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

Jean-Pierre Routy,Marion Pardons,Moti Ramgopal,Rémi Fromentin,Amélie Pagliuzza,Nicolas Chomont,Pierre Gantner

doi:10.1038/s41467-020-17898-8

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.

Highlights

Clonal expansions occur in the persistent HIV reservoir as shown by the duplication of proviral integration sites
Clonotypic characterization of individual HIV-infected cells was performed by combining single-cell sorting of HIV-infected (p24+) cells by HIV-Flow[33] with multiplex PCR of the V–J junction of the TCRβ chain followed by sequencing (Supplementary Fig. 1a)
Cells containing duplicated T-cell receptor (TCR) harbored the exact same viral sequence, which were different than those retrieved in cells harboring distinct TCRs (Supplementary Fig. 4b, c). These results indicated that clonal expansion of an HIVinfected cell is the most likely explanation for the duplication of TCR sequences within the pool of p24+ cells

Summary

Introduction

Clonal expansions occur in the persistent HIV reservoir as shown by the duplication of proviral integration sites. We hypothesize that duplication of TCR clonotypes within the pool of HIV-infected cells will reflect the dynamics of clonal expansion as well as the persistence of individual HIV-infected clones[32]. Results TCRβ sequencing and phenotyping of single HIV-infected cells.

Results

Conclusion