THE MOLECULAR BASIS OF HIV-1 LATENCY INITIATION AND MAINTENANCE

The Human Immunodeficiency Virus Type 1(HIV-1) targets CD4 T helper cells and maintains an insidious life-long viral infection. Combined antiretroviral therapy can block viral replication and transmission yet fails to cure HIV-1 due to the presence of a latent reservoir of persistent, transcriptionally latent, DNA proviruses. HIV-1 cure research aims to identify the molecular biological and immunological basis for HIV-1 transcriptional latency and to use this insight to identify safe and effective means to reduce the size of the latent reservoir. One such approach is to develop latency reversal agents, or LRAs, to induce viral gene expression and make infected cells susceptible to immune-mediated clearance.This dissertation research project employs a combination of pharmacological inhibitors, genetic knockout studies, and observational genomic assays to explore the mechanisms through which the host-cell environment facilitates proviral latency. One key approach employed in this dissertation is to use genetics to define the mechanism-of-action of pharmacological agents. Chapter 2 describes a collaboration where a combination of CRISPR-CAS9 knockout approaches and single-cell transcriptomics were used to help define the molecular mechanism that underlies the synergy between IAPi and BETi LRAs. Chapter 3 builds upon previous work studying Histone Deacetylases (HDACs) and the HIV provirus to identify a specific role for HDACs in the establishment of HIV-1 latency. Studies across multiple modalities of inhibition defined a model where HDAC3 and HDAC1/2 contribute distinctly to the initiation of HIV latency. Finally, the unpublished Chapter 4 study reports efforts to establish a sensitive method to employ single-cell RNA sequencing to characterize latently infected cells from the gastrointestinal tissue resident T cells. Collectively these studies provide new insight into the molecular basis of the initiation, maintenance, and persistence of HIV-1 proviral latency.