# SINGLE-CELL TRANSCRIPTOMIC ANALYSIS OF HIV-INFECTED CD4 T CELLS IN BLOOD AND LYMPHOID TISSUE USING PCR-ACTIVATED CELL SORTING

> **NIH NIH U01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2020 · $455,980

## Abstract

Project Summary
Understanding how the CD4 T cells that harbor HIV in vivo differ from those that do not
may spur the development of prophylactic or therapeutic antiviral strategies.
Unfortunately, due to the complexity of HIV-infected CD4 T cell populations and to key
technical obstacles, the detection and manipulation of these rare cells in blood and
lymphoid tissue samples from HIV-positive individuals has previously been infeasible.
We have therefore developed a novel technology termed PCR-activated cell sorting
(PACS) that allows identification and manipulation of individual CD4 T cells in
microfluidically-generated water-in-oil emulsions by the presence of intracellular HIV
genomic DNA. In the proposed investigations, we will use this technology to sort single
HIV-infected CD4 T cells from blood and lymphoid tissue of HIV-positive individuals for
gene expression profiling by whole transcriptome deep sequencing. This
comprehensive approach will allow discovery of novel markers of HIV-infected CD4 T
cell in vivo, which will then be validated in follow-up tissue staining and cell sorting
studies. Importantly, access to well-characterized NIH Clinical Center cohorts of HIV-
positive study participants with spontaneous control of the virus, with uncontrolled
infection, and with virus suppression on antiretroviral therapy (ART) will allow targeted
study of these distinct clinical subgroups. Comparing results from these subgroups will
allow differences between HIV infected CD4 T cells under differing degrees of natural or
treatment-induced virologic suppression to be understood. By thus elucidating the
determinants of HIV target cell selection and persistence in vivo, these studies may lead
to the development of novel HIV cure strategies.

## Key facts

- **NIH application ID:** 9990648
- **Project number:** 5U01AI129206-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Adam R. Abate
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $455,980
- **Award type:** 5
- **Project period:** 2017-08-17 → 2022-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9990648

## Citation

> US National Institutes of Health, RePORTER application 9990648, SINGLE-CELL TRANSCRIPTOMIC ANALYSIS OF HIV-INFECTED CD4 T CELLS IN BLOOD AND LYMPHOID TISSUE USING PCR-ACTIVATED CELL SORTING (5U01AI129206-04). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9990648. Licensed CC0.

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