Bilzer, M., Roggel, F. & Gerbes, A. L. Role of Kupffer cells in host defense and liver disease. Liver Int. 26, 1175–1186 (2006).

CAS  PubMed  Article  Google Scholar 

Asahina, K. et al. Mesenchymal origin of hepatic stellate cells, submesothelial cells, and perivascular mesenchymal cells during mouse liver development. Hepatology 49, 998–1011 (2009).

CAS  PubMed  Article  Google Scholar 

Maroni, L. et al. Functional and structural features of cholangiocytes in health and disease. Cell. Mol. Gastroenterol. Hepatol. 1, 368–380 (2015).

PubMed  PubMed Central  Article  Google Scholar 

Raven, A. et al. Cholangiocytes act as facultative liver stem cells during impaired hepatocyte regeneration. Nature 547, 350–354 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Lu, W.-Y. et al. Hepatic progenitor cells of biliary origin with liver repopulation capacity. Nat. Cell Biol. 17, 971–983 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Poisson, J. et al. Liver sinusoidal endothelial cells: Physiology and role in liver diseases. J. Hepatol. 66, 212–227 (2017).

CAS  PubMed  Article  Google Scholar 

Aizarani, N. et al. A human liver cell atlas reveals heterogeneity and epithelial progenitors. Nature https://doi.org/10.1038/s41586-019-1373-2 (2019).

MacParland, S. A. et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat. Commun. 9, 4383 (2018).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Ramachandran, P. et al. Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature https://doi.org/10.1038/s41586-019-1631-3 (2019).

Segal, J. M. et al. Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors. Nat. Commun. 10, 3350 (2019).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Wang, X. et al. Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level. Cell Res. https://doi.org/10.1038/s41422-020-0378-6 (2020).

Forbes, S. J. & Alison, M. R. Knocking on the door to successful hepatocyte transplantation. Nat. Rev. Gastroenterol. Hepatol. 11, 277–278 (2014).

CAS  PubMed  Article  Google Scholar 

Kegel, V. et al. Protocol for isolation of primary human hepatocytes and corresponding major populations of non-parenchymal liver cells. J. Vis. Exp. https://doi.org/10.3791/53069 (2016).

Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Svensson, V., Teichmann, S. A. & Stegle, O. SpatialDE: identification of spatially variable genes. Nat. Methods 15, 343–346 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Gayoso, A. & Shor, J. DoubletDetection. Zenodo https://doi.org/10.5281/ZENODO.2658730 (2018).

Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291.e9 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Mcinnes, L., Healy, J., Saul, N. & Großberger, L. UMAP: Uniform Manifold Approximation and Projection. J. Open Source Softw. https://doi.org/10.21105/joss.00861 (2018).

Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. https://doi.org/10.1186/s13059-017-1382-0 (2018)..

Van Der Maaten, L., Courville, A., Fergus, R. & Manning, C. Accelerating t-SNE using tree-based algorithms. J. Mach. Learn. Res. 15, 3221–3245 (2014).

Google Scholar 

Godlewski, G., Gaubert-Cristol, R., Rouy, S. & Prudhomme, M. Liver development in the rat and in man during the embryonic period (Carnegie stages 11–23). Microsc. Res. Tech. 39, 314–327 (1997).

CAS  PubMed  Article  Google Scholar 

Antoniou, A. et al. Intrahepatic bile ducts develop according to a new mode of tubulogenesis regulated by the transcription factor SOX9. Gastroenterology 136, 2325–2333 (2009).

PubMed  Article  CAS  Google Scholar 

Si-Tayeb, K., Lemaigre, F. P. & Duncan, S. A. Organogenesis and development of the liver. Dev. Cell 18, 175–189 (2010).

CAS  PubMed  Article  Google Scholar 

Collardeau-Frachon, S. & Scoazec, J.-Y. Vascular development and differentiation during human liver organogenesis. Anat. Rec. Adv. Integr. Anat. Evol. Biol. 291, 614–627 (2008).

