Large-scale screening of HIV-1 T-cell epitopes restricted by 12 prevalent HLA-A allotypes in Northeast Asia and universal detection of HIV-1-specific CD8+ T cells

Background Although the immune response of host T cells to human immunodeficiency virus (HIV) significantly influences the progression of the infection, the development of T-cell-based vaccines and therapies, as well as the clinical evaluation of specific T-cell functions, is currently markedly hindered by the absence of broad-spectrum, functionally validated HIV T-cell epitopes that account for the polymorphisms of the human leukocyte antigen (HLA) within an indicated geographic population. This study aimed to identify T-cell epitopes derived from the GP160, GAG, and POL proteins of the HIV-1 strain, specifically linked to 12 prevalent HLA-A allotypes, that collectively represent approximately 91% of the total gene frequency in Northeast Asian populations. Methods A total of 134 epitopes were predicted in silico and selected as potential candidates for further validation. Subsequently, peripheral blood mononuclear cells (PBMCs) were collected from 96 individuals with HIV-1 and cocultured ex vivo with each epitope candidate peptide, followed by the detection of activated CD8 + T cells. Peripheral blood mononuclear cells (PBMCs) were collected from 96 individuals with HIV-1 and cocultured ex vivo with each candidate peptide epitope, followed by the detection of activated CD8+ T cells. A total of 69 epitopes were validated as real-world HIV T-cell epitopes presented by 12 dominant HLA-A allotypes. Furthermore, the HLA-A cross-restriction for each epitope candidate was identified through peptide competitive binding assays using 12 transfected HMy2.CIR cell lines. Results A total of 45 epitopes demonstrated high affinity, while 31 epitopes displayed intermediate affinity. A broad-spectrum CD8 + T-cell epitope library containing 141 validated epitope peptides was used to universally detect HIV-1-specific CD8 + T cells via peptide-PBMC ex vivo coculture and intracellular IFN- γ staining. In 52 people with HIV-1, the number of reactive HIV-1 specific CD8 + T cells was significantly higher in the CD4 + T-cell-high patient group compared to the CD4 + T-cell-low patient group, and it correlated with the CD4 + T-cell-low patient group (<200/μL). Conclusion This study provides a broad-spectrum CD8 + T-cell epitope library aimed at developing a T-cell-directed HIV vaccine that offers high population coverage in Northeast Asia. In addition, it establishes a universal detection method for the clinical assessment of HIV-1-specific CD8 + T-cell responses.