IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection

Abstract

Pathogen recognition receptor (PRR) signaling is critical for triggering innate immune activation and the expression of immune response genes, including genes that impart restriction against virus replication. RIG-I-like receptors and TLRs are PRRs that signal immune activation and drive the expression of antiviral genes and the production of type I IFN leading to induction of IFNstimulated genes, in part through the interferon regulatory factor (IRF) family of transcription factors. Previous studies with West Nile virus (WNV) showed that IRF3 and IRF7 regulate IFN expression in fibroblasts and neurons, whereas macrophages and dendritic cells (DCs) retained the ability to induce IFN-in the absence of IRF3 and IRF7 in a manner implicating IRF5 in PRR signaling actions. Here we assessed the contribution of IRF5 to immune gene induction in response to WNV infection in DCs. We examined IRF5-dependent gene expression and found that loss of IRF5 in mice resulted in modest and subtle changes in the expression of WNV-regulated genes.Anti-IRF5 chromatin immunoprecipitation with next-generation sequencing of genomic DNA coupled with mRNA analysis revealed unique IRF5 binding motifs within the mouse genome that are distinct from the canonical IRF binding motif and that link with IRF5-target gene expression.Using integrative bioinformatics analyses, we identified new IRF5 primary target genes in DCs in response to virus infection. This study provides novel insights into the distinct and unique innate immune and immune gene regulatory program directed by IRF5. K E Y W O R D S bone marrow-derived dendritic cells, ChIP-exo, interferon signaling, IRF5, RNA-seq, West Nile virus Within the IRF family, studies have focused extensively on IRF3 and IRF7 as the major IRFs that modulate antiviral gene expression. During infection with RNA viruses, such as the neurotropic flavivirus West Nile virus (WNV), cellular pathogen recognition receptors (PRRs), including RIG-I-like receptors (RLRs) and TLRs, recognize viral RNA motifs. 6,7 Signaling from PRRs leads to activation of downstream protein kinases that phosphorylate IRF3 and IRF7, resulting in the dimerization and nuclear translocation of these factors to induce target gene expression. 8 Types I and III IFNs, specific antiviral effector genes, and immunomodulatory genes, have been identified as IRF3 and IRF7 targets that coordinate an effective antiviral immune response. 9,10 Beyond IRF3 and IRF7, recent studies of WNV infection in mouse and human cells suggest that additional factors are at play to orchestrate immune response against virus infection. Irf3-/-Irf7-/double knockout (DKO) mice failed to control WNV replication,

Current Understanding of West Nile Virus Clinical Manifestations, Immune Responses, Neuroinvasion, and Immunotherapeutic Implications

“…Type I IFN may also diminish DC maturation, reduce production of IL-1β, and weaken antiviral T cell immunity in AXL receptor tyrosine kinase deficient (Axl −/− ) mice during WNV and influenza infection [70]. Recent studies showed that IL-1β, IFN regulatory factors (IRF) 3, 5 and 7 are important to induce DC-mediated antivirus IFN responses against WNV infection [71][72][73].…”

Promoter Binding and Nuclear Retention Features of Zebrafish IRF Family Members in IFN Response

“…Genetic data have revealed the relevance of IRF family members to IFN responses ( 6 – 10 ). IRF3 and IRF7 are two primary regulators of IFN expression downstream of signaling pathways triggered by TLRs (such as TLR3/7/9), RLRs and DNA sensors (such as cGAS) ( 1 ).…”