GSE196472
Single-cell RNA-sequencing of porcine submandibular lymph node cells from ASF-immune and nonimmune pigs
We describe the recall response to African swine fever virus (ASFV) by applying single-cell RNA-sequencing (scRNA-seq) of submandibular lymph node (LN) cells from a control and a vaccinated animal with the live attenuated BA71?CD2 vaccine prototype. Cell suspensions obtained from the digested tissues were in vitro stimulated for 16 hours with BA71?CD2 ASFV, and methanol-fixed prior sequencing using the 10x Genomics scRNA-seq platform. We identified 22 transcriptionally distinctive clusters which were assigned to different cell subsets based on canonical lineage markers. Interferon-stimulated genes (ISG) were significantly upregulated in several cell subsets from the vaccinated pig when compared to the control one. Several populations were overrepresented in LN cells from the vaccinated pig, suggesting their contribution to the ASFV-specific recall response. These included several B cell subsets such as plasmablasts and plasma cells, an undefined CD4 T cell subset, and ?d T cells. The proinflammatory CXCL10 chemokine was strongly upregulated in plasmablasts, in the undefined CD4 T cell subset, and in crosspresenting DCs, thus showing the induction of a Th1-biased recall response. Of particular interest was the presence of a robust vaccine-specific cytotoxic response characterized by elevated numbers of responding CD8 T cells. Indeed, these subset significantly upregulated GZMA.1, confirming their activated status, while it was similarly expressed in NK cells from both samples. Overall, scRNA-seq allowed deciphering the complex protective immune response against ASFV infection, demonstrating a major role of an early Th1-mediated inflammatory response concomitant with a rapid expansion of cytotoxic CD8 T cells. Overall design: 10x Genomics single-cell RNA-sequencing (scRNA-seq) of submandibular LN cells from a control and a BA71?CD2-vaccinated animal after in vitro stimulation for 16 hours with BA71?CD2 ASFV and methanol fixation.