Defining the single-cell epigenetic landscape of the HIV-1 reservoir for effective latency reversal

About This Grant

Project Summary/Abstract While the advent of antiretroviral therapy (ART) has improved the lives of many people with HIV (PWH), HIV infection remains persistent for the lifetime of most individuals. ART interruption leads to viral rebound and renewed disease progression, thus highlighting the existence of the latent HIV which exists even when viral RNA is undetectable in plasma during ART. To date, there is no broadly accessible cure for HIV. This requires most PWH to stay virally suppressed with a constant ART regimen. As such, there remains an urgent need to find functional cures of HIV and alleviate the need for a lifetime of costly ART and its associated long-term side effects. However, the complex nature of the HIV reservoir has impeded our collective efforts to understand the reservoir for elimination strategies. Viral transcription decreases over time on ART and can be nonexistent in many HIV+ cells, thus leading to evasion of immunosurveillance. The leading concept in the field for eliminating the reservoir is to reverse latency using pharmacological agents so that viral antigen is produced to render HIV+ cells permissive for elimination by an interventional therapy. However, current attempts at latency reversal are neither efficient nor complete as only a fraction of HIV+ cells are reactivated. This suggests that transcriptional regulation of the various proviruses (i.e. the integrated viral DNA) is highly heterogeneous. Evidence further suggests that proviral epigenetics, defined as the regulation of transcription at the chromatin level independent of sequence, is critical in understanding how the latent HIV reservoir is established, regulated, and disrupted. Some proviruses are situated in more condensed (heterochromatic) DNA without transcription, while others are in more accessible (euchromatin) DNA that is more conducive to transcription. This spectrum of reactivation potential means that reservoir elimination will first require a single-cell investigation to precisely define these proviral epigenetic states and assess their contribution to latency reversal. Therefore, the primary objective for this project is to define the ex vivo proviral epigenetic landscape at single-cell resolution and to develop a pioneering strategy to selectively reverse latency. The underlying central hypothesis is that HIV+ cells with heterochromatin-associated proviruses are more resistant to reservoir disruption and latency reversal. The central hypothesis will be tested through two specific aims: 1) define the proviral epigenetic landscape and its susceptibility to reservoir disruption from ART-treated PWH; and 2) determine the efficacy of mRNA-LNP delivery of HIV-specific transcription activator-like effectors (TALEs) for latency reversal. This proposal is highly innovative because it represents a major shift in how the field studies the HIV reservoir by using new single-cell methodology to circumvent the challenges inherent to studying the HIV reservoir. The outcomes will uniquely define the identities of the latent HIV reservoir and will offer additional opportunities to target and eliminate the HIV reservoir.