Understanding the Transcriptional Landscape of Chinese Hamster Ovary (CHO) Cell Lines Using Next-Generation Sequencing Technology, RNA-seq, under Industrially Relevant Conditions

Recombinant therapeutic proteins are widely used to treat life-threatening diseases including cancer. Chinese hamster ovary (CHO) cells have been used for over 25 years in the biopharmaceutical industry to produce recombinant therapeutics, where CHO cells produce almost one in three of the manufactured recombinant therapeutics. CHO cell lines are the preferred host for protein expression due to their ability to produce human-compatible protein glycosylation, mediate protein folding, ease of culturing in large-scale bioreactors and protein expression stability. However, several limitations exist in CHO cell bioprocessing, including low protein yields, resulting in high market prices of the biopharmaceuticals. Understanding of CHO cells in the biopharmaceutical industry has heavily relied on empirical results with a limited knowledge of the molecular dynamics. Transcriptomics is one such medium through which cellular mechanisms could be better understood by measuring gene expression. Moreover, with the recent establishment of both Chinese hamster and CHO-K1 cell line genome assemblies, it is now possible to leverage the genomic resources to better understand and further improve CHO cell bioprocessing. This dissertation work used the next generation sequencing technique, RNA-seq, to characterize the transcriptional response in CHO cells under several industrially relevant treatments, particularly to observe changes due to the adaptation of CHO cells to serum-free media, low temperature, low pH and medium glucose concentration. The information obtained from comprehensive transcriptome analysis can be leveraged to engineer CHO cells with desired phenotypes including high protein titers and used to control the bioreactor environment to reduce waste production