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Primate-Specific Mir-576-3P Sets Host Defense Signalling Threshold

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Primate-Specific Mir-576-3P Sets Host Defense Signalling Threshold ARTICLE Received 22 May 2014 | Accepted 12 Aug 2014 | Published 18 Sep 2014 DOI: 10.1038/ncomms5963 Primate-specific miR-576-3p sets host defense signalling threshold Melanie L. Yarbrough1, Ke Zhang1, Ramanavelan Sakthivel1, Christian V. Forst2, Bruce A. Posner3, Glen N. Barber4, Michael A. White1 & Beatriz M.A. Fontoura1 MicroRNAs (miRNAs) have been shown to regulate viral infection, but the miRNAs that target intracellular sensors and adaptors of innate immunity have not been fully uncovered. Here we conduct an miRNA mimic screen and validation with miRNA inhibitors in cells infected with vesicular stomatitis virus (VSV) to identify miRNAs that regulate viral–host interactions. We identify miR-576-3p as a robust regulator of infection by VSV and other RNA and DNA viruses. While an miR-576-3p mimic sensitizes cells to viral replication, inhibition of endogenous miR-576-3p prevents infection. miR-576-3p is induced by IRF3 concomitantly with interferon and targets STING, MAVS and TRAF3, which are critical factors for interferon expression. Interestingly, miR-576-3p and its binding sites are primate-specific and miR-576-3p levels are reduced in inflammatory diseases. These findings indicate that induction of miR-576-3p by IRF3 triggers a feedback mechanism to reduce interferon expression and set an antiviral response threshold to likely avoid excessive inflammation. 1 Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9039, USA. 2 Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, New York 10029-6574, USA. 3 Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9039, USA. 4 Department of Cell Biology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA. Correspondence and requests for materials should be addressed to B.M.A.F. (email: [email protected]). NATURE COMMUNICATIONS | 5:4963 | DOI: 10.1038/ncomms5963 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5963 lthough studies on the functions of host miRNAs during viability. After transfection of miRNA mimics, cells were infected viral infection are still at early stages, increasing evidence with a VSV strain that expresses GFP, so that the progression of Asuggests that miRNAs have a key role in the regulation of infection could be monitored in live cells by fluorescence viral infection1. While viruses may utilize cellular miRNAs to (Fig. 1b). Infection conditions were optimized so that control promote their replication, miRNA expression can also facilitate transfected cells exhibited approximately 50% cell death after 20 h the host antiviral response through interaction with viral RNA or of infection (Fig. 1c). This allowed for the identification of by negatively regulating host factors required for viral miRNAs that promote resistance or sensitivity to infection. proliferation. One example is miR-199a-3p, which has antiviral A total of 810 mimics representing 723 unique miRNAs were activity by regulating various pathways targeted by viruses such as analysed. Those mimics that resulted in toxicity upon transfection the PI3K/AKT and ERK/MAPK pathways, oxidative stress in the absence of VSV infection were excluded from further signalling and prostaglandin synthesis2. Studies in vivo by analysis (Fig. 1d and Supplementary Data 1). Otsuka et al.3 demonstrated that mice harbouring a mutant miRNAs that impact viral infection were identified by their Dicer allele were hypersusceptible to VSV infection, suggesting ability to increase or decrease cell viability in the presence of that host miRNAs contribute to host resistance to viral infection. VSV infection compared with non-targeting mimic control. Cell VSV is a useful model virus for understanding viral infection viability ratios between infected and uninfected cells expressing processes as well as innate and adaptive immune responses. VSV the same miRNA were calculated and ranked from highest to is a negative sense RNA virus that replicates in the cytoplasm of lowest (Supplementary Data 2). Those miRNAs that increased or most vertebrate and many invertebrate cell types4,5. During decreased cell viability were identified as resisters and sensitizers infection, viruses are susceptible to innate immune responses that of VSV infection, respectively, and the top hits were selected. For induce type I interferon (IFN) and inflammatory cytokines. confirmation, these miRNA hits were again transfected into Upon cytoplasmic entry, viral RNA is recognized by a family of HBECs followed by infection as in the primary screen (Fig. 1e) DExD/H-box helicases that include