Regulation of HIV Latency by Host Cell Transcriptional and Epigenetic Networks

Project summary:
Antiretroviral therapy (ART) has been successful at treating HIV infection and allowing people with HIV (PWH)
to lead relatively normal lives. Nevertheless, a cure for HIV has remained elusive, and interruption of ART
results in rapid viral rebound. HIV persists during therapy by its ability to enter a state of latent infection in CD4
T cells. A key challenge in the field is defining the molecular mechanisms that regulate HIV expression and
contribute to maintaining the latent state. HIV expression in latently infected cells is repressed by the
formation of heterochromatin at the integrated provirus that restricts access by key activating transcription
factors (TFs) and RNAPol2. Latency reversing agents (LRAs) have been developed that target HIV regulating
transcriptional pathways. However, most LRAs reactivate only a fraction of the reservoir, suggesting that
latency reversal is inefficient with single agents. We have carried out a set of single cell analyses to
characterize the transcriptomic and epigenomic states of latently infected cells, leading to the discovery of a
latency associated `signature' in primary CD4 T cells. Since then, we have performed a targeted CRISPR
screen of latency-associated genes as well as a chemical screen to identify a set of validated novel host cell
factors that individually regulate HIV latency. In this proposal we will capitalize on these findings to identify
novel combinations of gene knockouts and small molecule inhibitors that can synergize with our validated HIV
regulating factors to achieve broad reactivation of the clinical reservoir. To achieve this, we will take a novel
experimental approach involving both combination CRISPR/LRA screening and using cutting edge
interpretable machine learning tools to define the key drivers of HIV reactivation. Additionally, we will develop
a novel lipid nanoparticle platform for RNA-mediated reprogramming of latently infected cells to promote viral
reactivation.

Grant Number: 2R56AI143381-05
NIH Institute/Center: NIH
Principal Investigator: Edward Browne