Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells
Cite
Wellington, R., Cheng, X., Campbell, C.A., Trapnell, C., Espin-Palazon, R., Hadland, B. and Doulatov, S., 2024. Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells. bioRxiv.
https://doi.org/10.1101/2024.09.24.612755
Abstract
Hematopoietic stem cells (HSCs) arise in embryogenesis 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, while an FGF agonist had the opposite effect. Consistently, chemical inhibition of FGF signaling increased hematopoietic 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.
Datasets
1. sci-RNA-seq, Day 7-21 iPSC-Derived Embryoid Bodies
ExploreScrublet call
Sample ID
Ligation barcode
RT barcode
P7 barcode
P5 barcode
Cell line
Cell line - time point
Time point
Subject ID
Tissue type
Clustering (monocle)
Cell type
Assay
Disease
Sex
Tissue
MSC-iPS Day 824,785 cells 45-iPS Day 1119,210 cells MSC-iPS Day 717,761 cells MSC-iPS Day 1117,183 cells 45-iPS Day 1414,873 cells MSC-iPS Day 1812,720 cells MSC-iPS Day 1412,267 cells Reprogrammed CD45+ PBMCs, unknown donor81,094 cells splanchnic lpm19,921 cells sensory neuron15,966 cells neural progenitor10,381 cells sci-RNA-seq3, single-nucleus166,085 cells embryoid body166,085 cells 
2. Integration of Day 8 iPSC-Derived Embryoid Bodies with Human Embryo Published Data
ExploreCell type (Zeng)
AGM sample
Clustering (Calvanese)
Clustering (integrated_snn_res.1.2)
Clustering (Seurat)
Sample source
Cell type (Crosse)
Cell type (iPS)
Cell type (Calvanese)
Clustering (monocle)
Subject ID
Tissue type
Cell type
Assay
Disease
Sex
Tissue
Age
Age group
Sample ID
Human Embryo (Zeng et al)15,009 cells Human Embryo (Calvanese et al)13,433 cells Human Embryo (Crosse et al)4,871 cells Arterial Endothelium395 cells Hemogenic Endothelium108 cells EMX2+ Epithelium102 cells Venous Endothelium1,130 cells Hematopoietic (Erythro-Myelo Precursor)1,112 cells Arterial Endothelium823 cells Unknown Mesoderm/Stroma609 cells Kidney Fibroblast268 cells Liver Epithelium161 cells Hematopoietic (Myeloid Precursor)124 cells Erythroid Progenitor111 cells Zeng_2019_Embryo18,498 cells Reprogrammed CD45+ PBMCs, unknown donor8,357 cells Zeng_2019_Embryo25,746 cells Calvanese_2022_Embryo2-35,249 cells Calvanese_2022_Embryo15,153 cells Calvanese_2022_Embryo43,031 cells Crosse_2020_Embryo22,470 cells Crosse_2020_Embryo12,401 cells Zeng_2019_Embryo3765 cells pluripotent stem cell40,562 cells cardiac endothelial cell518 cells hematopoietic stem cell301 cells dorsal lateral plate region19,069 cells Carnegie stage 108,498 cells Carnegie stage 115,746 cells Carnegie stage 155,249 cells Carnegie stage 145,153 cells Carnegie stage 164,871 cells Carnegie stage 173,031 cells Carnegie stage 13765 cells embryonic period33,313 cells 
3. 10X sc-RNA-seq, Day 8 iPSC-Derived Embryoid Bodies
ExploreCluster (monocle)
Cell type
Sample source
Subject ID
Tissue type
Assay
Disease
Tissue
Sample ID
Leiden clustering
Venous Endothelium1,130 cells Hematopoietic (Erythro-Myelo Precursor)1,121 cells Arterial Endothelium825 cells Unknown Mesoderm/Stroma609 cells Kidney Fibroblast268 cells Liver Epithelium161 cells Hematopoietic (Myeloid Precursor)124 cells Reprogrammed CD45+ PBMCs, unknown donor7,056 cells 
Alias names
GSE274082, GSE274084