Inhibition of type I interferon signaling is a conserved function of gamma-herpesvirus-encoded microRNAs

ABSTRACT Herpesviruses encode multiple factors that disarm innate immune signaling to evade host anti-viral responses. Several viral microRNAs expressed by Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV) disrupt the induction of type I interferons (IFN) and/or the subsequent signaling events activated through type I IFN receptors. Here, we aimed to determine whether non-human primate (NHP) γ-herpesviruses (rhesus lymphocryptovirus [rLCV], rhesus rhadinovirus [RRV], and Japanese macaque rhadinovirus [JMRV]), closely related to EBV and KSHV, use similar microRNA (miRNA)-mediated strategies to regulate IFN responses. Through functional screens, we identified multiple viral miRNAs that attenuated type I IFN-mediated activation of an IFN-stimulated response element reporter and diminished expression of interferon-stimulated genes (ISGs). Infection of primary cells with miRNA-deficient rLCVs resulted in augmented expression of ISGs. Abrogation of EBV BART miRNA homologs from rLCV, in particular, led to heightened sensitivity of latently infected cells to exogenous type I IFN. Through sequence analysis and reporter assays, we show that targets of these viral miRNAs include transcripts encoding the type I IFN receptors (IFNAR1, IFNAR2) and core components of JAK/STAT signaling pathways (JAK1, IRF9). Taken together, these data demonstrate that suppression of type I IFN responses is a conserved function for NHP γ-herpesvirus miRNAs and provide important mechanistic insight into how these viral miRNAs regulate type I IFN signaling pathways. IMPORTANCE Gamma-herpesviruses establish life-long infections in their hosts. Evading anti-viral responses is a key component of long-term viral persistence. In this work, we show that small noncoding RNAs expressed by multiple non-human primate γ-herpesviruses regulate anti-viral responses by directly targeting components of the type I interferon (IFN) signaling pathway.