Mechanisms of HIV Latency

HIV-1 infection is currently incurable and necessitates lifelong antiretroviral therapy (ART) in order to suppress viral replication and prevent AIDS. While ART has radically changed the course of the HIV-1/AIDS pandemic and saved millions of lives worldwide, it does not fully prevent pathology nor restore normal lifespan. Thus, curative therapies are urgently needed.

HIV-1 persists under ART because of a reservoir of immune cells, which contain chromosomally integrated latent HIV-1 proviruses that are transcriptionally silent and immunologically inert, thereby making latently infected cells indistinguishable from uninfected cells.

The current approach to eliminate HIV latency – ‘Shock and Kill’ – consists in the use of small molecules that reactivate latent viruses under the cover of ART to prevent de novo infection. However, this approach faces many identified challenges including the heterogeneity of HIV-1 latency mechanisms, and the lack of evidence for efficient clearance of the ‘reactivated latent’ pool by the immune system. Recent studies have also illustrated that latent viruses may be differentially reactivated in response to various ‘Shock and kill’ lead compounds and that HIV-1 latency reactivation by small molecules may be stochastic in nature rather than deterministic.

Moreover, the inability to identify and purify latently infected patient-derived cells ex vivo has hampered the development of novel therapeutics, as well as our understanding of HIV-1 latency mechanisms.

Our work focuses on studying and characterizing the mechanisms responsible for HIV-1 latency establishment and maintenance. To do so, we are using 2 different approaches:

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    Diagram of the Derivation of Two-color Viral Construct

Diagram of the Derivation of Two-color Viral Construct

1 - We have conducted an unbiased genome-wide screen using a pooled ultracomplex shRNA library with a complexity of 495,000 shRNAs in the latent J-Lat 5A8 cell line that emulates the response of latently infected cells from HIV patients. We identified previously reported HIV transcriptional activators such as Polycomb-group proteins and the P-TEFb complex, as well as novel complexes as regulators of HIV-1 latency. We are validating the different hits using the CRISPR technology and characterizing the associated pathways.

2 – We have developed a dual-labeled virus which allow us to detect, quantify, and purify uninfected, latently and productively infected primary CD4 T-cells. Using this tool, we have performed a transcriptomic study of each population using RNAseq. Preliminary analysis indicates that latently infected cells exhibit distinct expression patterns for unique cell surface proteins as well as unique pathways and genes involved in HIV-1 latency establishment. We are now validating the different hits. In addition, we are studying the role of viral proteins in HIV-1 latency establishment.

Selected publications:

1. Battivelli E, Dahabieh MS, Abdel-Mohsen M, Svensson JP, Tojal Da Silva I, Cohn LB, Gramatica A, Deeks S, Greene WC, Pillai SK, Verdin E. Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cellsElife. 2018 May 1;7. pii: e34655. doi: 10.7554/eLife.34655.

2. Besnard E, Hakre S, Kapmann M, Lim HW, Hosmane NN, Martin A, Bassik MC, Verschueren E, Battivelli E, Chan J, Svensson JP, Gramatica A, Conrad RJ, Ott M, Greene WC, Krogan NJ, Siliciano RF, Weissman JS, Verdin E. The mTOR Complex Controls HIV Latency. Cell Host Microbe. 2016 Dec 14;20(6):785-797.doi:10.1016/j.chom.2016.11.001

3. Chavez L, Calvanese V, Verdin E. HIV Latency Is Established Directly and Early in Both Resting and Activated Primary CD4 T Cells. PLoS Pathog. 2015 Jun 11;11(6):e1004955

4. Calvanese V, Chavez L, Laurent T, Ding S, Verdin E. Dual-color HIV reporters trace a population of latently infected cells and enable their purification. Virology. 2013 Nov;446(1-2):283-92.