RNA-seq analysis of human tonsil macrophage subsets

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. Overall design: Tonsil macrophages were separated into 3 subsets based on the expression of CD36 and CD81. RNA-seq analysis was performed on each subset separately after cell sorting. Tonsil macrophages were selected after tissue digestion by density gradient, enriched by negative selection, and isolated by cell sorting.