Gene expression profile at single cell level of OVA+ cells elicited by LTA1/OVA vaccine at different time points and CD4+T cells from naïve spleen as control
Our previous work showed that vaccine elicited Klebsiella pneumoniae specific CD4+ tissue resident memory (TRM) cells in the lung provide serotype independent immunity against K. pneumoniae for up to 6 months.  However, vaccine efficacy wanes in proportion to lung CD4+ TRM cell number.  To study what controls TRM maintenance, apart from antigen, we developed an LTA/1Ovalbumin (OVA) model and tetramer pulldown method to enrich OVA+ lung CD4+ TRM cells over time. We applied single-cell RNA-sequencing (scRNA-seq) of these cells, collected on days 30, 90 and 184 after prime immunization with OVA and our prior Th17 adjuvant, E. coli heat labile toxin A1 (LTA1). As control, we used splenic CD4+ T cells from naive mice Overall design: OVA+ cells from different time points were enriched by OVA-tetramer pulldown and analyzed by scRNAseq.