Baby Hamster Kidney (BHK) cells, a widely used industrial cell line for recombinant protein production, still suffer from limitations in the availability of genomic resources in this information-rich age. We therefore applied high throughput sequencing to characterize and quantify transcript levels globally across six cDNA libraries prepared from Syrian hamster tissues as well as treated and untreated recombinant and parental BHK cell lines. Comparative analysis with the Chinese hamster revealed a high degree of homology, according the use of the Chinese hamster genome as backbone for an efficient transcriptome assembly. Overall, this effort aims to achieve a near-complete repertoire of annotated, close-to-full-length genes, spanning a range of functional classes.
Transcript abundance levels, determined by alignment and frequency computation for each library against assembled transcripts, reveal a wide dynamic range spanning nearly five orders of magnitude. Visualization in a pathway context enables one to conjecture possible physiologically active pathways in these cultured cells. Comparative transcriptome analyses between the different libraries provide insight of perturbed physiological functions under chemical treatments, including the demethylation drug 5’azacytidine. The diversity of libraries sequenced in this study also allows the exploration of polymorphisms in transcripts across different cell line and tissue sources. Furthermore, comparative analysis to the Chinese hamster genome permits the examination of sequence orthology, and the variations in codon usage between the two species, especially for those functional classes important for recombinant protein production.
These genomic resources will provide valuable process diagnostic tools, providing further opportunities to fingerprint, engineer and enhance BHK cells in their role as recombinant protein producers.