Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses

Macrophages are the earliest emerging cells of the nascent immune system during embryonic development, and as innate immune cells constitutes an important first-line barrier against foreign organisms and pathogens. Rodent macrophages have been shown to infiltrate multiple organs at an early stage, developing symbiotically alongside these organs becoming tissue-resident macrophages (TRM) supporting tissue development and homeostasis. However, knowledge of the development and specialization of macrophages in the early human embryo is still limited. In order to study the spatiotemporal distribution and dynamic process of macrophage development in the early human embryo, we applied single-cell transcriptomic sequencing to generate a map of all CD45+CD235a- hematopoietic cells in human embryos of successive developmental stages from Carnegie stage (CS) 11 to 23. Here, we unravelled for the first time a map of macrophage heterogeneity across multiple anatomical sites and identified multiple macrophage subsets in the early human embryo, including various types of embryonic TRM (head, liver, lung and skin), and traced their developmental trajectories from yolk sac/embryonic liver-derived macrophages to their TRM specification in the head and liver based on core transcriptional factors. Altogether, our analyses provide a comprehensive characterization of the spatial and temporal dynamics of macrophage development in the early human embryo, and provides a reference for future study into human TRM function and embryonic development.