Myeloid cells, including dendritic cells (DCs) and macrophages, are essential for establishing central tolerance in the thymus by promoting T cell clonal deletion and regulatory T cell (Treg) generation. Previous studies suggest that the thymic DC pool consists of plasmacytoid DC (pDC), XCR1+ DC1, and SIRPα+ DC2. Yet the precise origin, development, and homeostasis, particularly of DC2, remain unresolved. Using single-cell transcriptomics and lineage-defining mouse models, we identify nine major populations of thymic myeloid cells and describe their lineage identities. What was previously considered to be "DC2" is actually composed of four distinct cell lineages. Among these are monocyte-derived DCs (moDCs) and monocyte-derived macrophages (moMacs), which are dependent on thymic IFN to upregulate MHCII and CD11c. We further demonstrate that conventional DC2 undergo intrathymic maturation through CD40 signaling. Finally, amongst DC2, we identify a novel thymic population of CX3CR1+ transitional DC (tDC), which represents transendothelial DCs positioned near thymic microvessels. Together, these findings reveal the thymus as a niche for diverse, developmentally distinct myeloid cells and elucidate their specific requirements for development and maturation.

Center for Immunology Department of Lab Medicine and Pathology University of Minnesota Medical School Minneapolis MN USA

Department of Cell Biology Faculty of Science Charles University Prague Czech Republic

Department of Molecular Biology University of California San Diego School of Biological Sciences La Jolla CA USA

Department of Pharmacology University of San Diego School of Medicine San Diego CA USA

bioRxiv. 2025 Jun 18:2025.06.13.659520. doi: 10.1101/2025.06.13.659520. PubMed

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