Genomic and Proteomic Profiling of Mammalian Cells Under High Productivity States (Paperback, Annotated edition)

Over the past decade, mammalian cell culture processes have become the most prominent production vehicle for biologicals. Chinese hamster ovary (CHO), Baby hamster kidney (BHK) and NS0 myeloma are amongst the most important host cell lines used in recombinant protein production. These cell lines that hardly secrete proteins in their native state, are now routinely engineered to produce antibodies and recombinant proteins at levels that rival the professional secretor - plasma cells, in vivo. Yet, there is little understanding of the genetic or physiological changes that enhance protein secretion in these cultured cell lines. Genomic research tools allow one to probe the global changes in mRNA and protein expression. This thesis research is enabled by the collection of annotated CHO ESTs (expressed sequence tags) and the construction of CHO cDNA microarrays and Affymetrix oligoarrays. This genomic infrastructure has facilitated gene expression profiling in CHO, and the closely related Baby Hamster Kidney (BHK) cell line. Comparison of hybridization results derived from same-species and cross-species hybridization platform has established the value for building the CHO genomic infrastructure. Sodium butyrate and low temperature have been used to increase specific productivity in mammalian cells. To unveil genes contributing to high productivity traits, comparative expression profile on two recombinant CHO cell lines under the separate treatment of butyrate, low temperature and a combined treatment of both conditions were analyzed. Microarray analysis revealed increased transcript levels of genes in vesicle-mediated secretion, protein transport and endocytosis pathways which accompanied the enhancement in protein productivity. Although transcriptome analysis is powerful for global survey, physiological insights can often be greatly enhanced by probing protein dynamics. To complement the microarray findings, the secretion rate of intracellular IgG was measured using stable isotope labeling in culture under the relevant high productivity culture conditions (low temperature and butyrate). In addition, global protein turnover was assessed in myeloma under conditions relevant to protein production. The revelation of the heterogeneity in protein turnover and protein secretion provide further hints on potential rate limiting steps in further enhancing recombinant protein productivity. This research has harnessed the application of functional genomics to delve into physiological mechanisms attributed to high productivity.