Developmental regulation of endothelial-to-hematopoietic transition from iPSCs [10X 3' sc-RNA-seq]
Hematopoietic stem cells (HSCs) arise in mid-gestation from a specialized hemogenic endothelium (HE). In this process, HE cells undergo a unique fate change termed endothelial-to-hematopoietic transition, or EHT. While induced pluripotent stem cells (iPSCs) give rise to HE with robust hemogenic potential, the generation of bona fide HSCs from iPSCs remains a challenge. Here, we map single cell dynamics of EHT during embryoid body differentiation from iPSCs and integrate it with human embryo datasets to identify key transcriptional differences between in vitro and in vivo cell states. We further map ligand-receptor interactions associated with differential expression of developmental programs in the iPSC system. We found that the expression of endothelial genes was incompletely repressed during iPSC EHT. Elevated FGF signaling by FGF23, an endothelial pathway ligand, was associated with differential gene expression between in vitro and in vivo EHT. Chemical inhibition of FGF signaling during EHT increased HSPC generation in the zebrafish system, while an FGF agonist had the opposite effect. Consistently, chemical inhibition of FGF signaling increased hemogenic output from iPSCs. In summary, we map the dynamics of EHT from iPSCs at single cell resolution and identify ligand-receptor interactions that can be modulated to improve iPSC differentiation protocols. We show, as proof of principle, that chemical inhibition of FGF signaling during EHT improves hematopoietic output in zebrafish and the iPSC system. Overall design: iPSCs were formed into embryoid bodies (day 0) and treated with 100ng/ml hSCF, 100ng/ml hFLT3, 50ng/ml hG-CSF, 25ng/ml IL-6 and 10ng/ml IL-3 starting on day 1 and throughout the rest of any given experiment. Unsorted cells from each time point (days 7, 8, 11, 18 and 21 of differentiation) were used for single-cell combinatorial indexing RNA-seq (sci-RNA-seq) samples.  CD34+, CD43+ or CD45+ were sorted using FACS for the 10X 3' sc-RNA-seq day 8 sample.