Host gene expression changes induced by an HIV-1 mutant associated with delayed AIDS progression reveal potential mechanisms

HIV-1 viral protein R (Vpr) is a multifunctional protein central to HIV-1 pathogenesis and progression to AIDS. Polymorphisms in vpr have been linked to varying rates of HIV-1 progression. Of note is the HIV-1 Vpr R77Q mutant, associated with delayed progression to AIDS (also as the long-term non-progressor phenotype, or LTNP). We previously demonstrated that the R77Q mutant promotes a non-inflammatory, apoptotic phenotype in CD4+ T cells. To investigate the mechanism underlying the R77Q-induced apoptotic phenotype, we performed RNA sequencing on a CD4+ T cell line, HUT78, infected with either a replication-competent wild-type strain (NL4-3) or the R77Q mutant. Our results show that at 72 hours post-infection, transcriptomes were heterogeneous, and differential expression analysis identified 289 differentially expressed genes (DEGs) in the R77Q vs. WT comparison. Functional enrichment analysis revealed enriched pathways associated with apoptosis. Gene ontology (GO) terms and GO connections also revealed an apoptotic signature. Although both viral strains upregulated pro-apoptotic genes, the R77Q mutant failed to upregulate some key anti-apoptotic genes such as bcl-2, while WT-infected cells displayed upregulation of those anti-apoptotic genes. Predicted protein-protein interaction within the Bcl-2 family local network also suggests that interactions within this network were substantially affected. Taken together, these findings provide a transcriptomic basis for our previous observations of enhanced apoptosis in R77Q-infected cells and highlight distinct host cell responses that may underlie delayed HIV-1 progression. These results may be useful in identifying new targets to delay AIDS progression. ImportanceThe R77Q mutant has been a long-standing variant of interest because of its association with long-term non-progressors (LTNPs), yet the mechanisms behind this phenotype remain poorly defined. We previously showed that the R77Q mutant is less cytotoxic, killing fewer cells than WT via a non-inflammatory apoptotic pathway while suppressing inflammatory cytokine release, possibly contributing to the LTNP phenotype. Here, we provide a transcriptomic basis for this phenotype and identify a potential novel loss-of-function mechanism in which R77Q-induced apoptosis arises from a failure to upregulate key anti-apoptotic genes. Defining host responses in the context of delayed HIV-1 progression offers novel insights into cellular networks that could inform future therapeutic strategies beyond the current antiviral approaches.