HIV-1 Vpu exerts broad immunosuppressive effects by inhibiting NF-?B-dependent gene expression

Using an unbiased RNA sequencing approach of primary CD4+ T cells infected with three wild type primary HIV-1 isolates and selective mutants thereof, Langer et al. show that the HIV-1 accessory protein Vpu exerts broad immunosuppressive effects, inhibiting the induction of innate and adaptive immune responses. Transcription factor network analyses reveal that Vpu suppresses the expression of NF-?B rather than IRF3 target genes. As a result, Vpu impairs the production of pro-inflammatory cytokines such as IFNß, CXCL10 and IL-6. Overall design: Human CD4+ T cells, isolated from 4 independent healthy donors, A1, X, Y and Z (corresponding to A, B, C and D in the publication), were infected with equal amounts of three different HIV-1 primary isolates, two of them being clade B viruses (HIV-1 CH077 and HIV-1 STCO1) and one of them being a clade C virus (HIV-1 CH293). In addition, CD4+ T cells were infected with mutant viruses of the aforementioned primary isolates. Specific mutations were introduced in these viruses to either abrogate Vpu expression ("vpu stop"), or selectively abrogate Vpu-mediated counteraction of the antiviral protein tetherin ("A20L/A24L" or "A15L/A19L") or NF-kB inhibition ("R50K" or "R45K"). Global RNA of infected cells was collected 72 hours post infection and processed for RNA-Seq analysis.