Transcriptome analysis of a CHO cell line expressing a recombinant therapeutic protein treated with inducers of protein expression

•RNA-Seq analysis was used to examine inducer effects on gene expression.•Inducer treatment increased RANK–Fc mRNA from 16% up to 45% of total cellular mRNA.•Specific productivity positively correlated to recombinant protein mRNA level.•Selectable marker and RANK–Fc were 2 out of 7 mRNAs positively correlated to qP.•Expression of many cell growth and housekeeping genes negatively correlated to qP.•Transcript level of the recombinant protein is a major qP determinant. The search for specific productivity (qP) determinants in Chinese hamster ovary (CHO) cells has been the focus of the biopharmaceutical cell line engineering efforts aimed at creating “super-producer” cell lines. In this study, we evaluated the impact of small-molecule inducers and temperature shift on recombinant protein production, and used transcriptomic analysis to define gene-phenotype correlations for qP in our biological system. Next-generation RNA Sequencing (RNA-Seq) analysis revealed that each individual inducer (caffeine, hexamethylene bisacetamide (HMBA) and sodium butyrate (NaBu)) or a combination treatment had a distinct impact on the gene expression program of the RANK–Fc cell line. Temperature shift to 31°C impacted inducer action with respect to transcriptional changes and phenotypic cell line parameters. We showed that inducer treatment was able to increase expression level of the Fc- fusion mRNA and the selectable marker mRNA from 16% up to 45% of total mRNA in the cell. We further demonstrated that qP exhibited a strong positive linear correlation to transcript levels of both the RANK–Fc fusion protein and the dihydrofolate reductase (DHFR) selectable marker. In fact, these were 2 out of 7 transcripts with significant positive correlation to qP at both temperatures. Many more transcripts were anti- correlated to qP, and gene set enrichment analysis (GSEA) revealed that those were involved in cell cycle progression, transcription, mRNA processing, translation and protein folding. Therefore, we postulate that the transcript level of the recombinant protein is a major qP determinant in our biological system, while downregulation of routine activity within the cell is necessary to divert cellular resources towards recombinant protein production.