Single-cell comparison of day 7 vaccine, listeria and vaccinia virus elicited CD8 T cells

Protection from pathogens relies on both humoral (antibody-mediated) and cellular (T cell-mediated) responses. While infections robustly elicit both of these types of immunity, currently approved vaccine adjuvants largely fail to induce significant T cell responses. However, recent work by our lab and others suggests that the mechanisms governing vaccine-elicited T cells (Tvac) may be substantially different than those governing infection-elicited T cells (Tinf). We have recently demonstrated that optimal subunit vaccine-elicited T cell responses rely on different cytokine signals (IL-27 and 15) and metabolic function (oxidative phosphorylation vs. aerobic glycolysis) leading to phenotypically and functionally different outcomes (memory vs. effector). Our goal was to investigate the transcriptional programming that promotes Tvac formation. Using a single-cell RNA-seq approach, we compared Tvac and Tinf at day 7 post-immunization or infectious challenge to determine the heterogenity of CD8 T cell responses at this peak timepoint. A small number (500) of congenically marked (CD45.1) OT-I T cells were adoptively transferred into a naïve B6 recipient (CD45.2). These recipients were then immunized intravenously against OVA using our combined adjuvant vaccine (poly I:C, anti-CD40), infection with Listeria monocytogenes-OVA (LM) or Vaccinia Virus-OVA (VV). T cells were isolated on day 7 post immunization using FACS sorting of CD45.1+ CD8+ cells. Cells from an individual condition (adjuvant, LM or VV) were stained with an unique oligo-tagged anti-CD45 “hashtag” antibody (Biolegend) and then combined into one sample. ------------------- HTO barcode sequence hashtagged sample TotalSeq-A0301 anti-mouse Hashtag 1 Antibody ACCCACCAGTAAGAC Adjuvant TotalSeq-A0302 anti-mouse Hashtag 2 Antibody GGTCGAGAGCATTCA Listeria monocytogenes TotalSeq-A0303 anti-mouse Hashtag 3 Antibody CTTGCCGCATGTCAT Vaccinia Virus