Genomics and proteomics in process development: opportunities and challenges

Trends in Biotechnology

Volumn 25, Issue 7, 2007, Pages 324-330

  Gupta, Prateek ^a   Lee, Kelvin H ^a  

^a Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; DRUG PRODUCTS; PRODUCTIVITY; PROTEINS; RESEARCH AND DEVELOPMENT MANAGEMENT;

DRUG DISCOVERY; GENOMIC ANALYSIS; PROCESS DEVELOPMENT; PROTEOMIC ANALYSES;

GENE EXPRESSION;

BIOLOGICAL PRODUCT; BUTYRIC ACID; HUMAN GROWTH HORMONE; PROTEIN CAPZ; PYRUVATE KINASE; TISSUE PLASMINOGEN ACTIVATOR; ZINC SULFATE;

BIOPROCESS; CELL CULTURE; CELL FUNCTION; CELL SELECTION; DNA FLANKING REGION; DNA LIBRARY; DNA MICROARRAY; DNA SEQUENCE; DOWNSTREAM PROCESSING; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC MANIPULATION; GENETIC STABILITY; GENOMICS; HUMAN; HYPEROSMOLARITY; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN EXPRESSION; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; TEMPERATURE;

ANIMALS; CELL CULTURE TECHNIQUES; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; PROTEOMICS;

MAMMALIA;

EID: 34250169808     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2007.04.005     Document Type: Review

References (75)

