HIV-1 Vpu exerts broad immunosuppressive effects by inhibiting NF-κB-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‑κB rather than IRF3 target genes. As a result, Vpu impairs the production of pro-inflammatory cytokines such as IFNβ, CXCL10 and IL-6. 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.