Advancements in single-cell techniques for examining the HIV reservoir: pathways to a cure

Abstract

Human immunodeficiency virus (HIV) is largely incurable, due to the presence of a viral reservoir, which primarily consists of resting CD4⁺ T cells and other long-lived cells like macrophages. These reservoir cells, which persist despite suppressive antiretroviral therapy (ART), are thought to be influenced by several key factors such as position and orientation of chromosomal proviral integration, proviral intactness, and antigen specificity. The host's immune status and immune selection pressures also likely play a significant role. Recent data suggest that the HIV provirus integrates into specific chromosomal regions, such as centromeric areas with low RNA expression, allowing the virus to evade detection. To effectively disrupt HIV latency, enhance immune recognition, and eliminate reservoir cells, a precise understanding of these viral reservoirs at single-cell level will be crucial. Gaining insights into the unique characteristics of these reservoir cells, including data on integration sites and gene expression profiles, is essential for designing targeted interventions. This review highlights current single-cell approaches, including single-cell sequencing, chromatin accessibility assays, and multiomic techniques, as tools for uncovering the heterogeneity and resilience of HIV reservoirs. Taken together, these methods aim to reveal the complexities of the HIV reservoir and promote the development of novel therapeutic strategies.

Keywords: HIV cure; HIV-1; HIV-1 reservoir; single-cell.

Fig 1

Tissue and cellular dynamics of the HIV reservoir and the application of single-cell technologies for characterization. The HIV reservoir is distributed across multiple anatomical sites, including peripheral blood, lymphoid tissues (spleen, thymus, bone marrow, and lymph nodes), the central nervous system, lungs, gastrointestinal tract, and adipose tissue. Cellular reservoirs include CD4⁺ T cells, macrophages, dendritic cells, astrocytes, and microglial cells. Advances in single-cell technologies, such as scDNA-seq, scATAC-seq, scRNA-seq, and multiomic approaches (ECCITE-seq and DOGMA-seq), enable a more detailed analysis of viral genome persistence, epigenetic modifications, transcriptomic activity, and proteomic characteristics across these reservoir sites. This image was created using BioRender (BioRender.com).