Whole genome DNA methylation analysis of human CD8 T cell specific for the Yellow fever virus vaccine

Central questions regarding the origin of memory CD8 T cells, their turnover and longevity in vivo are not well-defined in humans. Here, we have used the highly efficacious live yellow fever virus vaccine (YFV-17D) to address these issues in the context of a primary acute viral infection. We interrogated genome-wide CpG methylation of YFV tetramer-specific CD8 T cells. These findings provide a better understanding of how memory CD8 T cells are formed and maintained in humans. A2-NS4B214 tetramer+ CD8 T cells were isolated by FACS from one donor vaccinated with YFV-17D 14 days previously (effector) and a different donor vaccinated 166 days previously (memory). To obtain the required cell numbers from the memory donor, a leukapheresis procedure was performed. Total naive CD8 T cells from the memory donor were used as a control. Methylation profiling was performed using the Me-DIP sequencing services from Active motif. Briefly, genomic DNA was fragmented, denatured and a 5-methyl cytosine specific antibody was used for immunoprecipitation based enrichment of methylated DNA regions, the enriched DNA samples were amplified and Next-gen sequencing performed.