Genomics

Dataset Information

45

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


ABSTRACT: 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. Overall design: 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.

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

ORGANISM(S): Homo Sapiens

SUBMITTER: Rama S Akondy 

PROVIDER: GSE75533 | GEO | 2017-12-13

SECONDARY ACCESSION(S): PRJNA304496

REPOSITORIES: GEO

Dataset's files

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Action DRS
GSE75533_rpkm_summary.csv.gz Csv
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Publications


The differentiation of human memory CD8 T cells is not well understood. Here we address this issue using the live yellow fever virus (YFV) vaccine, which induces long-term immunity in humans. We used in vivo deuterium labelling to mark CD8 T cells that proliferated in response to the virus and then assessed cellular turnover and longevity by quantifying deuterium dilution kinetics in YFV-specific CD8 T cells using mass spectrometry. This longitudinal analysis showed that the memory pool originat  ...[more]

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