Extended Data Fig. 5: HepOrg in MM and HM-Wnt media show some degree of zonation.
From: Mouse liver assembloids model periportal architecture and biliary fibrosis
a. Bulk RNA sequencing analysis of HM-Wnt and MM media HepOrg compared to freshly isolated hepatocytes. Heatmap represents the log10(TPM + 1) (transcripts per million) values from the RNAseq for the indicated genes, Z-scored across each gene (n = 3 biological replicates). For HM-Wnt, some genes are reproduced from Extended Data Fig. 3b. b. Zonation score calculated from scRNAseq data of HM-Wnt and MM media HepOrg shows that HM-Wnt-grown HepOrg are on average more pericentrally zonated, while the score is shifted periportally for MM-grown HepOrg. c. Dot plot shows gene expression from scRNAseq of HM-Wnt and MM media HepOrg for pericentral and periportal genes, as well as zonated cholesterol metabolism genes. d. UMAP representing the hepatocytes from HM-Wnt and MM media HepOrg and expression of selected periportal (Cdh1, Alb) and pericentral (Cyp1a2, Cyp2e1) genes in the two media. e. Expression of periportal (Gls2, white) and pericentral (Cyp1a1, magenta) gene RNA visualised by RNAscope in HepOrg from MM media, representative of n = 3. Alb (green) and nuclei (DAPI, blue) are also shown. Scale bar, 50 µm, zoom-in, 20 µm. f. Immunofluorescence staining of periportal (E-CAD, E-cadherin, green and Fire LUT), pericentral (CYP2E1, magenta, and Fire LUT), Actin (Phalloidin, grey) and nuclei (DAPI, blue) in HepOrg cultures (P2) grown in HM-Wnt and transferred to MM for 7 days, compared to liver tissue. Representative images from 4 independent experiments are shown. Scale bar, 50 µm.
