Embryonic and neonatal waves generate distinct populations of hepatic ILC1s

Group 1 innate lymphoid cells (ILCs) comprising circulating natural killer (cNK) cells and tissue-resident ILC1s are critical for host defense against pathogens and tumors. Despite a growing understanding of their role in homeostasis and disease, the ontogeny of group 1 ILCs remains largely unknown. Here, we used fate mapping and single-cell transcriptomics to comprehensively investigate the origin and turnover of group 1 ILCs. While cNK cells are continuously replaced throughout life, we uncovered tissue-dependent development and turnover of ILC1s. A first wave of ILC1s emerges during embryogenesis in the liver and transiently colonizes fetal tissues. After birth, a second wave quickly replaces ILC1s in most tissues apart from the liver, where they layer with embryonic ILC1s and persist until adulthood undergoing a unique developmental program. While embryonically-derived ILC1s give rise to a cytotoxic subset, the neonatal wave establishes a helper-like subset. Our findings uncover key ontogenic features of group 1 ILCs and their association with unique cellular identities and functions. Overall design: 1) Embryonic, neonatal and adult hepatic group 1 innate lymphoid cells of WT and Hobit KO mice were obtained by Fluorescence-Activated Cell Sorting (FACS) and their gene expression analyzed by means of single-cell RNA sequencing (sc-RNA seq) using the 10X sequencing platform. 2) Neonatal and adult murine bone marrow was processed and analyzed by sc-RNA seq using the 10X sequencing platform to assess the developmental pathways leading to the hematopoiesis of group 1 innate lymphoid cells in mice.