1. Walsh G. Biopharmaceutical benchmarks 2006. Nat. Biotechnol. 24 (2006) 769-776
2. Lee P.S., and Lee K.H. Genomic analysis. Curr. Opin. Biotechnol. 11 (2000) 171-175
3. Dutt M.J., and Lee K.H. Proteomic analysis. Curr. Opin. Biotechnol. 11 (2000) 176-179
4. Burbaum J., and Tobal G.M. Proteomics in drug discovery. Curr. Opin. Chem. Biol. 6 (2002) 427-433
5. Butcher E.C., et al. Systems biology in drug discovery. Nat. Biotechnol. 22 (2004) 1253-1259
6. Kramer R., and Cohen D. Functional genomics to new drug targets. Nat Rev Drug D iscov. 3 (2004) 965-972
7. Onyango P. The role of emerging genomics and proteomics technologies in cancer drug target discovery. Curr. Cancer Drug Targets 4 (2004) 111-124
8. Wurm F.M. Production of recombinant protein therapeutics in cultivated mammalian cells. Nat. Biotechnol. 22 (2004) 1393-1398
9. Wlaschin K.F., et al. Toward genomic cell culture engineering. Cytotechnology 50 (2006) 121-140
10. Wlaschin K.F., et al. EST sequencing for gene discovery in Chinese hamster ovary cells. Biotechnol. Bioeng. 91 (2005) 592-606
11. Boone C.W., et al. Quality control studies on fetal bovine serum used in tissue culture. In Vitro 7 (1971) 174-189
12. Zheng X., et al. 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 (2006) 1294-1300
13. Allison D.W., et al. Development and optimization of cell culture media - genomic and proteomic approaches. BioProcess Int. 3 (2005) 2-7
14. Wong V.V., et al. Zinc as an insulin replacement in hybridoma cultures. Biotechnol. Bioeng. 93 (2006) 553-563
15. Wurm F.M., and Petropoulos C.J. Plasmid integration, amplification and cytogenetics in CHO cells: questions and comments. Biologicals 22 (1994) 95-102
16. Yoshikawa T., et al. Amplified gene location in chromosomal DNA affected recombinant protein production and stability of amplified genes. Biotechnol. Prog. 16 (2000) 710-715
17. Barnes L.M., et al. Molecular definition of predictive indicators of stable protein expression in recombinant NS0 myeloma cells. Biotechnol. Bioeng. 85 (2004) 115-121
18. Jones D., et al. High level expression of recombinant IgG in the human cell line PER.C6. Biotechnol. Prog. 19 (2003) 163-168
19. Barnes L.M., et al. Molecular analysis of successful cell line selection in transfected GS-NS0 myeloma cells. Biotechnol. Bioeng. 96 (2007) 337-348
20. Jiang Z., et al. 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 (2006) 313-318
21. Smales C.M., et al. Comparative proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnol. Bioeng. 88 (2004) 474-488
22. Dinnis D.M., et al. Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnol. Bioeng. 94 (2006) 830-841
23. Korke R., et al. Large-scale gene expression profiling of metabolic shift of mammalian cells in culture. J. Biotechnol. 107 (2004) 1-17
24. Ideker T., et al. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2 (2001) 343-372
25. Kuczenski R.S., et al. Improved understanding of gene expression regulation using systems biology. Expert Rev. Proteomics 2 (2005) 915-924
26. Seth G., et al. Large-scale gene expression analysis of cholesterol dependence in NS0 cells. Biotechnol. Bioeng. 90 (2005) 552-567
27. Lee K.H., et al. Two-dimensional electrophoresis of proteins as a tool in the metabolic engineering of cell cycle regulation. Biotechnol. Bioeng. 50 (1996) 336-340
28. Lee K.H., et al. 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 (1996) 273-279
29. Renner W.A., et al. Recombinant cyclin E expression activates proliferation and obviates surface attachment of Chinese hamster ovary (CHO) cells in protein-free medium. Biotechnol. Bioeng. 47 (1995) 476-482
30. Bloemkolk J.W., et al. Effect of temperature on hybridoma cell cycle and MAb production. Biotechnol. Bioeng. 40 (1992) 427-431
31. Fox S.R., et al. Maximizing interferon-gamma production by Chinese hamster ovary cells through temperature shift optimization: experimental and modeling. Biotechnol. Bioeng. 85 (2004) 177-184
32. Furukawa K., and Ohsuye K. Effect of culture temperature on a recombinant CHO cell line producing a C-terminal α-amidating enzyme. Cytotechnology 26 (1998) 153-164
33. Hendrick V., et al. Increased productivity of recombinant tissular plasminogen activator (tPA) by butyrate and shift of temperature: a cell cycle phase analysis. Cytotechnology 36 (2001) 71-83
34. Al-Fageeh M.B., et al. The cold-shock response in cultured mammalian cells: harnessing the response for the improvement of recombinant protein production. Biotechnol. Bioeng. 93 (2006) 829-835
35. Kaufmann H., et al. Influence of low temperature on productivity, proteome and protein phosphorylation of CHO cells. Biotechnol. Bioeng. 63 (1999) 573-582
36. Baik J.Y., et al. Initial transcriptome and proteome analyses of low culture temperature-induced expression in CHO cells producing erythropoietin. Biotechnol. Bioeng. 93 (2006) 361-371
37. Chen Z., Liu H., and WU B. Hyperosmolality leads to an increase in tissue-type plasminogen activator production by a Chinese hamster ovary cell line. Biotechnol. Tech. 12 (1998) 207-209
38. Ryu J.S., et al. Osmoprotective effect of glycine betaine on foreign protein production in hyperosmotic recombinant Chinese hamster ovary cell cultures differs among cell lines. Biotechnol. Bioeng. 70 (2000) 167-175
39. Lee M.S., et al. Proteome analysis of antibody-expressing CHO cells in response to hyperosmotic pressure. Biotechnol. Prog. 19 (2003) 1734-1741
