RT Journal Article SR Electronic T1 Single-cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches JF bioRxiv FD Cold Spring Harbor Laboratory SP 2024.10.14.618250 DO 10.1101/2024.10.14.618250 A1 Torcq, Léa A1 Vivier, Catherine A1 Schmutz, Sandrine A1 Loe-Mie, Yann A1 Schmidt, Anne A. YR 2024 UL http://biorxiv.org/content/early/2024/10/15/2024.10.14.618250.abstract AB Hematopoietic stem cells (HSCs) and more committed progenitors (collectively referred to as HSPCs) emerge from vessels during development, via Endothelial-to-Hematopoietic Transition (EHT). Recently, using the zebrafish embryo, we showed that two EHT cell types emerge from the aorta, raising the question of their subsequent fate. To address this issue, we established a complex pipeline based on single-cell photoconversion and transgenic lines to characterize the transcriptomic profiles of single EHT cell type progenies. We obtained, at unprecedented resolution in the early larva, a cartography of HSPCs and highly diversified differentiated populations, notably NK-like cell types, innate lymphoid cells and early eosinophils. We show that the two EHT cell types previously characterized indeed lead to differentially fated cells, with significant differences in thymus colonization and T-lymphoid lineage commitment. Using HSPC signatures retrieved from our datasets – namely gata2b and cd34/podocalyxin -, and to address niches, we performed in situ gene expression analyses via RNAscope. Unexpectedly, we unveil a niche contacting the supra-intestinal artery. Finally, integration with previous datasets reveal that our populations contain potential developmental HSCs bearing signatures highly similar with adult HSCs.Summary Statement Single cell photoconversion of emerging hematopoietic precursor cells and transcriptomics unravel the diversity of hematopoietic stem and progenitor cell populations and homing in developmental niches in toto, during zebrafish development.Competing Interest StatementThe authors have declared no competing interest.