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Mouse liver assembloids model periportal architecture and biliary fibrosis

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Abstract

Modelling liver disease requires in vitro systems that replicate disease progression1,2. Current tissue-derived organoids fail to reproduce the complex cellular composition and tissue architecture observed in vivo3. Here, we describe a multicellular organoid system composed of adult hepatocytes, cholangiocytes and mesenchymal cells that recapitulates the architecture of the liver periportal region and, when manipulated, models aspects of cholestatic injury and biliary fibrosis. We first generate reproducible hepatocyte organoids with functional bile canaliculi network that retain morphological features of in vivo tissue. By combining these with cholangiocytes and portal fibroblasts, we generate assembloids that mimic the cellular interactions of the periportal region. Assembloids are functional, consistently draining bile from bile canaliculi into the bile duct. Strikingly, manipulating the relative number of portal mesenchymal cells is sufficient to induce a fibrotic-like state, independently of an immune compartment. By generating chimeric assembloids of mutant and wild-type cells, or after gene knockdown, we show proof-of-concept that our system is amenable to investigating gene function and cell-autonomous mechanisms. Taken together, we demonstrate that liver assembloids represent a suitable in vitro system to study bile canaliculi formation, bile drainage, and how different cell types contribute to cholestatic disease and biliary fibrosis, in an all-in-one model.

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Authors and Affiliations

Authors

Corresponding author

Correspondence to Meritxell Huch.

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Figure 2, Supplementary Table 7 and Supplementary References.

Reporting Summary

Supplementary Figure 1

Cytokine array raw data. Cytokine array blots from 2 biological replicates, presented as raw scans of the signal, and overlay with the blot brightfield image. Images are annotated for the sample name. Supernatants from monocultures of CholOrg, or HepOrg or Msc cells or from assembloids from homeostatic or fibrotic-like conditions were analysed.

Peer Review File

Supplementary Table 1

Supplementary Table 1.1-1.7.

Supplementary Table 2

bulk RNA sequencing TPM values. TPM values from bulk RNA sequencing for each gene were used for heatmaps in Extended Data Figure 3b (HM-Wnt HepOrg vs freshly isolated hepatocytes); Extended Data Figure 5a (HM-Wnt and MM media HepOrg vs freshly isolated hepatocytes); Extended Data Figure 10a (7 days or 2.5 weeks homeostasis and fibrotic-like assembloids).

Supplementary Table 3

GSEA comparing cells from homeostasis-like assembloids. Gene set enrichment analysis (GSEA) of hepatocytes, cholangiocytes and portal mesenchyme; Related to Extended Data Figure 7k-m. Databases used are GO_Biological_Process_2023 (GO_BP), GO_Cellular_Component_2023 (GO_CC) and GO_Molecular_Function_2023 (GO_MF).

Supplementary Table 4

LIANA Inferred cell-cell interactions. 4_1: Interactions from fibrosis-like assembloids and the bile duct ligation (BDL) and CCl4 models from Yang et al., 2021; Related to Figure 4d, Top 100 significant interactions from all models; 4_2: Interactions from fibrosis-like and homeostasis assembloids; Related to Extended Data Figure 12a; Top 30 significant interactions from all models.

Supplementary Table 5

GSEA comparing fibrosis-like versus homeostasis assembloids. Related to Figure 4e; GSEA Homeostasis and Fibrosis-like Assembloids using KEGG, reactome and MSigDB_Hallmarks databases; Related to Extended Data Figure 10e-g; GSEA of cells from fibrosis-like versus homeostasis assembloids for hepatocytes (e), cholangiocytes (f), and mesenchyme (g).

Supplementary Table 6

Differential gene expression (DGE) between HepOrg and freshly isolated hepatocytes. Differential gene expression for comparison of HepOrg in HM-Wnt or MM media cultured at passage 2 for 1 week or 2 weeks, compared to freshly isolated hepatocytes.

Supplementary Video 1

Bubbly/grape-like shaped HepOrg metabolise 5-CFDA. Maximum intensity projection of a live cell imaging of a bubbly-shaped HepOrg at passage 2. HepOrg was treated with 5-CFDA (pseudo-coloured Royal LUT). Scale bar, 50 µm.

Supplementary Video 2

Ball-shaped HepOrg cannot metabolise 5-CFDA. Maximum intensity projection of a live cell imaging of a ball-shaped HepOrg at passage 2. HepOrg was treated with 5-CFDA (pseudo-coloured Royal LUT). Scale bar, 50 µm.

Supplementary Video 3

HepOrg transport CLF, CMFDA and fluorescent Phosphatidylcholine (PC). Maximum intensity projection of a live cell imaging of a bubbly-shaped HepOrg in MM media at passage 2, showing functional update and transport of CLF (Video 3), CMFDA (Video 4) and fluorescent PC (Video 5). Dyes are visualised with pseudo-coloured Royal LUT). Scale bar, 50 µm.

Supplementary Video 4

HepOrg transport CLF, CMFDA and fluorescent Phosphatidylcholine (PC). Maximum intensity projection of a live cell imaging of a bubbly-shaped HepOrg in MM media at passage 2, showing functional update and transport of CLF (Video 3), CMFDA (Video 4) and fluorescent PC (Video 5). Dyes are visualised with pseudo-coloured Royal LUT). Scale bar, 50 µm.

Supplementary Video 5

HepOrg transport CLF, CMFDA and fluorescent Phosphatidylcholine (PC). Maximum intensity projection of a live cell imaging of a bubbly-shaped HepOrg in MM media at passage 2, showing functional update and transport of CLF (Video 3), CMFDA (Video 4) and fluorescent PC (Video 5). Dyes are visualised with pseudo-coloured Royal LUT). Scale bar, 50 µm.

