 96, 337, 10.1002/bit.21119 Jiang, 2006, Regulation of recombinant monoclonal antibody production in Chinese hamster ovary cells: a comparative study of gene copy number, mRNA level and protein expression, Biotechnol. Prog., 22, 313, 10.1021/bp0501524 Smales, 2004, Comparative proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate, Biotechnol. Bioeng., 88, 474, 10.1002/bit.20272 Dinnis, 2006, Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate, Biotechnol. Bioeng., 94, 830, 10.1002/bit.20899 Korke, 2004, Large-scale gene expression profiling of metabolic shift of mammalian cells in culture, J. Biotechnol., 107, 1, 10.1016/j.jbiotec.2003.09.007 Ideker, 2001, A new approach to decoding life: systems biology, Annu. Rev. Genomics Hum. Genet., 2, 343, 10.1146/annurev.genom.2.1.343 Kuczenski, 2005, Improved understanding of gene expression regulation using systems biology, Expert Rev. Proteomics, 2, 915, 10.1586/14789450.2.6.915 Seth, 2005, Large-scale gene expression analysis of cholesterol dependence in NS0 cells, Biotechnol. Bioeng., 90, 552, 10.1002/bit.20429 Lee, 1996, Two-dimensional electrophoresis of proteins as a tool in the metabolic engineering of cell cycle regulation, Biotechnol. Bioeng., 50, 336, 10.1002/(SICI)1097-0290(19960505)50:3<336::AID-BIT12>3.0.CO;2-L Lee, 1996, Deregulated expression of cloned transcription factor E2F-1 in Chinese hamster ovary cells shifts protein patterns and activates growth in protein-free medium, Biotechnol. Bioeng., 50, 273, 10.1002/(SICI)1097-0290(19960505)50:3<273::AID-BIT6>3.0.CO;2-D Renner, 1995, Recombinant cyclin E expression activates proliferation and obviates surface attachment of Chinese hamster ovary (CHO) cells in protein-free medium, Biotechnol. Bioeng., 47, 476, 10.1002/bit.260470409 Bloemkolk, 1992, Effect of temperature on hybridoma cell cycle and MAb production, Biotechnol. Bioeng., 40, 427, 10.1002/bit.260400312 Fox, 2004, Maximizing interferon-gamma production by Chinese hamster ovary cells through temperature shift optimization: experimental and modeling, Biotechnol. Bioeng., 85, 177, 10.1002/bit.10861 Furukawa, 1998, Effect of culture temperature on a recombinant CHO cell line producing a C-terminal α-amidating enzyme, Cytotechnology, 26, 153, 10.1023/A:1007934216507 Hendrick, 2001, Increased productivity of recombinant tissular plasminogen activator (tPA) by butyrate and shift of temperature: a cell cycle phase analysis, Cytotechnology, 36, 71, 10.1023/A:1014088919546 Al-Fageeh, 2006, The cold-shock response in cultured mammalian cells: harnessing the response for the improvement of recombinant protein production, Biotechnol. Bioeng., 93, 829, 10.1002/bit.20789 Kaufmann, 1999, Influence of low temperature on productivity, proteome and protein phosphorylation of CHO cells, Biotechnol. Bioeng., 63, 573, 10.1002/(SICI)1097-0290(19990605)63:5<573::AID-BIT7>3.0.CO;2-Y Baik, 2006, Initial transcriptome and proteome analyses of low culture temperature-induced expression in CHO cells producing erythropoietin, Biotechnol. Bioeng., 93, 361, 10.1002/bit.20717 Chen, 1998, Hyperosmolality leads to an increase in tissue-type plasminogen activator production by a Chinese hamster ovary cell line, Biotechnol. Tech., 12, 207 Ryu, 2000, Osmoprotective effect of glycine betaine on foreign protein production in hyperosmotic recombinant Chinese hamster ovary cell cultures differs among cell lines, Biotechnol. Bioeng., 