Distinct transcriptome profiles of Gag-specific CD8+ T cells temporally correlated with the protection elicited by SIVΔnef live attenuated vaccine

S (SIVΔnef) live attenuated vaccine (LAV) confers the best protection among all the vaccine modalities tested in rhesus macaque model of HIV-1 infection. This vaccine has a unique feature of time dependent protection that is macaques are not protected at 3-5 weeks post vaccination (WPV), whereas immune protection emerges between 15 and 20 WPV. Although the exact mechanisms of the time dependent protection remain incompletely understood, recent studies suggested IgG antibodies specific to viral envelope glycoprotein gp41 trimers correlated spatially and temporally with the maturation of local protection against high dose pathogenic SIV vaginal challenge and SIV-specific CD8+ T cells quality rather than quantity may correlate with maturation of local protection. To further elucidate the mechanisms of protection induced by SIVΔnef vaccine, we longitudinally compared the global gene expression profiles of SIV Gag-CM9+ CD8+ (Gag-specific CD8+) T cells from peripheral blood of Mamu-A*01 rhesus macaques at 3 and 20 WPV using rhesus microarray. We found that gene expression profiles of Gag specific CD8+ T cells at 20 WPV are qualitatively different from those at 3 WPV. At 20 WPV, the most significant transcriptional changes of Gag specific CD8+ T cells were genes involved in cell activation, differentiation and maturation toward central memory cells with increased expression of CCR7, TCR-alpha, TCR-beta, CD28 and decreased expression of CTLA-4, IFN-γ, RANTES (CCL5), granzyme A and B. Our study indicates that a higher quality of SIV-specific CD8+ T cells elicited by SIVΔnef over time contributes to the maturation of time dependent protection.