Article  Google Scholar 

Asahina, K., Zhou, B., Pu, W. T. & Tsukamoto, H. Septum transversum-derived mesothelium gives rise to hepatic stellate cells and perivascular mesenchymal cells in developing mouse liver. Hepatology 53, 983–995 (2011).

CAS  PubMed  Article  Google Scholar 

Loo, C. K. C. & Wu, X. J. Origin of stellate cells from submesothelial cells in a developing human liver. Liver Int 28, 1437–1445 (2008).

PubMed  Article  Google Scholar 

Horsfall, D. & McGrath, J. Adifa software for single cell insights. Zenodo https://doi.org/10.5281/zenodo.5824896 (2022).

Wolf, F. A. et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20, 1–9 (2019).

Article  Google Scholar 

Alpert, A., Moore, L. S., Dubovik, T. & Shen-Orr, S. S. Alignment of single-cell trajectories to compare cellular expression dynamics. Nat. Methods 15, 267–270 (2018).

CAS  PubMed  Article  Google Scholar 

Pérez-Pomares, J. M. et al. Contribution of mesothelium-derived cells to liver sinusoids in avian embryos. Dev. Dyn. 229, 465–474 (2004).

PubMed  Article  Google Scholar 

Lotto, J. et al. Single-cell transcriptomics reveals early emergence of liver parenchymal and non-parenchymal cell lineages. Cell 183, 702–716.e14 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Patsch, C. et al. Generation of vascular endothelial and smooth muscle cells from human pluripotent stem cells. https://doi.org/10.1038/ncb3205 (2015).

Coll, M. et al. Generation of hepatic stellate cells from human pluripotent stem cells enables in vitro modeling of liver fibrosis.Cell Stem Cell 23, 101–113.e7 (2018).

CAS  PubMed  Article  Google Scholar 

Prior, N. et al. Lgr5+ stem and progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool. Dev. 146, 174557 (2019).

Article  CAS  Google Scholar 

Schmelzer, E., Wauthier, E. & Reid, L. M. The phenotypes of pluripotent human hepatic progenitors. Stem Cells 24, 1852–1858 (2006).

CAS  PubMed  Article  Google Scholar 

Hu, H. et al. Long-term expansion of functional mouse and human hepatocytes as 3D organoids. Cell 175, 1591–1606.e19 (2018).

CAS  PubMed  Article  Google Scholar 

Li, B. et al. Adult mouse liver contains two distinct populations of cholangiocytes. Stem Cell Rep. 9, 478–489 (2017).

CAS  Article  Google Scholar 

Stevens, K. R. et al. In situ expansion of engineered human liver tissue in a mouse model of chronic liver disease. Sci. Transl. Med. 9, aah5505 (2017).

Article  CAS  Google Scholar 

Huch, M. et al. Long-term culture of genome-stable bipotent stem cells from adult human liver. Cell 160, 299–312 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Huch, M. et al. In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration. Nature 494, 247–250 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Marsee, A. et al. Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids. Cell Stem Cell 28, 816–832 (2021).

CAS  PubMed  Article  Google Scholar 

Vento-Tormo, R. et al. Single-cell reconstruction of the early maternal–fetal interface in humans. Nature 563, 347–353 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Efremova, M., Vento-Tormo, M., Teichmann, S. A. & Vento-Tormo, R. CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat. Protoc. 15, 1484–1506 (2020).

CAS  PubMed  Article  Google Scholar 

Geisler, F. et al. Liver-specific inactivation of Notch2, but not Notch1, compromises intrahepatic bile duct development in mice. Hepatology 48, 607–616 (2008).

CAS  PubMed  Article  Google Scholar 

Clotman, F. et al. Control of liver cell fate decision by a gradient of TGFβ signaling modulated by Onecut transcription factors. Genes Dev. 19, 1849–1854 (2005).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).

CAS  PubMed  Article  Google Scholar 

Baxter, M. et al. Phenotypic and functional analyses show stem cell-derived hepatocyte-like cells better mimic fetal rather than adult hepatocytes. J. Hepatol. 62, 581–589 (2015).