70, 167, 10.1002/1097-0290(20001020)70:2<167::AID-BIT6>3.0.CO;2-P Lee, 2003, Proteome analysis of antibody-expressing CHO cells in response to hyperosmotic pressure, Biotechnol. Prog., 19, 1734, 10.1021/bp034093a Shen, 2006, Genome-wide analysis of the transcriptional response of murine hybridomas to osmotic shock, Biotechnol. Bioeng., 93, 132, 10.1002/bit.20691 Hayduk, 2005, Cytochalasin D can improve heterologous protein productivity in adherent Chinese hamster ovary cells, Biotechnol. Bioeng., 90, 354, 10.1002/bit.20438 Van Dyk, 2003, Identification of cellular changes associated with increased production of human growth hormone in a recombinant Chinese hamster ovary cell line, Proteomics, 3, 147, 10.1002/pmic.200390023 Chen, 2006, Effects of elevated ammonium on glycosylation gene expression in CHO cells, Metab. Eng., 8, 123, 10.1016/j.ymben.2005.10.002 Jaques, 1996, The glycosylation of Bowes melanoma tissue plasminogen activator: lectin mapping, reaction with anti-L2/HNK-1 antibodies and the presence of sulphated/glucuronic acid-containing glycans, Biochem. J., 316, 427, 10.1042/bj3160427 Harazono, 2004, Site-specific glycosylation analysis of human apolipoprotein B100 using LC/ESI MS/MS, Glycobiology, 15, 447, 10.1093/glycob/cwi033 Ackermann, 1995, Influence of cell-derived and media-derived factors on the integrity of a human monoclonal antibody after secretion into serum-free cell culture supernatants, Biotechnol. Bioeng., 45, 97, 10.1002/bit.260450202 Gawlitzek, 1995, Effect of different cell culture conditions on the polypeptide integrity and N-glycosylation of a recombinant model glycoprotein, Biotechnol. Bioeng., 46, 536, 10.1002/bit.260460606 Hooker, 1995, N-glycans of recombinant interferon-λ change during batch culture of Chinese hamster ovary cells, Biotechnol. Bioeng., 48, 639, 10.1002/bit.260480612 Neususs, 2005, Glycoform characterization of intact erythropoietin by capillary electrophoresis–electrospray–time-of-flight mass spectrometry, Electrophoresis, 26, 1442, 10.1002/elps.200410269 Wang, 2006, Monitoring of glycoprotein products in cell culture lysates using lectin affinity chromatography and capillary HPLC coupled to electrospray linear ion trap–Fourier transform mass spectrometry (LTQ/FTMS), Biotechnol. Prog., 22, 873, 10.1021/bp060005l Spellman, 1989, Carbohydrate structures of human tissue plasminogen activator expressed in Chinese hamster ovary cells, J. Biol. Chem., 264, 14100, 10.1016/S0021-9258(18)71649-9 Eaton, 1995, Host cell contaminant protein assay development for recombinant biopharmaceuticals, J. Chromatogr. A., 705, 105, 10.1016/0021-9673(94)01249-E Rathore, 2003, Analysis for residual host cell proteins and DNA in process streams of a recombinant protein product expressed in Escherichia coli cells, J. Pharm. Biomed. Anal., 32, 1199, 10.1016/S0731-7085(03)00157-2 Krawitz, 2006, Proteomic studies support the use of multi-product immunoassays to monitor host cell protein impurities, Proteomics, 6, 94, 10.1002/pmic.200500225 Hermann, 2004, Using functional genomics to improve productivity in the manufacture of industrial biochemicals, Curr. Opin. Biotechnol., 15, 444, 10.1016/j.copbio.2004.07.002 Lee, 2005, Systems biotechnology for strain improvement, Trends Biotechnol., 23, 349, 10.1016/j.tibtech.2005.05.003 Park, 2006, Rapid optimization of anti-botulinum toxin antibody fragment production by an integral approach