Proviral location affects cognate peptide–induced virus production and immune recognition of HIV-1–infected T cell clones
Filippo Dragoni, … , Francesco R. Simonetti, Joel N. Blankson
Filippo Dragoni, … , Francesco R. Simonetti, Joel N. Blankson
Published September 12, 2023
Citation Information: J Clin Invest. 2023;133(21):e171097. https://doi.org/10.1172/JCI171097.
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Clinical Research and Public Health AIDS/HIV

Proviral location affects cognate peptide–induced virus production and immune recognition of HIV-1–infected T cell clones

Abstract

BACKGROUND HIV-1–infected CD4+ T cells contribute to latent reservoir persistence by proliferating while avoiding immune recognition. Integration features of intact proviruses in elite controllers (ECs) and people on long-term therapy suggest that proviruses in specific chromosomal locations can evade immune surveillance. However, direct evidence of this mechanism is missing.METHODS In this case report, we characterized integration sites and full genome sequences of expanded T cell clones in an EC before and after chemoradiation. We identified the cognate peptide of infected clones to investigate cell proliferation and virus production induced by T cell activation, and susceptibility to autologous CD8+ T cells.RESULTS The proviral landscape was dominated by 2 large clones with replication-competent proviruses integrated into zinc finger (ZNF) genes (ZNF470 and ZNF721) in locations previously associated with deeper latency. A third nearly intact provirus, with a stop codon in Pol, was integrated into an intergenic site. Upon stimulation with cognate Gag peptides, infected clones proliferated extensively and produced virus, but the provirus in ZNF721 was 200-fold less inducible. While autologous CD8+ T cells decreased the proliferation of cells carrying the intergenic provirus, they had no effect on cells with the provirus in the ZNF721 gene.CONCLUSIONS We provide direct evidence that upon activation of infected clones by cognate antigen, the lower inducibility of intact proviruses in ZNF genes can result in immune evasion and persistence.FUNDING Office of the NIH Director and National Institute of Dental & Craniofacial Research; NIAID, NIH; Johns Hopkins University Center for AIDS Research.

Authors

Filippo Dragoni, Abena K. Kwaa, Caroline C. Traut, Rebecca T. Veenhuis, Bezawit A. Woldemeskel, Angelica Camilo-Contreras, Hayley E. Raymond, Arbor G. Dykema, Eileen P. Scully, Amanda M. Rosecrans, Kellie N. Smith, Frederic D. Bushman, Francesco R. Simonetti, Joel N. Blankson

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Figure 2

Persistence and expansion of 2 clones carrying intact proviruses integrated in ZNF genes.

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Persistence and expansion of 2 clones carrying intact proviruses integra...
(A) Experimental approach used to match integration site and proviral sequences of interest. (B) Nearly full-length (NFL) genome sequences from viral outgrowth isolates and intact proviruses integrated into ZNF721 and ZNF470 genes; black ticks show nucleotide differences from ZNF470i, indicated by the asterisk symbol; mutations in ZNF721i relative to ZNF470i are indicated with their positions relative to HXB2. (C) Genomic location and relative orientation of intact proviruses of interest; purple tracks indicate protein-coding genes, with the psudogene ABCA11P indicated in pink; black arrow heads indicate previously published integration sites; genes located outside the gray box are highlighted with arrows. (D) Representative 2D dPCR plots showing duplex amplification of total LTR R-U5 copies and proviruses of interest by integration site–specific assays. IS, integration site. (E) Longitudinal quantification of ZNF721i and ZNF470i proviruses before, during, and after treatment; the gray, green, and purple shaded areas indicate ART, chemoradiation, and immunotherapy, respectively, as in Figure 1A; open circles indicate values below the limit of detection; error bars indicate SEM; values above the graph area represent the percentage of proviruses of interest among all LTR R-U5 copies. (F) Fold increase of total LTR and proviruses of interest from day –6 to day 1000 from the start of chemoradiation. (G) Estimates of total-body clone size, expressed as million cells; the shaded gray area represents the uninfected fraction of each clonotype.