A Short Hairpin RNA Screen of Interferon-Stimulated Genes Identifies a Novel Negative Regulator of the Cellular Antiviral Response

Abstract

The type I interferon (IFN) signaling pathway restricts infection of many divergent families of RNA and DNA viruses by inducing hundreds of IFN-stimulated genes (ISGs), some of which have direct antiviral activity. We screened 813 short hairpin RNA (shRNA) constructs targeting 245 human ISGs using a flow cytometry approach to identify genes that modulated infection of West Nile virus (WNV) in IFN-β-treated human cells. Thirty ISGs with inhibitory effects against WNV were identified, including several novel genes that had antiviral activity against related and unrelated positive-strand RNA viruses. We also defined one ISG, activating signal cointegrator complex 3 (ASCC3), which functioned as a negative regulator of the host defense response. Silencing of ASCC3 resulted in upregulation of multiple antiviral ISGs, which correlated with inhibition of infection of several positive-strand RNA viruses. Reciprocally, ectopic expression of human ASCC3 or mouse Ascc3 resulted in downregulation of ISGs and increased viral infection. Mechanism-of-action and RNA sequencing studies revealed that ASCC3 functions to modulate ISG expression in an IRF-3- and IRF-7-dependent manner. Compared to prior ectopic ISG expression studies, our shRNA screen identified novel ISGs that restrict infection of WNV and other viruses and defined a new counterregulatory ISG, ASCC3, which tempers cell-intrinsic immunity.

Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein

“…Early studies attempting to evaluate the antiviral function of IFI6-16 showed that introduction of IFI6-16 in a KO cell line (HT1080_IFI6 −/− ) does not affect the replication of encephalomyocarditis virus, Semliki forest virus, or coccal virus, suggesting that IFI6-16 is not required to control these viral replications (61). In contrast, IFI6-16 was identified as a negative regulator that markedly inhibited the replication of yellow fever virus (31), DENV (62), and West Nile virus (63). The expression of the gene was also found to suppress respiratory syncytial virus replication and was down-regulated by the virus (64).…”

New insights into innate immune restriction of West Nile virus infection

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An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication

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