Developmental Timing Establishes Hematopoietic Stem and Progenitor Cell Lineage Bias

Embryonic development is a critical time window for the establishment of the hematopoietic and immune systems. During embryogenesis, hematopoietic stem and progenitor cells (HSPCs) that possess divergent differentiation preferences arise and sustain lifelong hematopoiesis. How the pace and differentiation repertoire of native hematopoiesis is set in development and how it evolves as the organism grows is incompletely elucidated. Here, we use temporal lineage tracing of the emerging hematopoietic system during zebrafish development coupled with single cell RNA sequencing to define the origins of larval and adult hematopoietic cells. In both larvae and adult tissues, HSPCs arising earlier during embryogenesis show a predilection for lymphoid lineage production while those arising later are skewed towards erythroid. Moreover, early arising HSPCs are the main contributors to adult tissue resident lymphocytes. Mechanistically, early and late arising HSPCs show divergent transcriptional signatures and differential sensitivities to the levels of the transcription factor Runx1. Additionally, we identified that young larvae possess a more heterogeneous set of lymphoid cells than previously recognized including diverse T-lymphocytes and Innate Lymphoid-like Cells (ILCs). We demonstrated that these newly described larval ILC-like cells reside in lymphoid and mucosal organs and are responsive to viral mimic immune stimulation, indicating their relevance in early vertebrate life. The work provides new fundamental knowledge on how the heterogeneous HSPC pool establishes early immune hierarchies during embryogenesis and its persistence in adulthood.