utilizing RC-SELDI mass spectrometry and statistical design, Biotechnol. Prog., 22, 233, 10.1021/bp050158t Aldor, 2005, Proteomic profiling of recombinant Escherichia coli in high cell-density fermentations for improved production of an antibody fragment biopharmaceutical, Appl. Environ. Microbiol., 71, 1717, 10.1128/AEM.71.4.1717-1728.2005 Champion, 2003, Comparison of the Escherichia coli proteomes for recombinant human growth hormone producing and non-producing fermentations, Proteomics, 3, 1365, 10.1002/pmic.200300430 Champion, 2001, Similarity of the Escherichia coli proteome upon completion of different biopharmaceutical fermentation processes, Proteomics, 1, 1133, 10.1002/1615-9861(200109)1:9<1133::AID-PROT1133>3.0.CO;2-S Han, 2003, Engineering Escherichia coli for increased productivity of serine-rich proteins based on proteome profiling, Appl. Environ. Microbiol., 69, 5772, 10.1128/AEM.69.10.5772-5781.2003 Jurgen, 2000, Monitoring of genes that respond to overproduction of an insoluble recombinant protein in Escherichia coli glucose-limited fed-batch fermentations, Biotechnol. Bioeng., 70, 217, 10.1002/1097-0290(20001020)70:2<217::AID-BIT11>3.0.CO;2-W Kim, 2004, Proteomic response analysis of a threonine-overproducing mutant of Escherichia coli, Biochem. J., 381, 823, 10.1042/BJ20031763 Raman, 2005, Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions, Biotechnol. Bioeng., 92, 384, 10.1002/bit.20570 Rinas, 1996, Synthesis rates of cellular proteins involved in translation and protein folding are strongly altered in response to overproduction of basic fibroblast growth factor by recombinant Escherichia coli, Biotechnol. Prog., 12, 196, 10.1021/bp9600039 Wang, 2005, Proteomic profiling of Escherichia coli proteins under high cell-density fed-batch cultivation with overexpression of phosphogluconolactonase, Biotechnol. Prog., 21, 1401, 10.1021/bp050048m Choi, 2003, Enhanced production of insulin-like growth factor I fusion protein in Escherichia coli by co-expression of the down-regulated genes identified by transcriptome profiling, Appl. Environ. Microbiol., 69, 4737, 10.1128/AEM.69.8.4737-4742.2003 Gill, 2001, Genomic analysis of high cell-density recombinant Escherichia coli fermentation and ‘cell conditioning’ for improved recombinant protein yield, Biotechnol. Bioeng., 72, 85, 10.1002/1097-0290(20010105)72:1<85::AID-BIT12>3.0.CO;2-H Haddadin, 2005, Transcriptome profiles for high cell-density recombinant and wild-type Escherichia coli, Biotechnol. Bioeng., 90, 127, 10.1002/bit.20340 Harcum, 2006, Global transcriptome response of recombinant Escherichia coli to heat-shock and dual heat-shock recombinant protein induction, J. Ind. Microbiol. Biotechnol., 33, 801, 10.1007/s10295-006-0122-3 Polen, 2003, DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate, Appl. Environ. Microbiol., 69, 1759, 10.1128/AEM.69.3.1759-1774.2003 Wei, 2001, High-density microarray-mediated gene expression profiling of Escherichia coli, J. Bacteriol., 183, 545, 10.1128/JB.183.2.545-556.2001 Yoon, 2003, Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture, Biotechnol. Bioeng., 81, 753, 10.1002/bit.10626 Lee, 2001, Proteomics: a technology-driven and a technology-limited discovery science, Trends Biotechnol., 19, 217, 10.1016/S0167-7799(01)01639-0 Aggarwal, 2006, Shotgun proteomics using the iTRAQ isobaric tags, Brief. Funct. Genomic. Proteomic., 5, 112, 10.1093/bfgp/ell018