# Characterizing HIV-1 reservoirs in the central nervous system

> **NIH NIH R01** · MASSACHUSETTS GENERAL HOSPITAL · 2024 · $831,792

## Abstract

Abstract
A considerable number of clinical, neuropathological, immunohistochemical and immunological studies suggest
that human brain cells, in particular those of myeloid origin, are susceptible to HIV-1 infection; infection of these
cells may contribute to neurocognitive dysfunction and viral long-term persistence despite ART. However, among
all anatomical tissue locations in the human body, the central nervous system (CNS) arguably represents the
most difficult one to access and to evaluate for viral infection and persistence. Recently, we and others have
made significant progress in defining viral reservoirs at a single-cell and single-molecule resolution, using a
platform of novel next-generation sequencing assays allowing to simultaneously analyzing near full-length
proviral sequences, the corresponding chromosomal integration sites and the respective HIV-1 RNA expression
profile from individual viral reservoir cells. Using such technologies, we observed evidence for immune-mediated
selection mechanisms that enable long-term persistence of viral reservoir cells with features of deep latency,
while reservoir cells with higher susceptibility to reactivation signals seemed to be actively selected against; in
rare cases of individuals with “elite control”, such selection mechanism resulted in a highly-restricted viral
reservoir configuration consisting of intact proviruses located in heterochromatin positions not permissive to viral
transcription. Here we will propose to use this established and fully-operational technology pipeline for a detailed
analysis of the frequency, clonality and replication competence of proviruses isolated from sorted CNS cells, in
particular from myeloid parenchymal microglia, from myeloid perivascular macrophages and astrocytes
(Specific Aim 1). In addition, we will utilize novel next-generation sequencing assays for characterizing the
chromosomal locations of intact and defective proviruses, and their associated epigenetic chromatin
microenvironment, using ATAC-Seq, ChIP-Seq and Methylation-Seq assays (Specific Aim 2). For a functional
evaluation of proviruses residing in the CNS, we will subsequently conduct reactivation assays with single
patient-derived virally-infected cells from the CNS, allowing us to determine how chromosomal positioning and
epigenetic features affect the transcriptional activity of proviruses and their susceptibility to latency-reversing
agents (Specific Aim 3). Together, these investigations will provide high-resolution insight into the dynamics of
HIV-1 persistence in myeloid CNS cell subsets and may be highly informative for targeted HIV-1 cure
interventions.

## Key facts

- **NIH application ID:** 10894324
- **Project number:** 5R01MH134823-02
- **Recipient organization:** MASSACHUSETTS GENERAL HOSPITAL
- **Principal Investigator:** Shibani Sharon Mukerji
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $831,792
- **Award type:** 5
- **Project period:** 2023-08-01 → 2028-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10894324

## Citation

> US National Institutes of Health, RePORTER application 10894324, Characterizing HIV-1 reservoirs in the central nervous system (5R01MH134823-02). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10894324. Licensed CC0.

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