Latently-infected CD4+ T cells are thought to be the main barrier to HIV eradication or functional cure, and viral reactivation from these cells likely contributes to the organ inflammation and damage observed on antiretroviral therapy. Major impediments to the development of more effective latency-reversing agents (LRAs) include the lack of knowledge about the mechanisms that govern latency and latency reversal in vivo, and the degree to which these are recapitulated by latency models in vitro. The lack of agreement between latency models and the incomplete success of human trials with LRAs suggest that it is critical to understand why different LRAs do or do not work in vivo. We have developed a new ?transcription profiling? approach that can simultaneously measure the degree to which different mechanisms contribute to reversible inhibition of HIV transcription in vivo. By applying this approach to cells from ART-suppressed patients, we have generated preliminary data suggesting a new paradigm in which latency is not (as commonly assumed) due to a block to HIV transcriptional initiation, the block to proximal elongation is greater and more pervasive than previously realized, and the main reversible blocks to HIV transcription are a previously-unrecognized block to distal transcription/polyadenylation (completion) and a block to multiple-splicing. In addition, we have intriguing new data suggesting that LRAs may act selectively on the different mechanistic blocks to HIV transcription. This study will utilize samples from clinical trials of humans treated with LRAs (aims 1 and 2) to better understand how they reverse the mechanisms of latency in vivo and to identify the optimum model to test new agents in vitro (aim 3).
In aim 1, we will apply our transcription profiling approach to samples from humans treated with disulfiram, vorinostat, panobinostat, and romidepsin. We hypothesize that these agents preferentially increase HIV transcriptional initiation and elongation but have less ability to overcome blocks to completion and splicing.
In aim 2, we will apply our approach to blood and gut samples from clinical trials of humans treated with agonists of toll-like receptor (TLR) 7 and 9 to understand how these agents reverse latency and lead to death of infected cells in vivo. We hypothesize that TLR agonists can overcome later blocks to HIV transcription, increasing the completed transcripts (and HIV protein/antigen) that may facilitate clearance by intrinsic cell defenses or immune killing.
In aim 3, we will compare in vitro models of latency based on the degree to which they recapitulate in vivo mechanisms of latency and responses to LRAs. We will then select the best model and test new combinations of agents for their ability to increase completed/spliced transcripts and lead to death of infected cells. The results from these 3 aims should provide critical new insights on the degree to which existing LRAs reverse the different mechanisms of latency in vivo (aims 1 and 2), the effects that correlate with clearance of reactivated cells (aims 2 and 3), the best system to study LRAs in the laboratory (aim 3), and new combinations that can lead to more effective latency reversal and/or killing of infected cells (aim 3).

Public Health Relevance

The main barrier to cure of HIV is the ability of the virus to hide in some infected cells (called ?latent infection?) that can live a long time and are not recognized or killed by the body?s defenses. Our preliminary data reveal new insights into the different mechanisms allow HIV to establish latent infection and suggest that currently-available drugs may act selectively to reverse these different mechanisms. In this proposal, we will use blood and tissue samples from humans treated with these drugs to investigate the degree to which they reverse latent infection and lead to killing of HIV-infected cells, to select the best model to study latent infection in the laboratory, and to test new combinations of drugs that can lead to more effective reversal of latency and killing of HIV-infected cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI132128-04
Application #
9975686
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Lawrence, Diane M
Project Start
2017-07-21
Project End
2022-06-30
Budget Start
2020-07-01
Budget End
2021-06-30
Support Year
4
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Northern California Institute Research & Education
Department
Type
DUNS #
613338789
City
San Francisco
State
CA
Country
United States
Zip Code
94121
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