Single-cell immune profiling of Q fever vaccination in mice

Human Q fever is a worldwide zoonotic disease caused by intracellular Gram-negative bacterium, Coxiella burnetii. Human Q fever has high infectious nature. However, there is no FDA approved vaccine in the US. Previous studies showed that after serial passages in eggs and tissue cultures, C. burnetiid undergoes a lipopolysaccharide (LPS) phase variation in which its virulent smooth LPS phase I (PI) converts to an avirulent rough LPS phase II (PII). A formalin-inactivated PI vaccine (PIV) was demonstrated to be more protective than PII vaccine (PIIV) in guinea pigs. The research objective is to understand the mechanisms of vaccine-induced protective immunity against C. burnetii infection. To achieve this objective, we utilized 10x Genomics immune profiling technology to simultaneously assay T cell, B cell receptor sequences, transcriptional profiles and surface protein expression at single-cell level. We leverage Seurat Weighted Nearest Neighbor algorithm to integrate transcriptional profiles and surface protein expression to perform cell-clustering. After automatic and manual annotation, we focused on B cells and CD4+ T cells. We identified differentially expressed gene for each vaccinated group in the subpopulation of B cells and CD4+ T cells. We will also perform B cells trajectory inference in each vaccinated group and perform TCR and BCR V(D)J usage and clonotype analysis.