Single cell RNA-seq of HLA-E restricted UL40-specific T cells

Human cytomegalovirus infection (CMV) can stimulate robust human leukocyte antigen (HLA)-E restricted CD8 T cell responses. These T cells recognize a peptide from UL40, which differs by as little as a single methyl group from self-peptides that also bind HLA-E, challenging their capacity to avoid self-reactivity. We showed in one donor 2 distinct populations of UL40/HLA-E T cells, with vastly different T cell receptor (TCR) affinities for the UL40/HLA-E complex. However, paradoxically, lower cytokine responses were observed from UL40/HLA-E T cells bearing TCRs with high affinity for HLA-E. To identify why these T cells bearing high affinity T cell receptors were less responsive to antigens, we performed single cell RNAseq analysis. These 2 distinct populations of T cells were single-cell sorted into 96-well plates prior to single cell RNA-seq analysis.