Cellular identity of the intact HIV reservoir

The National Institute of Allergy and Infectious Diseases (NIAID) awarded $489,500 to The Children's Hospital of Philadelphia Research Institute on June 11, 2025, under the Allergy and Infectious Diseases Research program (CFDA 93.855). This two-year project, which extends through May 31, 2027, focuses on developing novel sequencing methodologies and analytical pipelines to identify and characterize intact human immunodeficiency virus (HIV) reservoir cells at the single-cell level. The research addresses critical gaps in current HIV cure research by generating technical and scientific approaches capable of detecting integrated provirus in closed chromatin environments and distinguishing intact from defective proviral sequences—capabilities essential for improving the targeting and elimination of latent HIV reservoirs.

The project delivers two primary scientific products: (1) experimental validation demonstrating that CD4+ T cells with provirus in closed chromatin exhibit distinct transcriptional profiles compared to cells with open chromatin provirus, and (2) comprehensive characterization of cells containing intact provirus through integrated transcriptional, epigenetic, and clonal analysis. These deliverables will produce an adjunctive technical and analytical framework designed for application across multiple HIV cure-directed clinical trial strategies, directly supporting the advancement of HIV eradication research by providing investigators with improved tools for reservoir identification and monitoring.

Abstract

Persistence of the HIV reservoir is a major barrier to cure. Many cure-directed clinical trials use novel interventions to reactivate the reservoir for immune targeting and reservoir reduction. Improving the targeting and elimination of HIV reservoir requires a cell-by-cell understanding of where reservoir is and how reservoir persists after cure interventions. However, current strategies to identify the multi-modal biology of cells with integrated provirus are not able to fully resolve the intact proviral reservoir: they cannot detect provirus in closed chromatin and cannot discern intact from defective provirus. This proposal will work to interrogate cellular programs of the total intact reservoir using two new sequencing approaches to address the problems of proviral intactness and integration in closed chromatin. In aim 1, we will test the hypothesis that CD4+ t cells with provirus in closed chromatin are transcriptionally distinct from cells with provirus in open chromatin. In aim 2, we will test the hypothesis that cells with intact provirus have distinct transcriptional, epigenetic, and clonal features. We will therefore work to identify the distinct features of the intact reservoir and to generate a technical and analytic pipeline for adjunctive use across multiple cure strategies.