ABSTRACT
Shock-and-kill is one of the most advanced, yet unrealized, concepts towards establishment of HIV-1 cure. Treatment with latency-reversing agents (LRAs), including histone deacetylase inhibitors (HDACis) exerting chromatin remodelling and gene expression reprogramming, combined with anti-retroviral therapy reactivates HIV-1 transcription in vitro, ex vivo and in vivo. However, LRA treatment so far failed to significantly reduce the size of the viral reservoir in people living with HIV-1 (PLHIV), indicating its insufficiency in terms of elimination of latently infected cells. Here, by combining single cell RNA-sequencing and functional approaches, we characterised HDACi treatment-induced alterations of CD4+ T-cell subset composition, subpopulation-specific transcriptional profiles, and HIV-1 reactivation, using Vorinostat and Panobinostat as two prototypic HDACis. Ex vivo exposure of CD4+ T-cells from three aviremic PLHIV with clinically applicable concentrations of Panobinostat, but not Vorinostat, markedly reduced the expression and functionality of genes mediating antiviral immunity and T-cell activation. These modulations occurred in a CD4+ T-cell subset-specific manner, with an PLHIV-specific exhausted CD4+ T-cell subset that was to a certain extent refractory to said gene modulations. Furthermore, specific cellular genes were differentially expressed in the small HIV-1 RNA-positive fraction of CD4+ T-cells from PLHIV. In latently HIV-1-infected J1.1 T-cells, specific genes correlated positively and negatively with the abundance of HIV-1 transcripts at the single cell level. In sum, we present LRA treatment-imposed gene expression changes and their functional implications, and present a list of gene candidates that may serve as biomarkers of T-cells with active HIV-1 transcription.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Shock-and-kill is one of the most advanced, yet unrealized, concepts towards establishment of HIV-1 cure. Treatment with latency-reversing agents (LRAs), including histone deacetylase inhibitors (HDACis) exerting chromatin remodelling and gene expression reprogramming, combined with anti-retroviral therapy reactivates HIV-1 transcription in vitro, ex vivo and in vivo. However, LRA treatment so far failed to significantly reduce the size of the viral reservoir in people living with HIV-1 (PLHIV), indicating its insufficiency in terms of elimination of latently infected cells. Here, by combining single cell RNA-sequencing and functional approaches, we characterised HDACi treatment-induced alterations of CD4+ T-cell subset composition, subpopulation-specific transcriptional profiles, and HIV-1 reactivation, using Vorinostat and Panobinostat as two prototypic HDACis. Ex vivo exposure of CD4+ T-cells from three aviremic PLHIV with clinically applicable concentrations of Panobinostat, but not Vorinostat, markedly reduced the expression and functionality of genes mediating antiviral immunity and T-cell activation. These modulations occurred in a CD4+ T-cell subset-specific manner, with an PLHIV-specific exhausted CD4+ T-cell subset that was to a certain extent refractory to said gene modulations. Furthermore, specific cellular genes were differentially expressed in the small HIV-1 RNA-positive fraction of CD4+ T-cells from PLHIV. In latently HIV-1-infected J1.1 T-cells, specific genes correlated positively and negatively with the abundance of HIV-1 transcripts at the single cell level. In sum, we present LRA treatment-imposed gene expression changes and their functional implications, and present a list of gene candidates that may serve as biomarkers of T-cells with active HIV-1 transcription.