GSE168402
Murine Norovirus (MNV) infection results in anti-inflammatory response downstream of amino acids depletion in macrophages.
Purpose: Characterisation of MNV induced host genetic reprogramming and translational control exerted over the host response by comparison of available cytoplasmic transcripts and their association with polysomes. Results: RNaseq data showed an inadequate response to MNV infection downstream of MDA5 activation coupled with a cellular response to a metabolic stress.  In particular, all 296 significantly regulated transcripts showed a strong correlation between a transcript availability in the cytoplasm and its recrutment to the polysomal fraction as addressed using the R package 'Anota2seq'.  Genome annotation analyses using Cytoscape highlighted the host response to the viral infection but showed a cluster of genes involved in response to stress and the related intrinsic apoptotic pathways suggesting a prevalence of a metabolic stress response over the innate immune response to the viral replication. Conclusions: Our study provides the first understanding analysis of the host response to MNV at the level of available cytoplasmic mRNA and their recruitment to the actively translating fractions. It described an absence of translational control over the host innate immune response but highlight and inadequate NF-kB response correlating with an ectopic anti-inflammatory response to amino acid starvation. Overall design: Methods: Cytoplasmic RNA were extracted  from cells infected with MNV or UV-irradiated MNV at different time post-infection (6 and 10hpi). For each sample,  half was purified directly (Total samples) and half loaded onto polysome gradient to obtain the RNA associated with the translation machinery (Polysomal samples) in triplicate.  Samples were enriched for polyA-tailed mRNA and sequenced on Illumina HiSeq4000, outputs quality checked via FastQC and mapped onto mouse genome (Gencode release M12 GRCm38.p5) using Hisat2 and to the Murine Norovirus genome MNV1-CW1 (DQ285629) coding sequences (ORF1: ABB90153.1, ORF2: ABB90154.1, ORF3: ABB90155.1) using  Bowtie. Genomic features of the host were defined using 'Rsubread' and in-built gene annotations for the mouse genome (NCBI RefSeq gene annotations Build 38.1). Host genomic features were then annotated using the R package 'org.Mm.eg.db', Ensembl and GenBank. The feature count matrix consisted of the set of Host and MNV feature count and genes annotated as rRNA, miRNA, snoRNA, snoRNA or scaRNA were filtered out of the feature count matrix.  Filtering of lowly expressed genes was performed after library size normalisation by keeping genes with at least 0.25 CPM in at least 25% of the samples in both Total and Polysomal fractions and differential expression addressed using the GLM implementation of EdgeR.  A final filtering criterion was applied to each individual significant gene using the genome visualisation tool Integrative Genome Viewer IGV hosted by the Broad Institute. qRT–PCR validation was performed using SYBR Green assays.