Understanding and targeting the HIV-expressing reservoir to reduce immune activation

Abstract Although ART can reduce morbidity and prolong life, it does not cure HIV or fully restore health. Despite ART, people living with HIV (PWH) continue to have higher average levels of inflammation and immune activation, which are thought to be a major cause for the higher incidence of diseases in many organ systems (non-AIDS morbidity) and reduced life expectancy that persist even after years of suppressive ART. While the causes of immune activation may be multifactorial, it is thought that a major cause is the continued expression of HIV RNA, protein, and/or virions by subsets of HIV-infected cells. Within the gut, where most infected cells reside, expression of these viral products likely contributes to dysfunction of the gut mucosal barrier and leakage of gut microbial products into the circulation, leading to further increases in inflammation and immune activation. However, it is not clear which viral products contribute to immune activation and the sequelae of treated HIV. To investigate this question, aim 1 will utilize stored and prospective samples from a cohort of ART-suppressed PWH to determine the degree to which low-level plasma HIV RNA, levels of different cell-associated HIV transcripts of varying maturity, and p24 protein expression in blood and gut correlate with the inflammatory proteome in plasma. It is also unclear what subsets of cells express these viral products, and what factors determine whether a given infected cell will express HIV. To answer these questions, aim 2 will utilize novel single cell approaches to characterize the cell phenotypes, chromatin accessibility, transcriptomes, clonotypes, and surface protein expression of single HIV-infected (HIV DNA+) and HIV-transcribing (HIV RNA+) cells from the blood and gut of ART-suppressed PWH (aim 2A), and will then test how genes identified through single cell RNA-seq (scRNA-seq) affect HIV expression (aim 2B). While HIV researchers have identified some drugs that can inhibit HIV transcription, there is a critical need for new therapies aimed at reducing HIV expression and/or blocking reactivation from latency. We have identified new drugs that appear to block activation-induced increases in HIV transcription and virion release. In aim 3, we will compare both published and new drugs for their ability to enhance baseline blocks to HIV transcription or prevent activation-induced reversal of the blocks to HIV transcription and splicing in cells from the blood and gut of HIV-infected individuals. The results from aims 1-3 could lead directly to the identification of new drug targets and new agents aimed at a functional cure and/or reducing HIV-associated immune activation.