Antigen-driven clonal selection shapes the persistence of HIV-1–infected CD4+ T cells in vivo
Francesco R. Simonetti, … , Janet D. Siliciano, Robert F. Siliciano
Francesco R. Simonetti, … , Janet D. Siliciano, Robert F. Siliciano
Published December 10, 2020
Citation Information: J Clin Invest. 2021;131(3):e145254. https://doi.org/10.1172/JCI145254.
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Research Article AIDS/HIV Immunology

Antigen-driven clonal selection shapes the persistence of HIV-1–infected CD4+ T cells in vivo

Abstract

Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to achieving a cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here, we show that it is possible to link antigen responsiveness, the full proviral sequence, the integration site, and the T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated CMV- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), the proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ and integration site analysis showed that infection could occur early or late in the course of a clone’s response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together, these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.

Authors

Francesco R. Simonetti, Hao Zhang, Garshasb P. Soroosh, Jiayi Duan, Kyle Rhodehouse, Alison L. Hill, Subul A. Beg, Kevin McCormick, Hayley E. Raymond, Christopher L. Nobles, John K. Everett, Kyungyoon J. Kwon, Jennifer A. White, Jun Lai, Joseph B. Margolick, Rebecca Hoh, Steven G. Deeks, Frederic D. Bushman, Janet D. Siliciano, Robert F. Siliciano

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Figure 1

Experimental approach to study HIV-1–infected, antigen-responding CD4+ T cells.

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Experimental approach to study HIV-1–infected, antigen-responding CD4+ T...
(A) Experimental design and gating logic to isolate cells responding to stimulation. CD8-depleted PBMCs were stimulated with no antigen, anti-CD3/anti-CD28–conjugated beads, CMV lysates, or HIV-1 Gag peptides. CD4+ T cells upregulating both activation markers CD40L and CD69 were sorted. For CMV and Gag stimulations, nonresponding cells with high CD40RO expression were also isolated (highlighted in green). (B) Frequencies of CD4+ T cells responding to the indicated stimulation. Mean values of all time points are shown for each of 10 participants; horizontal bars show the median and interquartile values. Statistical significance was determined by 1-way ANOVA. (C) Experimental design to characterize the clones of the HIV-1–infected antigen-responding cells. Samples from follow-up time points were processed as in A; responding cells were sorted in small pools and subjected to WGA. Pools containing infected cells were detected by u5-gag or env PCR. Proviruses matching potential clones previously identified by single-genome sequencing were detected by Sanger sequencing. Whole-genome–amplified DNA was then used for integration site analysis, full proviral genome sequencing, the intact proviral DNA assay, and TCRβ sequencing. Ag, antigen.