Systems Analysis of a RIG-I Agonist Inducing Broad Spectrum Inhibition of Virus Infectivity

Goulet, Marie-Line; Olagnier, David; Xu, Zheng-Yun; Paz, Suzanne; Belgnaoui, S. Mehdi; Lafferty, Erin I.; Janelle, Valérie; Arguello, Meztli; Paquet, Marilène; Ghneim, Khader; Richards, Stephanie; Smith, Andrew T.; Wilkinson, Peter; Cameron, Mark J.; Kalinke, Ulrich; Qureshi, Salman T.; Lamarre, Alain; Haddad, Elias K.; Sékaly, Rafick Pierre; Peri, Suraj; Balachandran, Siddharth; Lin, Rongtuan; Hiscott, John

doi:10.1371/journal.ppat.1003298

Cited by 111 publications

(148 citation statements)

References 87 publications

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“…The panhandle structures of most negativestrand RNA viruses are only partially complementary (5,47). Very limited data obtained with authentic viral sequences, such as those of rabies virus and vesicular stomatitis virus, led to the conclusion that RIG-I tolerates partial complementarity in initiating the IFN response (5,48). Indeed, we have demonstrated that the partially complementary IAV panhandle structure is able to bind to and activate RIG-I.…”

Section: Resultsmentioning

confidence: 88%

Influenza A Virus Panhandle Structure Is Directly Involved in RIG-I Activation and Interferon Induction

Liu¹,

Park²,

Pyo

et al. 2015

J Virol

110

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Retinoic acid-inducible gene I (RIG-I) is an important innate immune sensor that recognizes viral RNA in the cytoplasm. Its nonself recognition largely depends on the unique RNA structures imposed by viral RNA. The panhandle structure residing in the influenza A virus (IAV) genome, whose primary function is to serve as the viral promoter for transcription and replication, has been proposed to be a RIG-I agonist. However, this has never been proved experimentally. Here, we employed multiple approaches to determine if the IAV panhandle structure is directly involved in RIG-I activation and type I interferon (IFN) induction. First, in porcine alveolar macrophages, we demonstrated that the viral genomic coding region is dispensable for RIG-I-dependent IFN induction. Second, using in vitro-synthesized hairpin RNA, we showed that the IAV panhandle structure could directly bind to RIG-I and stimulate IFN production. Furthermore, we investigated the contributions of the wobble base pairs, mismatch, and unpaired nucleotides within the wild-type panhandle structure to RIG-I activation. Elimination of these destabilizing elements within the panhandle structure promoted RIG-I activation and IFN induction. Given the function of the panhandle structure as the viral promoter, we further monitored the promoter activity of these panhandle variants and found that viral replication was moderately affected, whereas viral transcription was impaired dramatically. In all, our results indicate that the IAV panhandle promoter region adopts a nucleotide composition that is optimal for balanced viral RNA synthesis and suboptimal for RIG-I activation. IMPORTANCEThe IAV genomic panhandle structure has been proposed to be an RIG-I agonist due to its partial complementarity; however, this has not been experimentally confirmed. Here, we provide direct evidence that the IAV panhandle structure is competent in, and sufficient for, RIG-I activation and IFN induction. By constructing panhandle variants with increased complementarity, we demonstrated that the wild-type panhandle structure could be modified to enhance RIG-I activation and IFN induction. These panhandle variants posed moderate influence on viral replication but dramatic impairment of viral transcription. These results indicate that the IAV panhandle promoter region adopts a nucleotide composition to achieve optimal balance of viral RNA synthesis and suboptimal RIG-I activation. Our results highlight the multifunctional role of the IAV panhandle promoter region in the virus life cycle and offer novel insights into the development of antiviral agents aiming to boost RIG-I signaling or virus attenuation by manipulating this conserved region.

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Section: Resultsmentioning

confidence: 88%

Influenza A Virus Panhandle Structure Is Directly Involved in RIG-I Activation and Interferon Induction

Liu¹,

Park²,

Pyo

et al. 2015

J Virol

110

View full text Add to dashboard Cite

show abstract

“…35,36 Conceivably, at lower concentrations of RIG-I in the resting state, RIG-I surveys and binds only the ends of 5′trisphor-phylated RNA, but upon IFN induction and the concomitant increase in cellular levels of RIG-I protein, RIG-I molecules may start to bind internally near the RIG-I-capped RNA. 35,37 A distinct conformation of RIG-I bound internally to the duplex RNA is therefore highly desirable, which may provide a second-similar but not identical-means to activate RIG-I. Carefully designed experiments are needed to further clarify the functional implications of this RNA end capping preference vs. the duplex internal binding activity of RIG-I in vivo.…”

