Abstract BACKGROUND: In vitroexperiments in which HIV-infected CD4 +T cells are co-cultured with natural killer (NK) cells yield incomplete elimination of the infected cells. We therefore hypothesize that cell-intrinsic pathways in CD4 +T cells are differentially regulated in HIV-infected cells to mediate resistance to NK cell-mediated killing. METHODS: Mock-infected and HIV-89.6-infected CD4 +T cells from 6 HIV −donors were co-cultured overnight +/− autologous NK cells. Following co-culture, cells were stained for the surface exposed HIV envelope protein using fluorescently conjugated HIV antibodies. Fluorescence activated cell sorting was then used to isolate infected and uninfected cells, followed by bulk RNA-sequencing. Transcripts from infected and uninfected cells co-cultured overnight with versus without NK cells were compared. RESULTS: RNA-seq analysis of CD4 +T cells that survived co-culture with NK cells revealed dozens of differentially expressed genes in infected, but not uninfected cells. This included upregulation of interferon-stimulated genes, including PD-L1 (p adj=3×10 −6), and NF-kB-related genes. Additional upregulated genes in the surviving infected cells included c-Fos (p adj=1.9×10 −5), c-Jun (p adj=4.9×10 −8), and cathepsin L (p adj=5×10 −3). CONCLUSIONS: NF-kB genes that are downregulated in infected cells, potentially through Vpu activity, are normalized in surviving infected cells. This may be due to NK cell targeting of Vpu-mediated HLA-C downregulation. Deconvolution of the relative contributions of specific genes/proteins to target cell resistance will reveal novel targets for the development of therapeutics to eliminate the HIV reservoir.