Single-cell RNA-seq analysis of macaque tonsil antigen presenting cells

Numerous studies have shown in mouse that identity and function of macrophage populations are imprinted by their tissue of residence. By contrast, the properties of human tissue macrophages remain poorly understood. Here, we characterized human tonsil macrophages and identified 3 macrophage subsets with distinct phenotype, ontogeny and function. Using RNA-seq analysis, we found that CD36hi macrophages were transcriptionally related to monocytes, while CD36lo macrophages showed features of embryonic origin and CD36int macrophages had a mixed profile. Using scRNA-seq profiling of naïve and inflamed tonsils from non-human primates, we showed that monocyte engraftment did not pre-exist an immune challenge. We compared a naïve animal with macaques infected intra-nasally with Influenza A virus (H3N2 strain). Tonsils were sampled at day 5 or 14 post-infection. We profiled tonsil mononuclear phagocytes using scRNA-seq after cell enrichment for antigen presenting cells.