Single-cell RNA sequencing reveals different subsets of macrophage and dendritic cells in human skin

Abstract Objective Single-cell RNA sequencing(scRNA-seq) was performed to cells from whole human skin without pre-purifying to reveal the transcriptional landscape and heterogeneity of macrophages and dendritic cell (Mϕ/DC) subsets. Methods Single-cell RNA sequencing was implemented to ten enzymatically-digested human skin biopsies and analysis was performed with Seurat, then with gene ontology (GO) enrichment analysis and immunofluorescent staining. Results Upon scRNA-seq, 27869 cells from ten skin samples were analyzed in Seurat and 22 distinct clusters were identified using smart local moving clustering. One cluster highly specifically expressed MS4A4A, CD1C, HLA genes and other Mϕ/DC traditional markers, verifying as Mϕ/DC. Upon reanalysis of this cluster (988 cells), we identified three macrophage subsets, marked by high expression of CCR1, MARCO or TREM2; six dendritic cell subsets, marked by high expression of CXorf21, MCOLN2, CLEC9A, KIAA0101 or LAMP3 and one Langerhans cell subset. The KIAA0101 subset expressed a set of marking proliferation genes and all were in G2M phase, indicating represent a progenitor population. GO enrichment analyses indicated different putative functions of Mϕ/DC subsets. Then, the two major macrophage subsets could be defined immunofluorescently by CCR1 and MARCO double staining. And immunofluorescent staining of TREM2 and MS4A4A verified the existence of TREM2 macrophages. Conclusion Using scRNA-seq, we were able to uncover the transcriptional landscape and phenotypic heterogeneity of Mϕ/DC subsets in human skin, which will open up more opportunities to explore distinct immune cell populations and their roles in health and pathological conditions.