# Investigating the latent HIV-1 reservoir in lymphoid tissue using multiplexed imaging and spatial transcriptomics

> **NIH NIH F31** · STANFORD UNIVERSITY · 2022 · $39,375

## Abstract

PROJECT SUMMARY/ABSTRACT
The introduction of combination antiretroviral therapy (ART) has led to a dramatic improvement in lifespan for
individuals infected with HIV-1, but any interruption of treatment leads to rapid resumption of viral replication,
requiring patients to follow a strict drug regimen. HIV-1 establishes a stable reservoir within days of
transmission before the virus can be detected in the peripheral blood and can persist as replication-competent
proviruses inside cells, known as the latent reservoir. ART is incapable of targeting these latent reservoirs;
therefore, a cure for HIV-1 is needed. Treatments that target the latent reservoir have thus far been
unsuccessful, largely because the latent reservoir is poorly understood. Due to ease of sample access, the
vast majority of studies of the latent viral reservoir have been performed with peripheral blood. However,
lymphoid tissue are the principal sites of viral replication and HIV-1 has been shown to persist in lymphoid
tissue of patients on ART who have undetectable viral loads in the blood. The few prior studies of the latent
reservoir in lymphoid tissue were limited by approaches that could only target a few markers or required the
preparation of cell suspensions, which can lead to changes in cell phenotype or loss of cells, as well as loss of
spatial information. Our group has previously developed Multiplexed Ion Beam Imaging, which uses secondary
ion mass spectrometry to visualize up to 40 proteins at subcellular resolution in a single tissue. By combining
this novel imaging technology with spatial transcriptomics to assess immune features in lymphoid tissue, we
will be able to identify the cells and mechanisms important for viral persistence. We recently applied this
method in rhesus macaque tissue, demonstrating an immunosuppressive microenvironment in SIV+ macaque
lymph nodes. Building on this work, I hypothesize that applying novel imaging and spatial transcriptomic
methods will reveal an immunosuppressive phenotype in lymphoid tissue of HIV+ patients. This work will yield
a comprehensive picture of the infected cells, cell function, and tissue structure within the vicinity of the HIV-1
reservoir. In Aim 1, I will extend MIBI to the imaging of HIV RNA and DNA using in situ hybridization, enabling
the simultaneous quantification of viral RNA and DNA and cellular protein to fully characterize infected cells. In
Aim 2, I will assess the spatial structure and follicle heterogeneity within the lymphoid tissue of viremic patients
to identify features of the microenvironment in which cells are actively responding against the virus. In Aim 3, I
will compare the immune features between viremic patients, aviremic patients, and healthy individuals to
uncover features of the immune microenvironment that are important to viral persistence after ART. This work
will improve our understanding of the latent viral reservoir in lymphoid tissue, which is a critical barrier to HIV-1
eradicat...

## Key facts

- **NIH application ID:** 10480969
- **Project number:** 1F31AI165180-01A1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** CANDACE LIU
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $39,375
- **Award type:** 1
- **Project period:** 2022-03-28 → 2024-03-27

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10480969

## Citation

> US National Institutes of Health, RePORTER application 10480969, Investigating the latent HIV-1 reservoir in lymphoid tissue using multiplexed imaging and spatial transcriptomics (1F31AI165180-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10480969. Licensed CC0.

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