# Multiomic strategies to assess HIV reservoir persistence

> **NIH NIH R01** · UNIVERSITY OF PENNSYLVANIA · 2024 · $844,008

## Abstract

Persistence of the latent HIV reservoir in people living with HIV (PLWH) remains the critical barrier to an HIV
cure. Numerous reservoir reduction and control studies have met with only limited success due to our profound
lack of understanding of the cellular mechanisms that allow the HIV reservoir to persist during antiretroviral
therapy (ART). The goals of this proposal and RFA AI-22-025 are to define the characteristics of the HIV
reservoir enabling cell death resistance and to determine whether these mechanisms impact reservoir
reduction strategies in PLWH. Previous studies have examined the viral reservoir from the aspect of the
integrated provirus, including viral diversity, intactness, and integration site, but have not been able to directly
define potential cell death resistance mechanisms that perpetuate the viral reservoir. Similarly, challenges in
identifying and characterizing resting infected cells ex vivo, including rarity, heterogeneity, and absence of a
defining phenotypic marker, have limited our ability to determine how the HIV reservoir is maintained under
ART. To address these issues, we developed a novel single cell strategy to identify HIV+ cells via integrated
proviral DNA with simultaneous epigenetic and cell surface profiling (Assayfor Transposase Accessible
Chromatinsequencing with cell surface profiling and viral alignments,V-ASAPseq). Using this strategy, we
have directly profiled the HIV reservoir in ART treated PLWH at the single cell level, finding extensive reservoir
heterogeneity within and between individuals, but the potential for shared regulatory characteristics directly
relating to cell death resistance. Here, we will apply V-ASAPseq and V-TEAseq (transcriptome, epigenome,
and surface profiling) to define cell death resistance mechanisms of the HIV reservoir. Our central
hypothesis is that reservoir persistence over time under ART and after immunotherapeutic challenge is
associated with targetable cellular features, some of which are shared and others distinct between
subpopulations of HIV+ CD4+ T cells. In Aim 1 we will determine reservoir-associated changes in cell death
resistance signatures over time, between anatomical compartments and after reactivation. In Aim 2, we will
determine the epigenetic and transcriptional features of HIV+ cells that drive cell death susceptibility in vitro
and persistence in vivo after reservoir-targeting immunotherapies from human clinical trials. Together these
studies will define targetable features of reservoir persistence and cell death both at rest, during ART, and in
the context of reservoir-targeting immunotherapies with the ultimate goal of reducing the HIV reservoir.

## Key facts

- **NIH application ID:** 10816606
- **Project number:** 5R01AI176597-02
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Michael R Betts
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $844,008
- **Award type:** 5
- **Project period:** 2023-04-01 → 2028-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10816606

## Citation

> US National Institutes of Health, RePORTER application 10816606, Multiomic strategies to assess HIV reservoir persistence (5R01AI176597-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10816606. Licensed CC0.

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