Understanding HIV-1 latency in 3D

Human immunodeficiency virus (HIV-1) gradually destroys the immune system, which becomes unable to protect from the attack of other microorganisms. HIV-1 infection can be treated but not cured because the virus persists indefinitely. If treatment is stopped, the virus quickly bounces back. Hence it is critical to find a cure for HIV-1 infection. HIV-1 persists in a "latent" form, unaffected by the immune system and the drugs, but we do not understand well how HIV-1 becomes latent or how it comes out of latency. HIV-1 integrates permanently into the DNA genome of infected cells. Recent research has shown that the spatial organization of the genome it very important to regulate its function. For example, several genes may cluster into one region of the genome to be expressed in tandem. This results in co-expression of genes important for, say, a specific cell function, or a specific cell type. We want to understand if the spatial location where HIV-1 integrates in the host cell genome regulates the expression of HIV-1 genes and determines if the virus becomes latent or not. We will study the 3D organization of the genome where HIV-1 has integrated, how this affects the virus and how this spatial organization may change when the infected cells change their function. In the longer term, this knowledge will be important to find drugs that, by targeting specific regions of the genome, can switch the latent HIV-1 on or off and help cure HIV-1 infection.

A cure for HIV-1 infection is a priority. Treatment interruption triggers viral rebound from a "reservoir" largely composed of memory CD4+ T cells latently infected with HIV-1. HIV-1 cure strategies aim either at reactivating latent HIV-1 to trigger immune-recognition and elimination of infected cells, or to make latency irreversible to prevent virus rebound upon treatment interruption. However, we have limited understanding of how HIV-1 latency is established or reversed, which presents a major barrier to either of these strategies.

Spectacular advances in chromosome conformation capture techniques (3C) are revealing how the three dimensional (3D) organization of chromatin regulates gene expression in a cell type specific way. For example, genes and enhancers that are vastly distant from one another on the "linear" genome can cluster together in proximity in the folded chromatin, resulting in their transcriptional co-regulation. It is known that HIV-1 preferentially integrates into groups of active genes. It is not known how HIV-1 expression is influenced by the spatial organization of the genes in which the virus preferentially integrates.

We hypothesize that the spatial location of the integrated provirus within chromatin is key to understand regulation of HIV-1 gene expression and latency. Specifically, we hypothesize that a) HIV-1 has evolved preferentially to integrate into specific spatial domains of chromatin resulting in coordinated expression of HIV-1 and groups of host genes located within the same domain and b) latency depends on the spatial rearrangement of such TADs and compartments. We will address these hypotheses by a combination of cutting-edge technologies to map HIV-1 integration sites onto 3D chromatin in active and latently infected cells, and determine if changes in 3D chromatin regulate latency.

This research will provide new key knowledge on HIV-1 latency potentially revealing ways to modulate it for therapeutic purposes.