40. Shen D., and Sharfstein S.T. Genome-wide analysis of the transcriptional response of murine hybridomas to osmotic shock. Biotechnol. Bioeng. 93 (2006) 132-145
41. Hayduk E.J., and Lee K.H. Cytochalasin D can improve heterologous protein productivity in adherent Chinese hamster ovary cells. Biotechnol. Bioeng. 90 (2005) 354-364
42. Van Dyk D.D., et al. Identification of cellular changes associated with increased production of human growth hormone in a recombinant Chinese hamster ovary cell line. Proteomics 3 (2003) 147-156
43. Chen P., and Harcum S.W. Effects of elevated ammonium on glycosylation gene expression in CHO cells. Metab. Eng. 8 (2006) 123-132
44. Jaques A.J., et al. 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 (1996) 427-437
45. Harazono A., et al. Site-specific glycosylation analysis of human apolipoprotein B100 using LC/ESI MS/MS. Glycobiology 15 (2004) 447-462
46. Ackermann M., et al. 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 (1995) 97-106
47. Gawlitzek M., et al. Effect of different cell culture conditions on the polypeptide integrity and N-glycosylation of a recombinant model glycoprotein. Biotechnol. Bioeng. 46 (1995) 536-544
48. Hooker A.D., et al. N-glycans of recombinant interferon-λ change during batch culture of Chinese hamster ovary cells. Biotechnol. Bioeng. 48 (1995) 639-648
49. Neususs C., et al. Glycoform characterization of intact erythropoietin by capillary electrophoresis-electrospray-time-of-flight mass spectrometry. Electrophoresis 26 (2005) 1442-1450
50. Wang Y., et al. 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 (2006) 873-880
51. Spellman M.W., et al. Carbohydrate structures of human tissue plasminogen activator expressed in Chinese hamster ovary cells. J. Biol. Chem. 264 (1989) 14100-14111
52. Eaton L.C. Host cell contaminant protein assay development for recombinant biopharmaceuticals. J. Chromatogr. A. 705 (1995) 105-114
53. Rathore A.S., et al. 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 (2003) 1199-1211
54. Krawitz D.C., et al. Proteomic studies support the use of multi-product immunoassays to monitor host cell protein impurities. Proteomics 6 (2006) 94-110
55. Hermann T. Using functional genomics to improve productivity in the manufacture of industrial biochemicals. Curr. Opin. Biotechnol. 15 (2004) 444-448
56. Lee S.Y., et al. Systems biotechnology for strain improvement. Trends Biotechnol. 23 (2005) 349-358
57. Park J.T., et al. Rapid optimization of anti-botulinum toxin antibody fragment production by an integral approach utilizing RC-SELDI mass spectrometry and statistical design. Biotechnol. Prog. 22 (2006) 233-240
58. Aldor I.S., et al. Proteomic profiling of recombinant Escherichia coli in high cell-density fermentations for improved production of an antibody fragment biopharmaceutical. Appl. Environ. Microbiol. 71 (2005) 1717-1728
59. Champion K.M., et al. Comparison of the Escherichia coli proteomes for recombinant human growth hormone producing and non-producing fermentations. Proteomics 3 (2003) 1365-1373
60. Champion K.M., et al. Similarity of the Escherichia coli proteome upon completion of different biopharmaceutical fermentation processes. Proteomics 1 (2001) 1133-1148
61. Han M.J., et al. Engineering Escherichia coli for increased productivity of serine-rich proteins based on proteome profiling. Appl. Environ. Microbiol. 69 (2003) 5772-5781
62. Jurgen B., et al. Monitoring of genes that respond to overproduction of an insoluble recombinant protein in Escherichia coli glucose-limited fed-batch fermentations. Biotechnol. Bioeng. 70 (2000) 217-224
63. Kim Y.H., et al. Proteomic response analysis of a threonine-overproducing mutant of Escherichia coli. Biochem. J. 381 (2004) 823-829
64. Raman B., et al. Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions. Biotechnol. Bioeng. 92 (2005) 384-392
65. Rinas U. 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 (1996) 196-200
66. Wang Y., et al. Proteomic profiling of Escherichia coli proteins under high cell-density fed-batch cultivation with overexpression of phosphogluconolactonase. Biotechnol. Prog. 21 (2005) 1401-1411
67. Choi J.H., et al. 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 (2003) 4737-4742
68. Gill R.T., et al. Genomic analysis of high cell-density recombinant Escherichia coli fermentation and 'cell conditioning' for improved recombinant protein yield. Biotechnol. Bioeng. 72 (2001) 85-95
69. Haddadin F.T., and Harcum S.W. Transcriptome profiles for high cell-density recombinant and wild-type Escherichia coli. Biotechnol. Bioeng. 90 (2005) 127-153
70. Harcum S.W., and Haddadin F.T. Global transcriptome response of recombinant Escherichia coli to heat-shock and dual heat-shock recombinant protein induction. J. Ind. Microbiol. Biotechnol. 33 (2006) 801-814
71. Polen T., et al. DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate. Appl. Environ. Microbiol. 69 (2003) 1759-1774
72. Wei Y., et al. High-density microarray-mediated gene expression profiling of Escherichia coli. J. Bacteriol. 183 (2001) 545-556
73. Yoon S.H., et al. Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture. Biotechnol. Bioeng. 81 (2003) 753-767
74. Lee K.H. Proteomics: a technology-driven and a technology-limited discovery science. Trends Biotechnol. 19 (2001) 217-222
75. Aggarwal K., et al. Shotgun proteomics using the iTRAQ isobaric tags. Brief. Funct. Genomic. Proteomic. 5 (2006) 112-120