CD4 T cell transcriptomic response to HIV-1 infection: effects of time, viral strain, cell subtype, Vpr, and IFNa/b R2 blocking

Analysis of gene expression in primary CD4 T cells of multiple donors, following in vitro HIV-1 infection. Gene expression was measured at 4.5, 8, 12, 24 and 48h post infection and compared to mock-infected and HIV-1 delta-Env infected cells to determine and categorise the temporal expression profiles of genes affected by HIV-1 infection. Additional experiments determined: 1) the degree to which the accessory viral protein Vpr is responsible for the observed transcriptomic changes, 2) the effect of varying the viral strain, 3) the effect on the transcriptome of specifically memory CD4 T cells, the primary target cell subtype of HIV-1, in comparison with bulk CD4 T cells, and 4) the effect of blocking the Interferon alpha/beta receptor 2 during HIV-1 infection. 13 experiments involving 147 samples, all measuring gene expression after HIV-1 (or mock) infection at particular time points; two experiments are time courses with additional time points; the others each vary an additional factor such as cell type or viral strain.