Developmental trajectory of prehematopoietic stem cell formation from endothelium

Abstract

Hematopoietic stem and progenitor cells (HSPCs) in the bone marrow are derived from a small population of hemogenic endothelial (HE) cells located in the major arteries of the mammalian embryo. HE cells undergo an endothelial to hematopoietic cell transition (EHT), giving rise to HSPCs that accumulate in intra-arterial clusters (IAC) before colonizing the fetal liver. To examine the cell and molecular transitions between endothelial (E), HE, and IAC cells, and the heterogeneity of HSPCs within IACs, we profiled ~37,000 cells from the caudal arteries [dorsal aorta (DA), umbilical (U), vitelline (V)] of embryonic day 9.5 (E9.5) to E11.5 mouse embryos by single-cell RNA sequencing (scRNA-Seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-Seq). We identified a continuous developmental trajectory from E to HE to IAC cells, with identifiable intermediate stages. The intermediate stage most proximal to HE, which we term pre-HE, is characterized by increased accessibility of chromatin enriched for SOX, FOX, GATA, and SMAD motifs. A developmental bottleneck separates pre-HE from HE, with RUNX1 dosage regulating the efficiency of the pre-HE to HE transition. A distal candidate Runx1 enhancer exhibits high chromatin accessibility specifically in pre-HE cells at the bottleneck, but loses accessibility thereafter. Distinct developmental trajectories within IAC cells result in two populations of CD45+ HSPCs; an initial wave of lympho-myeloid-biased progenitors, followed by precursors of hematopoietic stem cells (pre-HSCs). This multi-omics single-cell atlas significantly expands our understanding of pre-HSC ontogeny.

Location, Location, Location: How Vascular Specialization Influences Hematopoietic Fates During Development

“…Although the relationship between HE and non-hemogenic arterial ECs has been debated (Ditadi et al, 2015;Gama-Norton et al, 2015), recent evidence using clonal analysis of lineage potential in vitro combined with single-cell RNA sequencing suggests that HSCcompetent HE and non-hemogenic arterial ECs diverge from a common arterial-like EC precursor shortly after E8 (Hou et al, 2020). Moreover, another recent study used single-cell RNA sequencing and ATAC-seq (assay for transposase-accessible chromatin sequencing) to identify a "pre-HE" state in a subset of arterial ECs with the potential to give rise to HSCs and LMPs in murine embryonic caudal arteries (dorsal aorta, umbilical artery, and vitelline artery) (Zhu et al, 2020). Specifically, pre-HE were shown to express arterial EC-specific and Notch pathway target genes (e.g., Hey2, Sox17) and simultaneously exhibit a chromatin accessibility profile indicating susceptibility to hematopoieticspecifying transcription factors.…”

Hematopoiesis: A Layered Organization Across Chordate Species

“…relied on the analysis of reporter and lineage tracing mouse lines. Corroborating these observations, single-cell transcriptional and epigenetic analysis of IAHC detected a population of lymphomyeloid-primed progenitors, suggesting an early differentiation process or an HSC-independent generation (Zhu et al, 2020). Alternatively, or complementarily, despite a transient expression of lymphoid transcripts, the reported YS-derived LMP were devoid of lymphoid potential and therefore do not qualify as lymphoid progenitors (Elsaid et al, 2020).…”

Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data

“…To alleviate this problem, we resorted to the concept of 'meta-cell', essentially borrowing information from neighboring single cells. Such an approach has been used to analyze other types of single cell data (Wagner et al 2017;van Dijk et al 2018;Gong et al 2018;Zhu et al 2020). Each meta-cell represents a group of individual cells that are in a similar state with a specific cell in the data (Fig.…”