SRA

Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells, the most commonly used cell line in biomanufacturing, to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited increased resistance to the prototype RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production. Overall design: We infected CHO-K1 cells with a panel of RNA viruses (VSV, EMCV and Reo) from diverse pretreatment (no treatment, or exogenously-added type I IFN or poly I:C). Viral stocks were generated in susceptible Vero cells as per standard practices using DMEM (Dulbecco's Modified Eagle's medium) supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin (DMEM-10). Library preparation was performed with Illumina's TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103).