Single-cell TCR sequencing reveals phenotypically diverse clonally expanded cells harboring inducible HIV proviruses during ART

Abstract

Clonal expansions occur in the persistent HIV reservoir as shown by the duplication of proviral integration sites. However, the source of the proliferation of HIV-infected cells remains unclear. Here, we analyze the TCR repertoire of single HIV-infected cells harboring translation-competent proviruses in longitudinal samples from eight individuals on antiretroviral therapy (ART). When compared to uninfected cells, the TCR repertoire of reservoir cells is heavily biased: expanded clonotypes are present in all individuals, account for the majority of reservoir cells and are often maintained over time on ART. Infected T cell clones are detected at low frequencies in the long-lived central memory compartment and overrepresented in the most differentiated memory subsets. Our results indicate that clonal expansions highly contribute to the persistence of the HIV reservoir and suggest that reservoir cells displaying a differentiated phenotype are the progeny of infected central memory cells undergoing antigen-driven clonal expansion during ART.

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

“…A total of 158 p24+ cells and 156 IS were retrieved. A large proportion of these stemmed from clonally expanded infected cells (74%, 116/156), defined by recurrent identical IS, confirming the often clonal nature of the translation-competent reservoir 17 .…”

“…2). In addition, the TCRβ chain of the host cell was sequenced as described 17 , and index sorting was used for post hoc determination of the memory phenotype of p24+ cells (Fig. 1a, Supplementary Fig.…”

“…Alternative assays have been developed to characterize and quantify infected cells harboring transcription-competent 22,40 or translation-competent 17,40–44 proviruses, therefore enriching for proviruses with a higher probability of contributing to viral rebound 45 . These assays use a potent stimulant to reactivate proviruses from latency, inducing transcription of viral genes and production of viral proteins.…”

“…Infected cells can then be identified and isolated by fluorescence-activated cell sorting (FACS). This allowed for the characterization of NFL proviral genome structure 22,43 , TCR sequences 17,43 and IS 22 from cells harboring an inducible provirus. However, none of these methodologies capture all three layers of information simultaneously.…”

Role of CD4+ T Cells in the Control of Viral Infections: Recent Advances and Open Questions

“…In the context of HIV infection, the loss of TCR repertoire diversity in both the CD4+ and the CD8+ T cell populations was also associated with disease progression in early studies [ 174 , 175 ]. TCR clonotypes are now being used as molecular markers to track the amplification of latently infected CD4+ T cell clones, demonstrating that HIV provirus persistence depends largely on homeostatic CD4+ T cell proliferation [ 176 ]. Interestingly, a subset of latently infected cells were shown to be specific for HIV and CMV, suggesting that viral reactivation episodes could also drive the amplification of the HIV reservoir [ 177 , 178 ].…”