Computational prediction and identification of dengue virus-specific CD4+ T-cell epitopes

In this study, we tried to identify dengue virus-specific CD4+ T-cell epitopes, which can induce PBMC (peripheral blood mononuclear cells) isolated from DF convalescent patients (dengue virus type 1 infection) to secrete IFN-γ. PBMC of DF convalescent patients were stimulated in vitro with dengue virus-derived peptides, which were prepared based on the prediction of dengue virus-specific CD4+ T-cell epitopes by using RANKpep online software. Subsequently, the frequency of IFN-γ producing T cells and percentage of IFN-γ+ CD4+ T cells were measured by using ELISPOT assay and ICS assay (intracellular cytokine straining), respectively. The positive response of PBMC by ELISPOT showed that the numbers of SFC (spots forming cells) ranged from 50 to 310 SFC/1 × 106 PBMC. The positive response of PBMC by ICS assay showed that the percentage of IFN-γ+ CD4+ T cells ranged from 0.03 to 0.27%. As a result, C45-57 (KLVMAFIAFLRFL), E396-408 (SSIGKMFEATARG), NS323-35 (YRILQRGLLGRSQ), and NS3141-155 (NREGKIVGLYGNGVV) were identified as dengue virus-specific CD4+ T-cell epitopes.