UNDO-HIV: UNDerstanding and Obliterating the active HIV reservoir

About This Grant

PROJECT SUMMARY A substantial fraction of the HIV reservoir that persists in the face of antiretroviral therapy (ART) actively expresses a multitude of HIV proteins, yet the mechanisms by which they avoid detection and/or elimination by the immune system is unclear. The features of these “translationally-active” HIV reservoir cells have remained elusive due to lack of tools to identify and characterize them at the single-cell level. In this proposal, we leverage three new technologies we have pioneered and/or adapted to both better understand these cells, as well as to target them therapeutically. The first technology, HIV-prex, is a single-cell sequencing technology we developed to simultaneously characterize the transcriptomes of translationally-active HIV reservoir cells from ART- suppressed people with HIV (PWH). The second technology is MIBI-TOF, a high-parameter imaging method enabling in-depth analysis of translationally-active reservoir cells in their local tissue microenvironments. The last technology is TRACeR, a bioengineered platform we developed to identify and target translationally-active HIV reservoir cells on the basis of their cell-surface presentation of HIV peptides bound to MHC class I (MHC-I). These approaches will be applied across three aims, using both banked and prospectively-collected blood and tissue specimens from the UCSF SCOPE cohort of PWH. In Aim 1, we will establish the transcriptional and proteomic features of translationally-active reservoir cells – including the HIV peptides presented by MHC-I on their cell surfaces – from ART-suppressed PWH, and compare their features to reactivated latent reservoir cells. The features of the active reservoir cells will be tracked longitudinally over the course of 2-20 years of suppressive ART, and be compared between men vs. women. In Aim 2, we will compare the features of translationally-active reservoir cells from blood and multiple tissue compartments (gut, lymph node), as well as establish the spatial context of these cells in the gut, the main site of HIV persistence. In Aim 3, we will develop a novel method to eliminate translationally-active reservoir cells, through re-engineering of the top HIV TRACeRs into BiTE therapeutics, the test their efficacy using in vitro models as well as ex vivo using specimens from PWH. Elimination of translationally-active reservoir cells has important translational value as it can diminish the chronic inflammation linked to co-morbidities in ART-treated PWH. Furthermore, it can help achieve HIV remission given the potential of these cells to cause immune dysfunction and lead to viral rebound upon ART interruption. Collectively, our aims will improve our understanding of translationally-active HIV reservoir cells – an important but poorly understood component of the HIV reservoir – and develop targeted strategies to directly eliminate them.