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.

Cognate Antigen Engagement Induces HIV-1 Expression In CD4+T Cells From People On Long-Term ART

“…Even though T cell activation is a prerequisite for latency reversal 88 , our data suggest that there is some discordance between Ag-driven T cell responses and latency reversal. This observation is consistent with studies demonstrating that for some proviruses latency reversal was achieved only after multiple rounds of T cell activation 16,32 , and that other factors, such as proviral location, can further reduce viral expression despite T cell activation and proliferation 66 . In addition, we showed that higher infection frequency among Ag-responding cells resulted in higher HIV-1 expression upon cognate Ag and PMA/I stimulation.…”

“…The latter finding was based on the QVOA, which relies on latency reversal with the mitogen phytohemagglutinin (PHA), raising the question of whether polyclonal activation with mitogens induced proviruses that would not be induced in vivo. Here, we extend the results from a recent case report 66 and show that Ag presented in a physiologic manner by autologous APCs can reverse latency and cause viral particle production, further supporting that even proviruses that have been selected during long-term ART can be reactivated and could contribute to viral rebound if ART is interrupted in the absence of exceptional immune control.…”

“…The percentage of CD69 + CD154 + cells did not correlate with HIV-1 RNA levels normalized by infected cell frequency (HIV-1 RNA/HIV-1 DNA) in either untreated cells (NoTx) or upon stimulation with PMA/I or cognate Ag (Figure S4D), likely due to the similar levels of CD69 and CD154 expression among participants in each condition. In addition, although T cell activation is required for latency reversal, the two processes are, to some degree, uncoupled 32,51,66 . As expected, we observed a significant correlation between HIV-1 RNA and the frequency of total proviruses (as calculated by IPDA, see Figure 1D) with both PMA/I and cognate Ag stimulation (Figure S4E).…”

Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells

“…It has been observed that certain infected cells may have some survival advantages compared to uninfected cells based on integration site locations or other mechanisms 44,45,47–50,85 . As a sensitivity analysis, we therefore added a positive “survival advantage” rate ζ i =1e-5 per day for a small fraction of HIV-infected clones f ζ =1/100.…”

“…The role of homeostatic proliferation in the maintenance of the reservoir is less clear. Factors related to provirus sequence 42,43 or integration site 26,27,37,44,45 may confer selective advantages or disadvantages to certain proviral clones and therefore contribute to the reservoir’s extraordinary clonality. While provirus integration into oncogenes is now thought to play only a minor role in reservoir clonal expansion 46 , there is evidence that integration into transcriptionally inactive heterochromatin may confer a survival advantage 44,47–50 .…”