Microarray analysis of total naïve and YFV-17D specific CD8 T cells in humans

CD8 T cells play an importart role in adaptive immunity to intracellular pathogens. Naïve CD8 T cells , that have not encountered antigen previously can be identified by virtue of their distinct phenotype. Upon antigenic encounter, they proliferate rapidly and undergo massive reprograming to differentiate to cytotoxic T lymphocytes. The yellow fever live virus vaccine (YF-17D) provides a model primary acute viral infection that can be used to follow this response.Here we characterize the resting, non-activated naive CD8 T cells in nine healthy adults and YF-specific CD8 T cells elicited in response to YF-17D vaccination from the same donors during the effector (2 weeks after vaccination) and memory (5-8 months later) stages. The dataset contains 3 sets of samples obtained using an IRB approved protocol and after informed consent of volunteers. Donors in this study were vaccinated with the yellow fever vaccine (subcutaneos, single immunization) and whole blood drawn in CPT tubes, total peripheral blood mononuclear cells (PBMC) were separated and used as a source for flow cytometry based isolation of CD8 T cell populations. The first set of samples is from nine healthy adults were recruited and naïve CD8 T cells (identified by their CD45RA+ CCR7+ CD3+ CD8+ phenotype) before vaccination and effector CD8 T cells (HLA-DR+CD38+ CD3+CD8+ T cells) 2 weeks after vaccination were sorted using a FACS vantage sorter. In the second set, 4 donors were recruited and naive CD8 T cells were isolated as before while effector CD8 T cells were isolated 2 weeks after vaccination using the HLA-A2 restricted NS4B-214 tetramers. Total RNA was isolated from the sorted cells and used for microarray analysis on Affymetrix Human Genome U133 plus 2.0 arrays. In the third set, pre vaccination samples were obtained as before and sorted tetramer-specific samples were acquired during the memory stage, 5 to 80 months after YF-17D vaccination. All tetramer specific sorts were done using the HLA-A2 restricted NS4B214 tetramer (Akondy et al, J. Immunol 2009).