Deep sequencing of the HIV latent reservoir to discern mechanisms of clonal proliferation and HIV persistence

PROJECT SUMMARY/ABSTRACT
The HIV latent reservoir (LR) is the major barrier to cure of HIV. The persistence of the LR in blood and tissues
in people living with HIV (PLWH) during ART is due to cellular proliferation of infected cells. Three mechanisms
are postulated to drive infected cell proliferation: integration of the provirus in or near genes associated with
cancer or cell proliferation; engagement of the infected CD4+ T cell receptor with its cognate antigen, leading to
proliferative bursts; and cytokine-mediated homeostatic proliferation. Recent evidence suggests that oncogene-
driven proliferation does not contribute significantly to infected cell proliferation. Meanwhile, antigen-driven
proliferation of infected cells appears to account for many or most of the most-highly expanded, or dominant,
infected cell clones. However, the degree to which homeostatic proliferation versus antigen-driven proliferation
maintains the overall reservoir is difficult to discern. Because infected cells are so clonal, shallow sampling
depths still reveal dominant clones (likely maintained by antigenic stimulation) while underestimating the extent
of the non-dominant clones (the ‘tail’ of the clonality distribution, likely maintained by homeostatic proliferation).
We will fill this knowledge gap by generating a near-full length HIV provirus sequencing dataset deep enough to
accurately assess clonality richness and by developing models to more precisely quantify the fractional
contribution of antigen-driven versus homeostatic proliferation to reservoir maintenance. In Aim 1, we will fully
characterize the intact and defective provirus clonality distributions in PLWH on ART by generating near-full
length HIV provirus sequencing datasets deep enough to approximate clonality richness saturation. We will test
the hypothesis that provirus clonality distributions mirror those of uninfected memory CD4+ T cells, with a small
number of dominant clones and a large number of non-dominant clones, and that they can be modeled with
similar power-law exponents. In Aim 2, we will first generate longitudinal characterizations of in vivo antigen-
driven and homeostatic CD4+ T cell proliferation of uninfected CD4s in PLWH on ART using T cell receptor
repertoires. Then we will use this information to construct mathematical models to estimate the fractional
contributions of antigen-driven and homeostatic proliferation to the persistence of the reservoir in PLWH on ART.
We will test the hypothesis that both antigen-driven and homeostatic proliferation contributes significantly to the
maintenance of the HIV LR. This work and the resulting models will help the HIV cure field design future
therapeutic strategies and help the field predict more precisely outcomes when HIV cure strategies such as anti-
proliferative therapies or personalized therapeutic vaccines are trialed.

Grant Number: 5R21AI186783-02
NIH Institute/Center: NIH
Principal Investigator: Annukka Antar