Validation and identification of reference genes in Chinese hamster ovary cells for Fc-fusion protein production

Abstract

Chinese hamster ovary cells are the predominant cell lines used for bio-therapeutic production. Real-time quantitative PCR (RT-qPCR) and transcriptomics are powerful tools to understand and optimize the Chinese hamster ovary cells for higher productivity or better control of product qualities. Reliable reference genes, which were proved to be experiment-specific, are critical yardsticks. In this study, we compared expression stability of 20 candidate reference genes at mRNA level, including commonly used housekeeping genes, previous literature reported genes in Chinese hamster ovary cells producing an intact antibody, and new candidates suggested by our RNA-seq transcriptomic database, in RT-qPCR reactions in Fc-fusion protein-producing Chinese hamster ovary cells with various productivity during long-term cultivation and fed-batch cultures at 26 different conditions. geNorm, NormFinder, BestKeeper, and ΔCt programs and methods were utilized to analyze the gene expression stability and gave an overall ranking. Akr1a1, Gpx1, and Aprt in long-term cultivation and Akr1a1, Rps16 in fed-batch culture, which have not been reported previously, exhibited the highest stability of gene expression, while Pabpn1, Hirip3, and Actb in both sets of experiments together with Atp5f1 in long-term passage process showed the weakest stability. The results were then validated using GLP1-Fc (Glucagon-like peptide-1 Fc fusion protein) gene as the target with determined expression level which were doubly confirmed by both absolute RT-qPCR and confocal microscopy. These new references should be considered for the investigations on Chinese hamster ovary cells in related research. Impact statement In order to reveal potential genotype-phenotype relationship, RT-qPCR reactions are frequently applied which require validated and reliable reference genes. With the investigation on long-term passage and fed-batch cultivation of CHO cells producing an Fc-fusion protein, four new reference genes–Akr1a1, Gpx1, Aprt, and Rps16, were identified from 20 candidates with the aid of geNorm, NormFinder, BestKeeper, and ΔCt programs and methods. This article provided more verified options in reference gene selection in related research on CHO cells.