Supplementary Video 6

Periportal assembloid formation. Maximum intensity projection of assembloid formation 2 days after seeding. Time in hours. Nuclei are depicted in white (SPY620), mesenchyme cells in green (Pdgfra-H2BGF), cholangiocytes in magenta (nuc-tdTomato). Brightfield is also shown. Assembloids can still recruit cells after being formed. Scale bar, 100 µm. Related to Extended Data Figure 7d.

Supplementary Video 7

Periportal assembloid formation. Maximum intensity projection of assembloid formation 2 days after seeding. Time in hours. Nuclei are depicted in white (SPY620), mesenchyme cells in green (Pdgfra-H2BGF), cholangiocytes in magenta (nuc-tdTomato). Brightfield is also shown. Assembloids can still recruit cells after being formed. Scale bar, 100 µm. Related to Extended Data Figure 7d.

Supplementary Video 8

Representative 3D-reconstruction showing the connection between bile canaliculi-bile duct in liver tissue. Animation of a 3D reconstruction of the interface of bile canaliculi-bile duct in mouse liver tissue. Example 1. Reconstruction was generated from multiphoton image showing a continuous lumen of bile canaliculi (CD13, green) entering bile duct (PCK, magenta). Hepatocytes, which connect their bile canaliculi to the bile duct lumen are visualised in different colours (red, yellow, cyan). Related to Fig. 3j.

Supplementary Video 9

Representative 3D-reconstruction showing the connection between bile canaliculi-bile duct in a periportal liver assembloid. Animation of a 3D reconstruction showing interface of bile canaliculi-bile duct in a mouse periportal assembloid. Example 1. Reconstruction was generated from high-resolution Airyscan 3D image showing a continuous lumen of bile canaliculi (ZO-1, green) entering bile duct (KRT19, magenta). Hepatocytes, which connect their bile canaliculi to the bile duct lumen are visualised in different colours (red, yellow). Related to Fig. 3j.

Supplementary Video 10

Representative 3D-reconstruction showing the connection between bile canaliculi-bile duct in liver tissue. Animation of a 3D reconstruction of the interface of bile canaliculi-bile duct in mouse liver tissue. Example 2. Reconstruction was generated from multiphoton image showing a continuous lumen of bile canaliculi (CD13, green) entering bile duct (PCK, magenta). Hepatocytes, which connect their bile canaliculi to the bile duct lumen are visualised in different colours (red, yellow, cyan). Related to Fig. 9b.

Supplementary Video 11

Representative 3D-reconstruction showing the connection between bile canaliculi-bile duct in a periportal liver assembloid Animation of a 3D reconstruction showing interface of bile canaliculi-bile duct in a mouse periportal assembloid. Example 2. Reconstruction was generated from confocal image showing a continuous lumen of bile canaliculi (CD13, green) entering bile duct (nuc-tdTomato, magenta). Hepatocytes, which connect their bile canaliculi to the bile duct lumen are visualised in different colours (red, yellow, cyan). Related to Fig. 9b.

Supplementary Video 12

Periportal assembloids transport bile acid analogue from bile canaliculi to bile duct lumens. Live imaging of the uptake and flow of the bile acid analogue cholyl-L-lysyl-fluorescein (CLF, pseudo-colour range) in assembloids shows functional transport of bile salts from bile canaliculi into the lumen of the bile duct lined by cholangiocytes (magenta). Time in minutes. Scale bar, 100 µm. Related to Fig. 3l (video 12) and Related to Extended Data Fig. 9h (video 13).

Supplementary Video 13

Periportal assembloids transport bile acid analogue from bile canaliculi to bile duct lumens. Live imaging of the uptake and flow of the bile acid analogue cholyl-L-lysyl-fluorescein (CLF, pseudo-colour range) in assembloids shows functional transport of bile salts from bile canaliculi into the lumen of the bile duct lined by cholangiocytes (magenta). Time in minutes. Scale bar, 100 µm. Related to Fig. 3l (video 12) and Related to Extended Data Fig. 9h (video 13).

Supplementary Video 14

Structures with aberrant cholangiocyte ratio and non-physiological BC-BD connection do not transport bile acid analogue. Live imaging of the uptake and flow of the bile acid analogue cholyl-L-lysyl-fluorescein (CLF, pseudo-colour range). CLF uptake is not observed in structures with aberrant architecture where cholangiocytes are not embedded in the organoid (mem-tdTomato, magenta). Nuclei are shown in white (SPY620). Time in minutes. Scale bar, 50 µm. Related to Fig. 9i.

Supplementary Video 15

Fibrotic-like assembloids show disruption of cell integrity. Maximum intensity projection of a 3D assembloid showing big bursts of cell-free DNA signal, imaging from 2 days after seeding. Time in hours. Nuclei are depicted in white (stained with SPY620), mesenchyme cells in green (nuc-GFP, Pdgfra-H2BGF) and cholangiocytes in magenta (nuc-tdTomato). Brightfield is also shown. Scale bar, 100 µm.

Supplementary Video 16

Fibrotic-like assembloids show no functional bile duct-bile canaliculi connection. Live imaging of the bile acid analogue cholyl-L-lysyl-fluorescein (CLF, pseudo-colour range) in fibrotic-like assembloids is not observed. Cholangiocytes (nuc-tdTomato, magenta) and mesenchyme (nuc-GFP, green), and brightfield are also shown. Time in minutes. Scale bar, 50 µm.

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Dowbaj, A.M., Sljukic, A., Niksic, A. et al. Mouse liver assembloids model periportal architecture and biliary fibrosis. Nature (2025). https://doi.org/10.1038/s41586-025-09183-9

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