Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level

Xin Wang,Zi-Ran Xu,Cheng-Ran Xu,Yan-Chun Wang,Ye Feng,Yi Wang,Jing Zhang,Li Yang

doi:10.1038/s41422-020-0378-6

Xin Wang, Zi-Ran Xu + Show 6 more

Open Access

https://doi.org/10.1038/s41422-020-0378-6

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Abstract

During embryogenesis, the liver is the site of hepatogenesis and hematopoiesis and contains many cell lineages derived from the endoderm and mesoderm. However, the characteristics and developmental programs of many of these cell lineages remain unclear, especially in humans. Here, we performed single-cell RNA sequencing of whole human and mouse fetal livers throughout development. We identified four cell lineage families of endoderm-derived, erythroid, non-erythroid hematopoietic, and mesoderm-derived non-hematopoietic cells, and defined the developmental pathways of the major cell lineage families. In both humans and mice, we identified novel markers of hepatic lineages and an ID3+ subpopulation of hepatoblasts as well as verified that hepatoblast differentiation follows the “default-directed” model. Additionally, we found that human but not mouse fetal hepatocytes display heterogeneity associated with expression of metabolism-related genes. We described the developmental process of erythroid progenitor cells during human and mouse hematopoiesis. Moreover, despite the general conservation of cell differentiation programs between species, we observed different cell lineage compositions during hematopoiesis in the human and mouse fetal livers. Taken together, these results reveal the dynamic cell landscape of fetal liver development and illustrate the similarities and differences in liver development between species, providing an extensive resource for inducing various liver cell lineages in vitro.

Highlights

The liver consists of greater than 20 cell types, including hepatocytes, biliary ductal cells, liver endothelial cells, hepatic stellate cells, Kupffer cells, mesothelial cells, and various circulatory immune cells, which are all organized to form the foundation for liver functions, including nutrient metabolism, drug detoxification, and immune responses.[1,2,3,4] Cell lineage differentiation and organogenesis mainly occur in the fetal stage
Doublet removal (Supplementary information, Fig. S1d), iterative clustering, and batch effect correction, we identified 13 major cell types across all developmental stages in both the human and mouse fetal livers based on marker gene expression (Fig. 1a; Supplementary information, Table S1)
Upregulated during hepatoblast-to-hepatocyte differentiation, whereas cholangiocytes expressed group-C/c genes, including many transcription factors (TFs), such as SOX4, SOX9, and SOX6, in both humans and mice (Fig. 4b; Supplementary information, Table S5). These results suggested that in both species, hepatoblasts default to the hepatocyte fate and follow a gradual and progressive transition to hepatocytes, while cholangiocyte differentiation requires escape from this default fate choice via de novo activation of regulatory factors

Summary

Introduction

The liver consists of greater than 20 cell types, including hepatocytes, biliary ductal cells (cholangiocytes), liver endothelial cells, hepatic stellate cells, Kupffer cells, mesothelial cells, and various circulatory immune cells, which are all organized to form the foundation for liver functions, including nutrient metabolism, drug detoxification, and immune responses.[1,2,3,4] Cell lineage differentiation and organogenesis mainly occur in the fetal stage. The development of certain cell lineages across fetal development in the mouse liver has been studied,[5,6,7,8] the cell type components and their development pathways during embryogenesis have not been comprehensively defined, especially in humans. A comparative study of fetal liver development between two important species, mice and humans, is critical to our understanding of the mechanisms of liver development and regeneration, but we know little about the degree to which liver development is conserved between humans and mice. Hepatoblasts that have begun to express hepatocyte function-related genes choose the default fate of becoming hepatocytes, while cholangiocyte differentiation involves a sharp detour from this default path via de novo activation of additional TFs and multiple signaling pathways, including the Sox[4], Sox[9], Hnf1b and Notch, Tgfb, Wnt, FGF, Hippo-Yap, and MAPK pathways.[5,15,16,17,18,19,20,21,22] whether this “default-directed” regulatory strategy is conserved in humans remains unknown

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