# Determinants of reservoir contraction and expansion in vivo, ex vivo, and in vitro

> **NIH NIH R37** · UNIVERSITY OF PENNSYLVANIA · 2020 · $556,548

## Abstract

The advent of antiviral therapy (ART) revealed a treatment-resistant reservoir in CD4+ T cells
capable of refueling HIV viremia when ART is stopped. This reservoir is a major barrier to
achieving a cure for HIV infection. Our recent work suggests the inherent reservoir decay is
more rapid than previously recognized. This decay is obscured due to an opposing force that
results in proviral clonal expansion. The driving forces behind proviral clonal expansion remain
mysterious, but integration into introns of oncogenes may play a role. Overall objective: In this
proposal, we dissect the drivers of reservoir contraction (Aim 1) and expansion (Aim 2). Our
approach will be to perturb both forces and to study the resulting effects. We will use proviral,
integration site, and RNA sequencing to understand how perturbing these forces affects the
genetic make-up of proviruses, their propensity to expand, and their expression. Our approach
is to perform massive deep sequencing in a few individuals rather than large sample size. We
believe our intriguing results validate our deliberate decision to limit sample size to obtain
deeper sequence information within each individual. With this approach, we recently provided
unprecedented depth and elucidated previously unknown selection pressures. Design and
Methods: In Aim 1, we isolate the role of immune clearance by measuring reservoir contraction
in vivo and in vitro. We also dissect the cytotoxicity induced by HIV proteins by mutating
individuals Open Reading Frames before infecting CD4 T cells with a barcoded virus. In Aim 2,
we dissect the drivers of clonal expansion, including HIV-driven cell division, by using a
barcoded virus. We also use longitudinal integration site analysis to compare the rate of clonal
expansion as well as the “character” of the expanded proviral clones in elite controllers, acutely
and chronically infected individuals on ART.
The premise of our proposal is largely based on our work showing that there are two
counterbalancing forces that cause (1) proviral contraction through viral cytotoxicity and immune
clearance and (2) proviral expansion through clonal proliferation. The significance of our
proposal includes that it may contribute to growing evidence that the reservoir is more visible
than previously realized. We envision this work could lead to approaches that enhance immune
clearance or target splicing to reduce reservoir size.

## Key facts

- **NIH application ID:** 10022993
- **Project number:** 1R37AI150556-01A1
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Una T O'Doherty
- **Activity code:** R37 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $556,548
- **Award type:** 1
- **Project period:** 2020-03-16 → 2025-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10022993

## Citation

> US National Institutes of Health, RePORTER application 10022993, Determinants of reservoir contraction and expansion in vivo, ex vivo, and in vitro (1R37AI150556-01A1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10022993. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*