Single-cell multi-omic analysis reveals serum amyloid A3 restrains alternative activations in macrophages derived from different origins

Abstract Alternatively activated macrophages (AAMs) play pivotal roles in regulating metabolism, anti-helminth infections, and tissue homeostasis. AAMs derived from different cellular origins are functionally and phenotypically distinct, but the regulatory networks mediating these differences remain unclear. Here, we use a combination of CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing; a 128 or 198 barcode-antibody panels) and genetic fate mapping, to profile F4/80 intCD206+ macrophage (Mφ) and F4/80 hiCD206-tissue-resident Mφ derived from CX3CR1+ precursors, in mice during homeostasis and Interleukin 4 (IL-4) or Heligmosomoides polygyrus initiated alternative activation. The analyses reveal greater complexity in embryonic-derived F4/80 hiCD206-tissue-resident Mφ than F4/80 intCD206+ Mφ or Mφ with tissue-resident phenotype from monocyte origins during homeostasis. We show that serum amyloid A3 (Saa3) is exclusively expressed in tissue-resident Mφ than other immune cell types and negatively associated with typical M2 markers such as Retnla, Mrc1, and Mgl2 expression in Interleukin 4 (IL-4) or Heligmosomoides polygyrus (H. Poly) initiated AAMs. The significant expansion of Retnla+ Mφ is observed in H. Poly- or IL-4 treated Saa3−/− mice and presents less worm burden and more M2 metabolic phenotypes than WT mice. Notably, we also identified a Folr2+ tissue-resident Mφ population that constitutively expresses Retnla and is associated with leukocyte and T-cell activation. Hence, single-cell multi-omic analysis allowed us to identify novel regulatory networks and distinct Mφ properties from different origins during alternative activation.