Fig. 4: Periportal assembloids mimic aspects of biliary fibrosis in vitro.
From: Mouse liver assembloids model periportal architecture and biliary fibrosis
a, Schematic of the experimental design. b, Immunofluorescence images of assembloids with homeostatic (left) and 10× excess (right) of mesenchyme. n > 3 experiments. Scale bars: 50 µm (main images), 10 µm (zoom view). c, UMAP of fibrotic-like assembloid data (from this study) integrated with datasets from liver damage models. d, Circular plots represent the inferred cell–cell interactions from fibrotic-like assembloids, bile duct ligation (BDL) and CCl4 models from Yang et al.33. Interactions reported in the literature and shared with BDL and CCl4 models are shown in red, interactions that are shared but not mentioned in the literature are in cyan and unique interactions are shown in black. Selected from the top 100 significant interactions for BDL. e, Gene set enrichment analysis (GSEA) of fibrosis-like versus homeostatic-like assembloids using MSigDB_Hallmark_2020 (black), KEGG_2019 (red) and Reactome_2022 (cyan) gene datasets. EMT, epithelial to mesenchymal transition; NES, normalized enrichment score. f, Cell composition of homeostatic-like and fibrotic-like assembloids. Dots show the percentage of cells per structure. Data are mean ± s.e.m. (3 independent experiments, n = 13 organoids); homeostatic-like data are reproduced from Fig. 3d. Mann–Whitney test, two-tailed. g, Left, immunofluorescence staining for cleaved caspase-3 (CASP3). Right, violin plot showing the median and quartiles of the percentage distribution of hepatocytes containing cleaved caspase-3 from three independent biological replicates. Each dot represents one organoid. Mann–Whitney test, two-tailed. Hom, homeostatic (n = 8); Fib, fibrotic-like (n = 7). Scale bars: 100 µm (left), 50 µm (middle), 25 µm (right). h, Left, SHG imaging reveals fibrous collagen deposition; cholangiocytes (nuc-tdTomato), mesenchyme (PDGFRα–H2B–GFP) and SiR-actin staining. Right, mean ± s.e.m. of the intensity of SHG signal from three biological replicates from n = 3 independent experiments. Mann–Whitney test, two-tailed. Homeostatic assembloids, n = 10; fibrotic-like assembloids, n = 4. Scale bars, 20 µm. i, Expression of selected genes in mesenchyme, presented as abundance, in homeostatic (Ctrl) and fibrosis-like (Damage) assembloids, or in damage or control tissue from BDL and CCl4 models from ref. 33.