retinoic acid inducible gene 1 and their basal levels were measured by microRNA array (RIG-I) and melanoma differentiation associated antigen 5 (Supplementary Data 3). Eight miRNA resisters (Fig. 1e) and (refs 6,7). Upon interaction with viral RNA, RIG-I and six miRNA sensitizers (Fig. 1f) were validated. miR-193b* was not melanoma differentiation associated antigen 5 associate with confirmed as hit (Fig. 1f). the adaptor protein MAVS (also known as IPS-1, VISA, or To determine if endogenous expression of the miRNAs could CARDIF) to facilitate activation of transcription factors that significantly impact viral infection, we transfected inhibitors of induce type I IFN signalling8–11. The efficient induction of each of the confirmed hits from the miRNA mimic screen into antiviral response to intracellular viral RNA and also foreign HBECs and infected them with VSV. The inhibitors are single- DNA was shown to involve a central adaptor molecule STING stranded oligonucleotides that compete with a target mRNA for (stimulator of IFN genes), an ER-associated protein that interacts binding to endogenous mature miRNA. Transfection of inhibitors with RIG-I and MAVS12,13. Recently, it was shown that foreign of miRNAs that resist VSV infection resulted in significantly DNA such as that released by viruses in the cytoplasm is sensed decreased cell viability upon VSV infection for several hits, by the enzyme cyclic GMP-AMP synthase (CGAS), which including miR-802, let-7e, let-7a, miR-98 and miR-125b (Fig. 1g). synthesizes cyclic-di-GMP-AMP molecules that are recognized miR-98, let-7 miRNAs and miR-125b have been previously by STING to induce IFN signalling14,15. Thus, type I IFN shown to regulate responses to microbial infection, serving as interferon production represents a major antiviral response validation to our screen17–19. Inhibition of miRNAs that pathway and STING is a key mediator of this response. sensitized HBECs to viral infection resulted in increased cell In this manuscript, we identify a novel primate-specific viability during VSV infection for many of the top hits. This effect microRNA-driven feedback mechanism that prevents excessive was observed with five miRNAs including miR-576-3p, miR-550, innate immune signalling that can lead to abnormal inflamma- miR-138, miR-888* and miR-625 (Fig. 1h). tion. By using an unbiased genome-wide screening approach to Since transfection of the mimic and inhibitor of miR-576-3p search for miRNAs that regulate viral–host interactions, we produced significant opposing effects on VSV infection (Fig. 1f,h) identified miR-576-3p, which is induced by IRF3 and in turn and because it more strongly promoted viral replication as downregulates key constituents of the IFN expression pathway, compared with other novel hits, using the conditions shown in such as STING, MAVS and TRF3, to avert sustained immune Fig. 2a, we investigated the unknown function of miR-576-3p in signalling. viral infection. Overexpression of miR-576-3p in VSV-GFP infected HBECs resulted in increased GFP production (Fig. 2a) and virus replication, as supernatants from these cells yielded an Results and Discussion increase in viral titre compared with control transfected cells Identification of miRNAs that regulate viral infection.To (Fig. 2b). Additional results of VSV replication in the presence of identify novel miRNAs that are key regulators of viral infection, miR-576-3p mimic or inhibitor are shown in Supplementary we analysed the impact of expressing a library of human miRNA Fig. 1. Indeed, enhanced viral replication (Fig. 2b and mimics on the viability of cells infected with VSV (Fig. 1a). The Supplementary Fig. 1a) is corroborated by the increase in viral miRNA mimics are synthetic RNA duplexes, which are func- protein levels on overexpression of miR-576-3p (Fig. 2c; tionally equivalent to mature miRNAs that have been processed Supplementary Fig. 6). In contrast, inhibition of endogenous by Dicer. Upon transfection into cells, the mimics lead to miR-576-3p function dramatically decreased viral protein levels downregulation of target genes. The screen was conducted in (Fig. 2c; Supplementary Fig. 6) and viral replication human bronchial epithelial cells (HBECs)16, which represent a (Supplementary Fig. 1b). To determine if regulation of the host common site of viral infection. To determine that transfection of response to viral infection by miR-576-3p is specific to VSV, we miRNA mimics themselves do not impact viral infection, a non- infected cells treated with miR-576-3p with influenza virus. As targeting miRNA mimic from Caenorhabditis elegans was used as shown in Fig. 2d, miR-576-3p significantly sensitized HBECs to a negative control and was
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