Single-cell multi-omic analysis identify heterogeneity and distinct features in fate-mapped tissue-resident alternatively activated macrophages

Peritoneal cavity cells play pivotal roles in inflammation, repair, and maintaining homeostasis in response to pathogenic infections and tissue injury. Two major tissue-resident macrophages (TRMs) are large peritoneal macrophages (LPMs) and small peritoneal macrophages (SPMs). These are the major macrophage subsets in the peritoneal cavity and originate from embryogenic (LPMs) or bone-marrow-derived myeloid precursors (SPMs). CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) provides simultaneous information for single cells in both cell-surface protein and gene expression levels. Here, we used CITE-seq to profile peritoneal cells by an oligonucleotide-labeled antibody panel designed to react with 189 unique mouse cell surface antigens. We identify 14 markers exclusively expressed on TRMs but not other immune cell types. These markers can classify phenotype differences between LPMs and SPMs during IL-4 stimulation. We further profile fate-mapped TRMs by scRNA-seq and identified more heterogenous phenotypes of TRMs that originated from embryogenic rather than bone-marrow-derived myeloid precursors. Notably, serum amyloid A-3 (Saa3) and platelet factor 4 (Pf4), can distinguish TRM clusters from alternative activation to IL-4 stimulation and Heligmosomoides polygyrus infection. Hence, we identify distinct markers that can be used to distinguish the different origins and heterogenous TRM phenotypes under steady state and type 2 immune responses.