# Selection and Evolution of HIV-1 reservoir cells in blood and tissues

> **NIH NIH R01** · BRIGHAM AND WOMEN'S HOSPITAL · 2020 · $802,651

## Abstract

Abstract
Viral reservoir cells are an extremely small but highly durable population of HIV-1-infected CD4 T cells that
persist despite treatment with highly-effective antiretroviral therapy and are responsible for viral rebound once
treatment is interrupted. Understanding and characterizing the physiology of these cells will likely be critical for
any effort to successfully target these cells but has turned out to be extremely difficult, due to their low fractional
abundance and considerable heterogeneity in blood and tissues. Moreover, there is growing evidence
suggesting that viral reservoir CD4 T cells are dynamically evolving over time, and subject to selection
mechanisms that favor the long-term persistence of some reservoir cells, while eliminating others. Here, we plan
to take advantage of recent progress in molecular single-cell and imaging analysis techniques and propose to
comprehensively profile the longitudinal evolution of viral reservoir cells in blood and tissues. We hypothesize
that continuous suppressive antiretroviral therapy selects for intact proviruses with features of deeper latency,
likely as a result of immune selection mechanisms that preferentially eliminate proviruses more susceptible to
reactivation signals, while proviruses in deeper latency persist. These studies will be conducted using samples
of a unique, prospectively followed cohort of HIV-1-patients who were identified in acute infection and started
antiretroviral treatment immediately after diagnosis. In Specific Aim 1, we will use novel next-generation
sequencing technologies to longitudinally profile the chromosomal position of intact and defective proviruses
from blood and tissues, and evaluate their microanatomical location in lymphoid tissues. Subsequently, we will
characterize the epigenetic chromatin environment within chromosomal proximity to intact proviruses from blood
and tissues, using a platform of next-generation sequencing assays to evaluate chromatin accessibility, inhibitory
or activating histone modifications and DNA methylation (Specific Aim 2). In Specific Aim 3, we will perform
novel, functional single-cell assays to simultaneously analyze the proviral sequence, the corresponding
integration sites and HIV-1 RNA expression profile of single virally infected cells from blood and tissues; this
assay will allow us to individually characterize the viral gene expression pattern of single infected cells encoding
for intact and defective proviruses, and enable testing the hypothesis that continuous antiretroviral therapy is
associated with progressive accumulation of proviruses with deeper levels of latency and lower responsiveness
to viral reactivation stimuli. Together, these studies have the potential to provide significant advances in
understanding the complexity and longitudinal evolution of viral reservoir cells and may allow to identify
susceptibilities and vulnerabilities of residual HIV-1-infected cells that could be therapeutically target...

## Key facts

- **NIH application ID:** 10176754
- **Project number:** 1R01AI152979-01A1
- **Recipient organization:** BRIGHAM AND WOMEN'S HOSPITAL
- **Principal Investigator:** JACOB D ESTES
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $802,651
- **Award type:** 1
- **Project period:** 2020-09-23 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10176754

## Citation

> US National Institutes of Health, RePORTER application 10176754, Selection and Evolution of HIV-1 reservoir cells in blood and tissues (1R01AI152979-01A1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10176754. Licensed CC0.

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