Tracking spatio-temporal dynamics of the endothelial niche during fetal hematopoiesis

The emergence of the hematopoietic system occurs in temporal waves across different tissues during mouse development. During these waves, the endothelial niche serves as a source of hematopoietic cells and provides molecular cues that potentially shape the tissue-specific lineage output. Although the endothelial-to-hematopoietic transition in the aorta-gonad-mesonephros is well understood, a systematic analysis of hematopoietic progenitors and their endothelial niche across fetal tissues is lacking. Here, we leverage single-cell RNA-sequencing of micro-dissected fetal tissues during their peak of hematopoietic activity to systematically compare hematopoietic progenitors and the endothelial niche. We predict stage-specific interactions accompanying the transition of yolk sac endothelium to primitive and definitive hematopoietic fates and reveal distinct roles for fetal liver vascular niches. Furthermore, we provide in vitro evidence that lipid signaling by sphingosine-1-phosphate producing erythrocyte progenitors supports hematopoietic stem cell expansion in fetal liver. Our resource deciphers the temporal waves of hematopoietic development within distinct vascular niches. Overall design: Single-cell RNA-sequencing was performed on hematopoietic (c-Kit+, CD34+) and endothelial (CD31+) cells isolated from micro-dissected fetal tissues (yolk sac = YS, aorta-gonad-mesonephros = AGM, placenta = PL, fetal liver = FL) between embryonic day (E) 8.5-14.5. For all samples, dead cells were excluded via Zombie staining. The lineage (Lin) cocktail used included: CD3e, B220, Gr-1, Ter119, SiglecH and CD19.