Decoding single-cell transcriptomic landscape and physiological roles of RUNX1 in macaque embryonic hematopoiesis

Blood birth during embryogenesis consists of multiple waves generating diverse progenies and is governed by spatiotemporally specific mechanisms1. Despite extensive studies in animal models, our current understanding of embryonic hematopoiesis in primates is very limited, particularly regarding the physiological roles of the presumed key regulators. Here, we firstly constructed a comprehensive single-cell RNA-seq atlas of embryonic hematopoiesis in rhesus macaque, involving multiple hematopoietic tissues (yolk sac, aorta-gonad-mesonephros region and fetal liver). We revealed high conservation of hematopoietic cell types and gene regulatory networks between human and macaque, and demonstrated a previously unrecognized dual-path specification of fetal liver monocytes in primate embryos, namely directly from lymphoid-featured progenitors in addition to from canonical granulocyte–monocyte progenitors. By generating RUNX1-null macaque embryos through CRISPR–Cas9-based approach, we revealed the indispensable role of RUNX1 in formation of most blood lineages during primate embryogenesis. Of note, in the absence of RUNX1, besides the completely blocked endothelial-to-hematopoietic transition, mesenchymal-priming characteristics were found in the arterial endothelial cells from which hematopoietic stem cells should emerge. Taken together, this study presented the first in vivo evidence of molecular mechanism regulating embryonic hematopoiesis in primates, providing novel insights for decoding blood ontogeny and regeneration in human being. Here, we provided a single-cell transcriptome atlas of hematopoiesis in human and rhesus macaque embryos using cells from hematopoietic tissues, including yolk sac, dorsal aorta and fetal liver. The developmental stage of human and macaque embryo span carnegie stage 10 to 15 and E28 to E34 respectively.