Background: To target the persistence of quiescent HIV-1 during ART, HDAC inhibitors have been used to induce viral transcription, which could potentially facilitate viral clearance. It is important that all replication competent proviruses are activated to fully purge infection. Therefore, we performed an in-depth analysis of the panobinostat clinical trial to determine whether the observed increases in unspliced cell-associated RNA (CA RNA) were due to transcription from a subset or a broad range of proviruses.
Methods: Panobinostat was administered to 15 patients on suppressive ART three times a week every other week for eight weeks (i.e., four cycles of drug). Cell-associated DNA (CA DNA) and RNA were extracted from PBMCs collected before, twice while receiving and four weeks after the final dose of panobinostat treatment. Additionally, plasma samples were collected prior to initiation of ART (nine patients) and during a post-panobinostat analytical treatment interruption (ATI, nine patients) to assess circulating HIV-1. Single-genome sequencing of the env region was used to characterise the virus from the cell-associated DNA and RNA and plasma RNA.
Results: The sequences obtained from the preART plasma reflected the infection status of the patient (acute vs. chronic). Phylogenetic analysis revealed that the panobinostat-induced viral RNA intermingled extensively with the CA DNA sequences from the equivalent time points, indicating that panobinostat activates transcription from a broad range of proviruses. The rebound virus from the ATI plasma was composed of expansions of homogenous sequences, and the sequences from this virus were genetically similar to the panobinostat-induced CA RNA sequences. Furthermore, CA DNA sequences that were identical to the rebound virus were detected. A significantly higher percentage of the sequences from the CA RNA were hypermutated compared to the CA DNA (p=0.04).
Conclusions: Panobinostat non-selectively activates transcription from quiescent proviruses in patients on suppressive ART, supporting its ability to activate HIV-1 from latency. Furthermore, panobinostat activated virus that was genetically similar to that observed during ATI, indicating that it targets virus that drives rebound following treatment discontinuation. The high percentage of hypermutated HIV CA RNA that was detected stresses the need for assays that measure replication competent virus when assessing latency reversing agents.