Comparative analysis of the DNA methylation landscape in CD4, CD8, and B memory lineages

There is considerable evidence that epigenetic mechanisms and DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common pathways in distinct cell types for immunological processes such as immune activation. Further, it remains unclear if the memory cell subtypes differentiate distinctly by cell lineages. We used the Illumina EPIC array to characterize the DNA methylation similarities and differences in B cell, CD4 T, and CD8 T naïve and memory cells states. Our data describe considerable overlap in CpG dinucleotides and genes with altered DNA methylation in the process of naïve to memory activation across the three lineages, clearly suggesting that common pathways exist for immune memory generation. Further, our analyses revealed specific CpG dinucleotides and genes in CD4 T and CD8 T central to effector memory differentiation. Finally, we identified unique DNA methylation patterns in TEMRA CD8 T cells compared to other CD8 T memory cell subtypes. Bisulphite converted, EPIC arrayed DNA from naïve and memory B and T lymphocytes: B naïve (n=6), B memory (n=7), CD4 naïve (n=6), CD4 central memory (n=6), CD4 effector memory (n=6), CD8 naïve (n=12), CD8 central memory (n=5), CD8 effector memory (n=4), CD8 TEMRA (n=5).