Background:
CD4 T cells with latent HIV-1 infection persist despite treatment with currently available antiretroviral agents and represent the main barrier to HIV-1 cure. Pharmacological disruption of viral latency may increase the immunological vulnerability of HIV-1 infected cells, but the efficacy of latency-reversing agents for reducing HIV-1 persistence remains to be proven
Methods:
We conducted a randomized controlled human clinical trial in which panobinostat (PBT), a potent histone deacetylase inhibitor (HDACi), was evaluated in combination with pegylated IFNα2a (PEG-IFNα2a). ART-treated participants were randomized to receive PBT alone (n=4), the combination of PBT and PEG-IFNα2a (n=9) or PEG-IFNα2a alone (n=4). We quantified CD4 T cell-associated HIV-1 RNA by RT-ddPCR and proviral HIV-1 DNA using the intact proviral DNA assay (IPDA). Cellular immune responses were analyzed by flow cytometry and CD4 T cell gene expression profiling was conducted by RNA-Seq. The integration sites were collected using ISLA or LM-PCR and we conducted a genome-wide assessment of H3K27ac histone marks using CUT&RUN sequencing.
Results:
The combined treatment with PBT and PEG-IFNα2a increased CD4 T cell-associated HIV-1 RNA (fold increase 1.83, p=0.0029). In parallel, the study medication induced activation of cDC2, pDCs, and cytotoxic NK cells and enhanced the expression of IFN-stimulated genes. The combined treatment also resulted in a trend for reduced frequencies of intact proviruses, determined by IPDA (p=0.0547). To evaluate effects of the study medication on the proviral landscape, we collected 2,695 integration sites; these studies showed that the combined treatment induced a structural transformation of the HIV-1 reservoir cell pool, characterized by an accumulation of HIV-1 proviruses integrated in ZNF genes (p=0.032), in chromatin regions with reduced H3K27ac marks, and, to a lesser extent, in centromeric/satellite DNA regions.
Conclusions:
Treatment with PBT and PEG-IFNα2a can induce notable changes in the proviral reservoir landscape, with preferential elimination of proviruses in proximity to H3K27ac marks, the molecular target site for PBT. Together, these results provide proof-of-principle that the viral reservoir is vulnerable to ‘shock and kill’ interventions.