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

Yan Ding ^1* Jialai Yan ^2* Ling Huang ^1* Jinhong Yu ^1* Yandan Wu ^3* Chuanlai Shen ^3* Anning Fang ^4*

• ¹ the Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Department of Clinical Laboratory, Nanjing, China
• ² Anhui Medical College, School of Medical Technology, Hefei, China
• ³ Medical School of Southeast University, Department of Microbiology and Immunology, Nanjing, China
• ⁴ Anhui Medical College, School of Basic Medicine, Hefei, China

Background: Although the immune response of host T cells to human immunodeficiency virus (HIV) has been shown to have a significant effect on infection progression, the development of T-cell-based vaccines and therapies, as well as the clinical assessment of specific T-cell functions, is currently markedly hindered by the lack of broad-spetrum HIV T-cell epitopes that are functionally validated and cover the polymorphisms of the human leukocyte antigen (HLA) in an indicated geographic population. This study aimed to screen the T-cell epitopes derived from the GP160, GAG, and POL proteins of the HIV-1 strain, which are represented by 12 prevalent HLA-A allotypes, accounting for approximately 91% of the total gene frequency in Northeast Asian populations. Methods: A total of 134 epitopes were predicted in silico and selected as epitope candidates for further validation. Then, peripheral blood mononuclear cells (PBMCs) were collected from 96 people with HIV-1 and cocultured ex vivo with each epitope candidate peptide, followed by the detection of activated CD8 + T cells. Sixty-nine epitopes were validated as realworld HIV T-cell epitopes presented by 12 dominant HLA-A allotypes. Furthermore, 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 had high affinity, and 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 IFNγ intracellular staining. For 52 people with HIV-1, the number of reactive HIV-1 specific CD8 + T cells was significantly greater in the CD4 + T-cell-high patient group than in the CD4 + T-cell-low patient group, and was correlated with CD4 + T-cell-low (< 200/μL).This study provides a broad-spectrum CD8 + T-cell epitope library for a T-celldirected HIV vaccine with high population coverage in Northeast Asia and establishes a universal detection method for the clinical assessment of HIV-1-specific CD8 + T-cell responses.