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Cytotechnology

, 50:121 | Cite as

Toward genomic cell culture engineering

  • Katie F. Wlaschin
  • Gargi Seth
  • Wei-Shou HuEmail author
Original Paper

Abstract

Genomic and proteomic based global gene expression profiling has altered the landscape of biological research in the past few years. Its potential impact on cell culture bioprocessing has only begun to emanate, partly due to the lack of genomic sequence information for the most widely used industrial cells, Chinese hamster ovary (CHO) cells. Transcriptome and proteome profiling work for species lacking extensive genomic resources must rely on information for other related species or on data obtained from expressed sequence tag (EST) sequencing projects, for which burgeoning efforts have only recently begun. This article discusses the aspects of EST sequencing in those industrially important, genomic resources-poor cell lines, articulates some of the unique features in employing microarray in the study of cultured cells, and highlights the infrastructural needs in establishing a platform for genomics based cell culture research. Recent experience has revealed that generally, most changes in culture conditions only elicit a moderate level of alteration in gene expression. Nevertheless, by broadening the conventional scope of microarray analysis to consider estimated levels of transcript abundance, much physiological insight can be gained. Examples of the application of microarray in cell culture are discussed, and the utility of pattern identification and process diagnosis are highlighted. As genomic resources continue to expand, the power of genomic tools in cell culture processing research will be amply evident. The key to harnessing the immense benefit of these genomic resources resides in the development of physiological understanding from their application.

Keywords

cDNA library Data analysis Mammalian cell culture Microarray Proteome Transcriptome 

Notes

Acknowledgements

The support from Pfizer, Inc. and Bayer Healthcare for the cell culture research work in W-S. Hu’s laboratory are gratefully acknowledged. KFW was supported by the NIH Biotechnology Training Grant (GM08347). The bioinformatic support was provided by The Minnesota Supercomputing Institute.

