Spatial transcriptome analysis of the human developmental haematopoietic stem cell niche

During human embryonic development the first definitive haematopoietic stem cells (HSCs) arise in the aorta-gonad-mesonephros (AGM) region between Carnegie stages (CS) 13 to 17. More specifically, these HSCs are considered to derive from the endothelial cells of the dorsal aorta which undergo an endothelial-to-haematopoietic transition and bud into the lumen to form intra-aortic clusters of haematopoietic cells. This process is localised to the ventral domain and spatial polarisation of signals along the dorsal-ventral axis of the dorsal aorta has been shown to be essential for HSC emergence in the mouse AGM. This PhD project utilised laser capture microscopy coupled with RNA-Sequencing (LCM-Seq) to generate a spatial transcriptome map of the human embryonic AGM region and in doing so revealed many polarised genes and signalling pathways. Single cell and bulk sorted population RNA-Seq analysis of the dorsal and ventral portions of the aorta further resolved signalling in the AGM both elucidating a gene signature for haematopoietic progenitors and mapping niche signals to cell populations. Genes encoding the blood pressure regulators renin and endothelin-1 were amongst the most ventrally enriched factors with elements of their signalling pathways expressed across the niche on perivascular, endothelial, haematopoietic progenitor and mature cells. Renin, endothelin-1 and endothelin-2 were functionally assessed for their role in promoting HSC emergence and were shown to enhance HSC production in culture of E9.5 caudal tissues of the mouse embryo as validated by enhanced reconstitution of the haematopoietic system of irradiated mice. The “transcriptome map” dataset generated in this study can be utilised to identify signals that promote HSC emergence and can be a reference for improving haematopoietic differentiation cultures from pluripotent stem cells