Transcriptional profiles reveal a stepwise developmental program of memory CD8⁺ T cell differentiation

The generation of CD8⁺ T-cell memory is a major aim of vaccination. While distinct subsets of CD8⁺ T-cells are generated following immunization that differ in their ability to confer long-term immunity against infection, the transcriptional profiles of these subsets within endogenous vaccine-induced CD8⁺ T cell responses have not been resolved. Here, we measure global transcriptional profiles of endogenous effector (T_EFF), effector memory (T_EM) and central memory (T_CM) CD8⁺ T-cells arising from immunization with three distinct prime-boost vaccine regimens. While a proportion of transcripts were uniquely regulated within distinct CD8⁺ T cell populations, we observed progressive up- or down-regulation in the expression of a majority of differentially expressed transcripts when subsets were compared in the order T_N>T_CM>T_EM>T_EFF. Strikingly, when we compared global differences in gene expression between T_N, T_CM, T_EM and T_EFF cells with known transcriptional changes that result when CD8⁺ T cells repetitively encounter antigen, our analysis overwhelmingly favored a model whereby cumulative antigen stimulation drives differentiation specifically from T_N>T_CM>T_EM>T_EFF and this was common to all vaccines tested. These findings provide insight into the molecular basis of immunological memory and identify potential biomarkers for characterization of vaccine-induced responses and prediction of vaccine efficacy.