Background
HIV-1 infection in chronic progressors (CPs) is characterized by dysfunctional HIV-specific T cell responses. HIV controllers (HICs) maintain superior HIV-specific T cell responses that control viral replication. Recent studies have shown that long-term antiretroviral therapy (ART) is associated with dominant HIV-specific CD8+ T cell clonotypes displaying signatures of stemness. We compared the proliferative capacity and transcriptional profile of HIV Gag-specific T cells as well as the Gag-specific T cell receptor (TCR) repertoire in CPs on long-term ART and HICs.
Methods
We performed 10-day expansion assays using PBMCs from 5 HIC and 14 CPs who have been on ART for more than 15 years. Cells were stimulated with overlapping Gag peptide pools and flow cytometry was used to measure HIV-specific CD4+ and CD8+ T cell cytokine responses. We used the functional expansion of specific T cells (FEST) assay with TCR sequencing to quantify Gag-specific TCR clonotypes in CD4+ T cells. Coupled single-cell TCRseq/RNA-seq was used to analyze the transcriptional profile of HIV-specific CD4+ T cells from 3 CPs and 3 HICs after 10 days of culture with Gag peptides.
Results
Gag-specific CD4+ T cell responses (IFN-γ+TNF-α+) were robust in both groups after 10 days of peptide stimulation, with median frequencies of 3.24% (range 0-13.2) in CPs and 7.09% (range 1.81-22.8) in HICs (P = 0.3275) after 10 days of culture with peptides compared to 0.08% (range 0-0.15) vs 0.36% (range 0.25-0.63) in cells cultured with DMSO. CD8+ T cell responses were similar between groups (median 0.69%, range 0-4.31 in CPs vs. 1.92%, range 0.107-17.16 in HICs after 10 days of culture with peptides, P = 0.124) compared to 0.13% (range 0-0.94) vs 0.65% (range 0.04-4.14) in cells cultured with DMSO. FEST analysis revealed comparable Gag-specific TCR repertoires in CD4+ T cells, with a median of 19 distinct Gag-specific TCRs (range 3-67) in CPs and 55 (range 4-73) in HICs (P = 0.19). Gag-specific CD4+ T cells in both groups exhibited a cytotoxic phenotype, marked by upregulation of GZMA, GZMB, and GNLY. A higher proportion of these cells were within the cytotoxic subset and expressed higher levels of GZMK in HICs.
Conclusions
Our results demonstrate that CPs on long-term ART exhibit HIV-specific T cell responses that are comparable to those present in HICs, although subtle differences remain. Further studies will be needed to determine whether these cells can effectively target the viral reservoir.