References

  1. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207CrossRefGoogle Scholar
  2. Alete DE, Racher AJ, Birch JR, Stansfield SH, James DC, Smales CM (2005) Proteomic analysis of enriched microsomal fractions from GS-NS0 murine myeloma cells with varying secreted recombinant monoclonal antibody productivities. Proteomics 5:4689–4704CrossRefGoogle Scholar
  3. Chakraborty A, Regnier FE (2002) Global internal standard technology for comparative proteomics. J Chromatogr A 949:173–184CrossRefGoogle Scholar
  4. Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SP (1996). Accessing genetic information with high-density DNA arrays. Science 274:610–614CrossRefGoogle Scholar
  5. Chen Z, Southwick K, Thulin CD (2004) Initial analysis of the phosphoproteome of Chinese hamster ovary cells using electrophoresis. J Biomol Tech: JBT 15:249–256Google Scholar
  6. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 1:19–20CrossRefGoogle Scholar
  7. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:681–685CrossRefGoogle Scholar
  8. Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge UK, Cambridge University PressGoogle Scholar
  9. Gadgil C, Rink A, Beattie CW, Hu WS (2002) A Mathematical Model for Suppression Subtractive Hybridization. Comp Funct Genomics 3:405–422CrossRefGoogle Scholar
  10. Gadgil M, Lian W, Gadgil C, Kapur V, Hu W-S (2005) An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays. BMC Genomics 6Google Scholar
  11. Gladney CD, Bertani GR, Johnson RK, Pomp D (2004) Evaluation of gene expression in pigs selected for enhanced reproduction using differential display PCR and human microarrays: I. Ovarian follicles. J Anim Sci 82:17–31Google Scholar
  12. Gu J, Gu X (2003) Induced gene expression in human brain after the split from chimpanzee. Trends Genet 19:63–65CrossRefGoogle Scholar
  13. Guo QM (2003) DNA microarray and cancer. Curr Opin Oncol 15:36–43CrossRefGoogle Scholar
  14. Gygi S, Rist B, Gerber S, Turecek F, Gelb M, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999CrossRefGoogle Scholar
  15. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 97:9390–9395CrossRefGoogle Scholar
  16. Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M (2002) A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res 30:1083–1090CrossRefGoogle Scholar
  17. Hayduk EJ, Choe LH, Lee KH (2004) A two-dimensional electrophoresis map of Chinese hamster ovary cell proteins based on fluorescence staining. Electrophoresis 25:2545–2556CrossRefGoogle Scholar
  18. Hayduk EJ, Lee KH (2005) Cytochalasin D can improve heterologous protein productivity in adherent Chinese hamster ovary cells. Biotechnology & Bioengineering 90:354–364CrossRefGoogle Scholar
  19. Hunt DF, Henderson RA, Shabanowitz J, Sakaguchi K, Michel H, Sevilir N, Cox AL, Appella E, Engelhard VH (1992) Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255:1261–1263CrossRefGoogle Scholar
  20. International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409:860–921CrossRefGoogle Scholar
  21. Kaufmann H, Mazur X, Fussenegger M, Bailey JE (1999) Influence of low temperature on productivity, proteome and protein phosphorylation of CHO cells. Biotechnol Bioeng 63:573–582CrossRefGoogle Scholar
  22. Kim H, Zhao B, Snesrud E, Haas B, Town C, Quckenbush J (2002) Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analysis. Biotechniques 33:924–930Google Scholar
  23. Korke R, De Leon Gatti M, Lau AL, Lim JW, Seow TK, Chung MC, Hu WS (2004) Large scale gene expression profiling of metabolic shift of mammalian cells in culture. J Biotechnol 107:1–17CrossRefGoogle Scholar
  24. Lee MS, Kim KW, Kim YH, Lee GM (2003) Proteome analysis of antibody-expressing CHO cells in response to hyperosmotic pressure. Biotechnol Prog 19:1734–1741CrossRefGoogle Scholar
  25. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, et al (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. 438:803–819Google Scholar
  26. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675–1680CrossRefGoogle Scholar
  27. Moody DE, Zou Z, McIntyre L (2002) Cross-species hybridisation of pig RNA to human nylon microarrays. BMC Genomics 3:27CrossRefGoogle Scholar
  28. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562CrossRefGoogle Scholar
  29. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386CrossRefGoogle Scholar
  30. Pattyn F, Speleman F, De Paepe A, Vandesompele J (2003) RTPrimerDB: the real-time PCR primer and probe database. Nucleic Acids Research 31:122–123CrossRefGoogle Scholar
  31. Rabilloud T (2002) Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2:3–10CrossRefGoogle Scholar
  32. Rat Genome Sequencing Project Consortium (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493–521CrossRefGoogle Scholar
  33. Rose K, Simona MG, Offord RE, Prior CP, Otto B, Thatcher DR (1983) A new mass-spectrometric C-terminal sequencing technique finds a similarity between gamma-interferon and alpha 2-interferon and identifies a proteolytically clipped gamma-interferon that retains full antiviral activity. Biochem J 215:273–277Google Scholar
  34. Ross P, Huang Y, Marchese J, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cellular Proteomics 3:1154–1169CrossRefGoogle Scholar
  35. Schneider LV, Hall MP (2005) Stable isotope methods for high-precision proteomics. Drug Discovery Today 10:353–363CrossRefGoogle Scholar
  36. Seow TK, Korke R, Liang R, Ong S-E, Ou K, Wong K, Hu WS, Chung M (2001) Proteomic investigation of metabolic shift in mammalian cell culture. Biotechnol Progr 17:1137–1144CrossRefGoogle Scholar
  37. Seth G, Philp RJ, Denoya CD, McGrath K, Stutzman-Engwall KJ, Yap MG, Hu W-S (2005) Large scale gene expression analysis of cholesterol dependence in NS0 cells. Biotech Bioeng 90:552–567CrossRefGoogle Scholar
  38. Seth G, Ozturk M, Hu W-S (2006) Reverting cholesterol dependence of NS0 cells by altering epigenetic gene silencing. Biotech Bioeng 93:820–827Google Scholar
  39. Shen D, Sharfstein ST (2006) Genome-wide analysis of the transcriptional response of murine hybridomas to osmotic shock. Biotechnol Bioeng 93:132–145CrossRefGoogle Scholar
  40. Smales CM, Dinnis DM, Stansfield SH, Alete D, Sage EA, Birch JR, Racher AJ, Marshall CT, James DC (2004) Comparative proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnol Bioeng 88:474–488CrossRefGoogle Scholar
  41. Talaat A, Howard S, Hale W, Lyons R, Garner H, Johnston S (2002) Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res 30Google Scholar
  42. Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071–2077CrossRefGoogle Scholar
  43. Van Dyk DD, Misztal DR, Wilkins MR, Mackintosh JA, Poljak A, Varnai JC, Teber E, Walsh BJ, Gray PP (2003) Identification of cellular changes associated with increased production of human growth hormone in a recombinant Chinese hamster ovary cell line. Proteomics 3:147–156CrossRefGoogle Scholar
  44. Williams B, Gwirtz R, Wold B (2004) Genomic DNA as a cohybridization standard for mammalian microarray measurements. Nucleic Acids Res 32Google Scholar
  45. Wlaschin K, Nissom PM, de Leon Gatti M, Fern PFO, Arleen S, Tan KS, Rink A, Cham B, Wong K, Yap M, Hu W-S (2005) EST sequencing for gene discovery in Chinese hamster ovary cells. Biotech Bioeng 91:592–606CrossRefGoogle Scholar
  46. Wong VVT, Nissom PM, Sim S-L, Yeo JHM, Chuah S-H, Yap MGS (2006) Zinc as an insulin replacement in hybridoma cultures. Biotechnol Bioeng 93:553–563CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  1. 1.Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolisUSA

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