sncRNA signatures underlying HIV-1 restriction in elite controllers

HIV controllers maintain low viral loads without therapy, offering a natural model for a functional cure. The regulatory role of the small non-coding RNA (sncRNA) transcriptome in CD4+ T cells has been scarcely explored. Our study aimed to characterize the sncRNA and coding RNA landscape in CD4+ T cells from HIV controllers and to assess the potential antiviral activity of key non-coding RNAs.

We performed sncRNA-Seq and RNA-Seq on CD4+ T cells from elite controllers (ECs, n=10), viremic controllers (n=6), and untreated (n=8) and treated (n=9) non-controllers. Differential expression analysis, miRNA-mRNA correlation, interaction mapping, and functional annotation were conducted. To assess antiviral activity, inhibitors for candidate miRNAs were transfected into CEM-NKR.CCR5 cells, which were then infected with a replication-competent HIV-1 clone.

The sncRNA compartment of elite controllers was distinct, including overexpression of specific transfer RNA (tRNA)-Lys isoacceptors and a cluster of five PIWI-interacting RNAs (piRNA) associated with tRNA-Lys genomic repeats. Noteworthy, miR-99b-5p and miR-125a-5p were significantly downregulated in elite controllers compared to both non-controller groups. Concurrently, the coding transcriptome of elite controllers displayed an enrichment in p53 signaling, inflammatory response, cell activation, and oxidative stress. Several genes upregulated in these processes (e.g., THBS1, DPM2) were identified as validated targets of miR-99b-5p and miR-125a-5p. Finally, in vitro experiments showed that miR-99b-5p and miR-125a-5p inhibition, individually or in combination, reduced viral replication by 17.6%, 16.3%, and 21.4%, respectively.

Elite controllers exhibit a distinctive sncRNA signature in CD4+ T cells. The coordinated downregulation of miR-99b-5p and miR-125a-5p may contribute to a restrictive cellular environment and reducing viral replication, revealing a novel layer of post-transcriptional regulation in natural HIV control. These findings underscore these miRNAs and their potentially regulated counterparts as potential targets for future therapeutic strategies.