Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing

Abstract

Tracing the emergence of the first hematopoietic stem cells (HSCs) in human embryos, particularly the scarce and transient precursors thereof, is so far challenging, largely due to the technical limitations and the material rarity. Here, using single-cell RNA sequencing, we constructed the first genome-scale gene expression landscape covering the entire course of endothelial-to-HSC transition during human embryogenesis. The transcriptomically defined HSC-primed hemogenic endothelial cells (HECs) were captured at Carnegie stage (CS) 12–14 in an unbiased way, showing an unambiguous feature of arterial endothelial cells (ECs) with the up-regulation of RUNX1, MYB and ANGPT1. Importantly, subcategorizing CD34+CD45− ECs into a CD44+ population strikingly enriched HECs by over 10-fold. We further mapped the developmental path from arterial ECs via HSC-primed HECs to hematopoietic stem progenitor cells, and revealed a distinct expression pattern of genes that were transiently over-represented upon the hemogenic fate choice of arterial ECs, including EMCN, PROCR and RUNX1T1. We also uncovered another temporally and molecularly distinct intra-embryonic HEC population, which was detected mainly at earlier CS 10 and lacked the arterial feature. Finally, we revealed the cellular components of the putative aortic niche and potential cellular interactions acting on the HSC-primed HECs. The cellular and molecular programs that underlie the generation of the first HSCs from HECs in human embryos, together with the ability to distinguish the HSC-primed HECs from others, will shed light on the strategies for the production of clinically useful HSCs from pluripotent stem cells.

Dissecting endothelial to haematopoietic stem cell transition by single-cell transcriptomic and functional analyses

“…1e; Supplementary information, Fig. S1h), supportive of the globally up-regulated transcriptional and translational activity during hemogenic specification, which was in line with the finding in human embryo that translational initiation is overrepresented in HSC-primed HECs than in arterial ECs 19 . We further evaluated the arteriovenous scores of the populations we defined, and found similar results in mouse and human that HEC rather than haematopoietic populations manifested certain arterial feature (Fig.…”

“…We also revealed several similarities regarding the molecular events underlying the development of HSC-primed HECs between in mouse and human embryos we have reported very recently 19 , including the arterial feature and the overrepresented ribosome and translational activity in the HSC-primed HECs. Such conservation further assures the mouse model as an adequate animal model for HSC development studies.…”

“…Moreover, HSCs and arterial ECs are proposed to arise from distinct precursors, characterized by different Notch signaling strengths 18 . Most recently, HSC-primed HECs have been transcriptionally identified in human embryos, which present an unambiguous arterial property, indicative of their arterial EC origin 19 .…”

Analysis of Endothelial-to-Haematopoietic Transition at the Single Cell Level identifies Cell Cycle Regulation as a Driver of Differentiation

“…10b ). Based on the level of expression of marker genes, in vitro generated endothelial cells displayed higher similarity to late haemogenic endothelial cells (late HECs), which give rise to true HSPCs in the AGM (64), rather than early haemogenic endothelial cells (early HECs). Interestingly, in vitro derived HPCs displayed similarities to end stage HSPCs from AGM, albeit maintaining expression of genes expressed in immature HSPCs such as active cell cycle genes ( Supplementary Fig.…”

“…The GEO dataset GSE135202 derived from human foetal AGM (64) was located and the relevant raw count data from the corresponding single-cell samples GSM3993420:CS10_body_10x, GSM3993421:CS11_CH_10x and GSM3993422:CS13_DA_10x were collected, including their annotation found in Table S3 (Cell annotation and coordinates of early and late populations), related to Figs. 1-4 of the main manuscript.…”