Section: Rig-i Prefers Capping the Ends Of Rna Duplex Rather Than Binmentioning

confidence: 99%

Toward a crystal-clear view of the viral RNA sensing and response by RIG-I-like receptors

Luo

2014

RNA Biology

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“…We note that KIN1400 treatment induced little if any expression of IFN-␤, type III IFN (IFN-2/3), or the proinflammatory cytokine interleukin-6 (IL-6) compared to the level of expression for the DMSO-treated control. Despite having identified KIN1400 and KIN1000 in similar screens that selected for small molecules that activate RLR-dependent signaling, the two compounds induced innate immune gene expression but little expression of type I and III IFNs, suggesting that they induce transcriptional activity that is distinct from that induced by IFN treatment alone and also different from that induced by RLR agonist RNA, which potently induces type I IFN expression (12,13). KIN1400 suppresses WNV in cultured cells.…”

Section: Kin1400 Triggers Irf3-dependent Innate Immune Antiviral Genementioning

confidence: 99%

“…These products act in concert to suppress and control virus infection. Synthetic and natural ligands that artificially induce PRR signaling and activate the innate immune response in cells and in mice show a proof of concept that triggering PRR pathways for innate immune induction can provide protection against virus infection (13,14). Signaling convergence to activate IRF3 is a common theme shared among PRRs (12).…”

mentioning

confidence: 99%

Targeting Innate Immunity for Antiviral Therapy through Small Molecule Agonists of the RLR Pathway

Pattabhi

Wilkins

Dong

et al. 2016

J Virol

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The cellular response to virus infection is initiated when pathogen recognition receptors (PRR) engage viral pathogen-associated molecular patterns (PAMPs). This process results in induction of downstream signaling pathways that activate the transcription factor interferon regulatory factor 3 (IRF3). IRF3 plays a critical role in antiviral immunity to drive the expression of innate immune response genes, including those encoding antiviral factors, type 1 interferon, and immune modulatory cytokines, that act in concert to restrict virus replication. Thus, small molecule agonists that can promote IRF3 activation and induce innate immune gene expression could serve as antivirals to induce tissue-wide innate immunity for effective control of virus infection. We identified small molecule compounds that activate IRF3 to differentially induce discrete subsets of antiviral genes. We tested a lead compound and derivatives for the ability to suppress infections caused by a broad range of RNA viruses. Compound administration significantly decreased the viral RNA load in cultured cells that were infected with viruses of the family Flaviviridae, including West Nile virus, dengue virus, and hepatitis C virus, as well as viruses of the families Filoviridae (Ebola virus), Orthomyxoviridae (influenza A virus), Arenaviridae (Lassa virus), and Paramyxoviridae (respiratory syncytial virus, Nipah virus) to suppress infectious virus production. Knockdown studies mapped this response to the RIG-I-like receptor pathway. This work identifies a novel class of host-directed immune modulatory molecules that activate IRF3 to promote host antiviral responses to broadly suppress infections caused by RNA viruses of distinct genera. IMPORTANCEIncidences of emerging and reemerging RNA viruses highlight a desperate need for broad-spectrum antiviral agents that can effectively control infections caused by viruses of distinct genera. We identified small molecule compounds that can selectively activate IRF3 for the purpose of identifying drug-like molecules that can be developed for the treatment of viral infections. Here, we report the discovery of a hydroxyquinoline family of small molecules that can activate IRF3 to promote cellular antiviral responses. These molecules can prophylactically or therapeutically control infection in cell culture by pathogenic RNA viruses, including West Nile virus, dengue virus, hepatitis C virus, influenza A virus, respiratory syncytial virus, Nipah virus, Lassa virus, and Ebola virus. Our study thus identifies a class of small molecules with a novel mechanism to enhance host immune responses for antiviral activity against a variety of RNA viruses that pose a significant health care burden and/or that are known to cause infections with high case fatality rates.

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Systems Analysis of a RIG-I Agonist Inducing Broad Spectrum Inhibition of Virus Infectivity

Cited by 111 publications

References 87 publications

Influenza A Virus Panhandle Structure Is Directly Involved in RIG-I Activation and Interferon Induction

Influenza A Virus Panhandle Structure Is Directly Involved in RIG-I Activation and Interferon Induction

Toward a crystal-clear view of the viral RNA sensing and response by RIG-I-like receptors

Targeting Innate Immunity for Antiviral Therapy through Small Molecule Agonists of the RLR Pathway

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