HIV-1 Vpr induces an NFAT-controlled transcriptional program in primary CD4+ T cells

HIV-1 Vpr has a major impact on the cellular transcriptome and proteome. Although Vpr is known to stimulate the nuclear factor of activated T cells (NFAT), it remained unclear to what extent transcriptional changes induced by Vpr are governed by NFAT. We, therefore, performed RNA sequencing and transcription factor network analyses of primary CD4+ T cells infected with HIV-1 harboring an intact or defective vpr open reading frame. Furthermore, we analyzed Vprs from HIV-1 groups M, N, O, and P to investigate whether Vpr-mediated NFAT activation is conserved among different clades of HIV-1. All Vprs stimulated NFAT and induced the expression of the T cell activation marker CD69, which is a bona fide target of NFAT in T cells. Our transcriptome analysis showed that NFAT controls 46.5% of 1,083 Vpr-deregulated genes in primary CD4+ T cells. Gene set enrichment analyses revealed that Vpr upregulates processes related to signaling, proliferation, and immunity, while downregulating cell cycle progression, ribosome activity, and cytoskeleton organization. Quantitative real-time PCR confirmed Vpr-mediated modulation of specific genes, i.e., upregulation of NEIL1, TNFS4, and CXCL10, as well as downregulation of CCNB1, CDC20, CENPA, and PLK1. Notably, NFAT inhibition abrogated Vpr-mediated enhancement of HIV-1 replication in primary CD4+ T cells and alleviated G2 arrest in Jurkat T cells. In conclusion, a significant proportion of Vpr-deregulated genes in CD4+ T cells are controlled by NFAT. Affected pathways are related to T cell activation, cell cycle progression, cytoskeleton, and chromosome organization. Thus, Vpr-mediated NFAT activation is a key regulatory event that reprograms the host cell transcriptome into an environment supportive of HIV-1 replication.

The HIV-1 accessory protein Vpr is known for its profound effect on the host proteome. It degrades many cellular proteins, including transcription factors and DNA-associated proteins. In addition, Vpr activates the nuclear factor of activated T cells (NFAT), a key transcription factor in T cells. However, it has remained unclear to what extent Vpr and consequently NFAT control changes in the transcriptome of HIV-1-infected primary CD4+ T cells. In this study, we show that Vpr significantly alters the transcriptome of CD4+ T cells, with almost half of the deregulated genes being under NFAT control. These changes involve pathways associated with increased immune activation and cell cycle regulation, shedding light on how Vpr contributes to CD4+ T cell depletion and HIV-1 pathogenesis.