Single cell analysis uncovers novel populations of CD4+ T cells associated with antifungal vaccine efficacy

Memory T cells underpin vaccine-induced immunity but are not yet fully understood. To distinguish features of memory cells that confer protective immunity, we used single cell transcriptome analysis to compare antigen-specific CD4+ T cells recalled to lungs of mice that received a protective or nonprotective subunit vaccine followed by challenge with a fungal pathogen. We unexpectedly found populations specific to protection that expressed a strong type I interferon response signature, whose distinctive transcriptional signature appeared unconventionally dependent on IFN? receptor. We also detected a unique population enriched in protection that highly expressed genes for chemokine CCL5 and natural killer cell marker NKG7. Lastly, we detected differences in TCR gene use and in Th1- and Th17-skewed responses after protective and nonprotective vaccine, respectively, reflecting heterogeneous Ifng- and Il17a-expressing populations. Our findings highlight key features of transcriptionally diverse and distinctive antigen-specific T cells associated with protective vaccine-induced immunity. Overall design: Mice were inoculated either intranasally (IN) or subcutaneously (SC) with Blastomyces dermatitidis endoglucanase-2 (Bl-Eng2) six weeks prior to pathogen challenge. Tetramer-positive CD4+ T cells were FACS sorted and sequenced 3 days after the pulmonary challenge with B. dermatitidis