Supplementary MaterialsAdditional file 1 41598_2019_45126_MOESM1_ESM. out these genes, the engineered CHO cells exhibited activation of cellular immune responses and increased resistance to the RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications. strong class=”kwd-title” Subject terms: Virus-host interactions, Next-generation sequencing, Cellular signalling networks Introduction Chinese hamster ovary (CHO) cells are extensively used to produce biopharmaceuticals1 for numerous reasons. While one advantage is their reduced susceptibility to many human virus families2,3, there have been episodes of animal viral contamination of biopharmaceutical production runs, mostly from trace levels of viruses in raw materials. These infections have led to expensive decontamination efforts and threatened the supply of critical drugs4,5. Viruses that have halted production of valuable therapeutics include RNA viruses such as Cache Valley virus6, Epizootic hemorrhagic disease virus7, Reovirus6 and Vesivirus 21178. IPI-145 (Duvelisib, INK1197) Thus, there is a critical need to understand the mechanisms by which CHO cells are infected and how the cells can be universally engineered to enhance their viral resistance9. For example, a strategy was proposed to inhibit infection of CHO cells by minute virus of mice by engineering glycosylation10. We present an alternative strategy to prevent infections of several RNA infections with different genomic constructions and ways of hinder the sponsor anti-viral defense. Many reports have looked into the cellular reaction to varied infections in mammalian cells, and detailed the innate immune responses that are activated upon infection. For example, type I interferon (IFN) responses regulate the innate immune response, inhibit viral infection11,12 and can be induced by treatment of cells with poly I:C13,14. However, the detailed mechanisms of virus infection and the antiviral response CACNLB3 in CHO cells remain largely unknown. Understanding the role of type I IFN-mediated innate immune responses in CHO cells could be invaluable for developing effective virus-resistant CHO bioprocesses. Fortunately, recent genome sequencing15C17 and RNA-Seq tools have enabled the analysis of complicated cellular processes in CHO cells18,19, such as virus infection. To unravel the response of CHO cells to viral infection, we infected CHO-K1 cells with RNA viruses from diverse virus families. The RNA viruses are of particular interest since viral RNAs are all sensed by the RIG-I/TLR3 receptor, so broadly active resistance strategies might be engineered upon targeting relevant downstream pathways. IPI-145 (Duvelisib, INK1197) We assayed the ability of activators of type I IFN pathways to induce an antiviral response in the cells. Specifically, we asked the following questions: (1) Can CHO-K1 cells mount a robust type I IFN response when infected by RNA viruses? (2) Can innate immune modulators trigger a type I IFN response of CHO-K1 cells and, if so, are the type I IFN levels produced sufficient to protect CHO-K1 IPI-145 (Duvelisib, INK1197) cells from RNA virus infections? (3) Which biological pathways and processes are activated during virus infection and/or treatment with innate immune modulators, and are there common upstream regulators that govern the antiviral response? (4) Upon the identification of common upstream regulators, how can we engineer virus resistance into CHO cells for mitigating risk in mammalian bioprocessing? Here we address these questions, illuminate antiviral mechanisms of CHO cells, and guide the development of bioprocess IPI-145 (Duvelisib, INK1197) treatments and cell engineering efforts to make CHO cells more resistant to viral infection. Materials and Methods CHO-K1 cells and RNA virus infections The susceptibility of CHO-K1 cells to viral infection has been previously reported3. Since infectivity was demonstrated for viruses of a variety of families (harboring distinct.