Spatial Multi-omic Analysis of HIV-infected Cell Reservoirs in the Tumor Microenvironment

National Institute Of Allergy And Infectious Diseases

Investigators

Abstract

The Vaccine Research Center (VRC) Virus Persistence and Dynamics Section (VPDS) seeks to address barriers to HIV cure by developing and applying new technologies that comprehensively describe the biology of HIV-infected cell reservoirs. Although resting memory CD4 T cells harboring HIV DNA under antiretroviral therapy (ART) have for decades been considered a “latent reservoir,” attempts to identify special cellular attributes that could allow these cells to silence HIV gene expression or otherwise avoid elimination in vivo have faced major technical obstacles. The central obstacle is that HIV DNA+ cells under ART are not known to express distinguishing virus- or host-encoded markers, making it impossible to isolate and characterize these cells by flow cytometry. Moreover, because HIV DNA+ cells are rare (i.e., <1% of all memory CD4 T cells), comprehensive “-omic” analysis of pooled CD4 T cells from ART-treated people with HIV (PWH) largely reflects the attributes of uninfected cells. To address these obstacles, VPDS and extramural engineering partners developed Focused Interrogation of cells by Nucleic acid Detection and sequencing (FIND-seq), which uses a series of custom microfluidic devices to isolate transcriptomes of HIV-infected cells based solely on HIV DNA detection. This single-cell analytical approach captures a transcriptome-wide profile of HIV DNA+ cells in their natural state, without the need for in vitro latency reversal that can change cellular attributes. Our initial application of FIND-seq to HIV DNA+ memory CD4 T cells under ART identified host cell transcriptomic signatures of HIV silencing and cell survival that help to explain HIV-infected CD4 T cell persistence despite the suppression of virus replication. These findings bolstered the latent reservoir concept, linked quiescence of HIV gene expression to host gene expression patterns that are specific to infected cells, and emphasized that further elucidating the biology of HIV-infected cell reservoirs in vivo can help advance the search for an HIV cure. The present study will advance the field's early understanding of the unique biology of HIV-infected cells, as described below.