Single Cell Analysis of HIV-1 Latent reservoir establishment in Humanized Mice

Abstract Human Immunodeficiency Virus (HIV) has infected 76 million people worldwide and caused the death of 38 million. Current treatments can reduce patient viral loads but fail to cure patients of infection. This is due to the ability of the virus to undergo latency during antiretroviral therapy. Latently infected cells are nearly indistinguishable from uninfected cells and there is no effective treatment to eliminate these cells. Our long- term goal is to describe at a single cell level, how early reservoir seeding occurs and the mechanisms that drive latency establishment. The proposed experiments in this grant are based on the hypothesis that during acute infection, a proportion of infected CD4+ T cells from diverse lineages of T cells such as resting CD4+ memory, activated T cells, naïve T cell, effector memory T cell undergo early latency and that transcriptional pathways such as mTOR and EIF2 signaling and provirus integration into transcriptionally repressive site are mechanisms of early latency establishment. This hypothesis is based on observations that: i) despite extremely early ART treatment, HIV latent reservoir may be established earlier than 72 hours after exposure ii) a diverse subset of T cells can harbor latent HIV iii) complex interactions between host and viral factors drive latency. First generation latency marking technology has been developed by the Chen lab to report the history of HIV infection through irreversible marking all HIV-infected cells called HIV-Induced Lineage Tracing (HILT). In this application, I propose a second-generation, innovative genetic marking technology, Enhanced HILT (EHILT), to further our knowledge the complexities of HIV latency. Using EHILT and validated small animal models of latency, I will define early latency kinetics in in vitro and in vivo acute and ART-treated infection using EHILT, identify transcriptional profiles and pathways associated with latency in vivo, and profile the integration sites of provirus with immediate latent phenotype.