Parallel spatial transcriptomics, single-cell and bulk RNA-Seq analysis of the human embryonic HSC niche, the dorsal aorta

Haematopoietic stem cells (HSCs) first emerge in the embryonic aorta-gonad-mesonephros (AGM) region. Studies on model organisms defined intersecting signalling pathways that converge to promote HSC emergence predominantly in the ventral domain of the dorsal aorta. Much less is known about mechanisms driving HSC development in human. Here, to identify secreted signals underlying human HSC development, we combined spatial transcriptomics analysis of dorso-ventral polarised signalling in the aorta with gene expression profiling of sorted cell populations and single cells. Our analysis revealed a subset of aortic endothelial cells with downregulated arterial signature and a predicted lineage relationship with the emerging HSC/ progenitor population. Analysis of the ventrally polarised molecular landscape identified endothelin 1 as an important secreted regulator of human HSC development. The obtained gene expression datasets will inform future studies on mechanisms of HSC development in vivo and on the generation of clinically relevant HSCs in vitro. Two LCM-Seq transcriptome analyses of spatially defined regions around the dorsal aorta (Carnegie Stages (CS) 16-17, N=6); RNA-Seq analysis of hematoendothelial populations from the dorsal and ventral portions of the dorsal aorta (AoV, AoD respectively) (CS15-16, N=2); single cell RNA-Seq analysis of the AoV (N=1) and central portion of the dorsal aorta (N=1).