RLR-mediated immunity is unique and critical in the response to West Nile Virus

Abstract

Abstract RIG-I-Like Receptors (RLRs) include RIG-I, MDA5, and LGP2. RLRs are vital pathogen recognition receptors in the defense against RNA viruses. West Nile Virus (WNV) is an emerging, neurotropic flavivirus that infects the central nervous system to cause disease and death. RIG-I and MDA5 work in tandem to initiate innate immune responses against WNV infection, though the role of LGP2 in this process is not well defined. To gain a deeper understanding of the contributions of each RLR in the innate immune response to WNV, we conducted a systems biology approach to assess the role of each RLR in immune programming. We conducted genome-wide RNAseq and bioinformatics analysis of WNV infection in bone marrow derived macrophages from the RLR-deficient mice. Here we show that the RLRs drive distinct immune gene activation and polarization of the immune response. In our data, the RLR-dependent, WNV-induced immune response polarization overshadows the classical drivers of viral innate immune responses, interferon I (IFN) and IFN-stimulated genes, thus underscoring the importance of innate immune activation for channeling the adaptive immune system into specific effector pathways. Bioinformatics analysis and computational modeling was used to define a unique gene signature of each RLR following WNV infection. Further, we dissected the complex virus-induced cytokine response utilizing multiplex analyses to link gene induction and cytokine protein output. These analyses reveal that distinct RLR-driven transcriptional programs lead to differential functional output in immune response initiation against WNV infection. Our study demonstrates a clear, defined role for RIG-I, MDA5, and LGP2 in immune programming against virus infection.