Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis

a Overall study design. Figure generated by BioRender. Human embryonic organoids (HEMOs) at D8, D15, and D18 were harvested for 10X Chromium scRNA-seq. D15 HEMOs were also harvested for 10X Visium spatial transcriptomics. b scRNA-seq analysis of time-series HEMO cells (n = 22,204) visualized by UMAP. CM-like cardiac mesoderm-like cells, Ect-like Ectoderm-like cells, Endo endothelium, Ery erythroid cells, Fibro fibroblasts, HPC hematopoietic progenitor cells, MP-1 myeloid progenitor 1, MEP megakaryocyte and erythrocyte progenitors, MP-2 myeloid progenitor 2, Mes-like mesoderm-like cells, Mk megakaryocytes, Mono: monocytes, NC neural crest, NE-like neural ectoderm-like cells, PSC-Ect pluripotent stem cells with ectoderm specification, PSC-like pluripotent stem cells-like, TB-like trophoblast-like cells, YSE yolk sac endoderm. c Area chart shows cell proportion changes during the differentiation. d Individual UMAP shows cell populations at D8 (n = 3124), D15 (n = 8350), D18 (n = 10,700). e UMAP of non-hematopoietic cell clusters. f UMAP of non-hematopoietic cell clusters grouped by Immature PSC, TB-like, Ectoderm (PSC-Ect, Ect-like, NE-like, NC), Mesoderm (Mes-like, CM-like, Fibro, Endo) and Endoderm (YSE) populations (n = 5477). g Marker gene expression of Immature PSC, TB-like, Ectoderm, Mesoderm, Endoderm clusters. h UMAP of cell populations in D15 HEMO. i WNT signaling pathway interaction among D15 HEMO cell populations. Wider lines indicate stronger interaction. j Gene expression pattern of NC specification and migration in D15 non-hematopoietic cells in HEMO. k UMAP shows the gene expression of WNT signaling in D15 HEMO. l UMAP of cell clusters of decomposed single-cell level spatial transcriptomic data by SpatialScope. m Stacked bar plot shows the cell composition of each HEMO. n Spatial plot of Ery, Mk, MkP, and YSE population within HEMO #1. The yolk sac erythro-megakaryopoiesis niche is pointed out by a dashed gray circle. o Spatial cell-cell interaction analysis conducted by CellPhoneDB. Pairs with a mean value above 0 indicate the activation of the ligand-receptor pairs. Pairs with a mean value below 0 indicate the inhibition of the pairs. Among these, VTN-ITGA2B exhibit the highest enriched score between YSE and Mk. p Gene expression pattern of VTN and ITGA2B on HEMO #1 in a spatial slice. q Gene expression of VTN and related downstream targets in imputed spatial data in HEMO #1. r Gene expression of VTN and related downstream targets in scRNA-seq dataset. t UMAP analysis of cell clusters of in vivo yolk sac hematopoiesis dataset (Wang et al., 2021). Ery erythrocyte, Mk megakaryocyte, MEP Mk-erythroid progenitor, Mac macrophage, YSMP YS-derived myeloid-biased progenitor, EC endothelial cell, Epi epithelial cell, Mes mesenchymal cell. s Heatmap indicates the correlation between HEMO sample and in vivo yolk sac sample. u UMAP shows the gene expression of VTN and ITGA2B in the yolk sac dataset. v Dot plot shows the gene expression of VTN and related downstream targets in the YS hematopoiesis dataset

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