GSE109806
Transcriptome profiling of alphaherpesvirus-infected cells treated with the HIV-integrase inhibitor raltegravir reveals profound and specific alterations in host transcription.
Purpose: To study the effects of raltegravir treatment for corneal cells on host gene expression during FHV-1 infection and in uninfected cells. Method: For examination of effects in infected cells, corneal cells were infected with FHV-1 for 2 hours and treated with raltegravir or DMSO for 2 h. For examination of effects in uninfected cells, corneal cells were infected with FHV-1 for 2 h. Data was analyzed using a standard pipeline. Follow up of results were done with SYBR green based qPCR and functional assays where relevant.  Results: In infected cells, we identifed 399 differentially expressed genes following raltegravir therapy. Many of these genes had functions as anti-angiogenic factors and in metabolic pathways. In contrast, in uninfected cells, only 27 genes were identified as differentially regulated by raltegravir, with little overlap with those modulated during infection and little shared biological functions. This indicates that raltegravir is unlikely to induce side effects in vivo. Conclusion: Our study represents the first, to our knowledge, use of RNAseq technology to study the effects of an antiviral on host gene expression during a virus infection. We conclude that such methodology will be useful in future studies to identify bystander effects of drug treatment. Overall design: RNAseq analysis of gene expression of antiviral treated, FHV-1 infected or uninfected corneal cells. For each sample, 3 independent biological replicates were performed