Fig. 5: Organoids phenotypes represent distinct tumour cell states with unique in vivo biological functions.
a, Scoring of the individual organoid phenotypes isolated from the E-mouse line ID: 9591 and the M-mouse line ID: 16992 for PDAC subtype-specific signatures35. Graph represents mean ± s.e.m., each dot represents an independent experiment. b, Violin plots of scRNA-seq from the parental epithelial and mesenchymal cells scored for the organoid phenotype signatures. The y-axis represents the AUCell scores for the specific signatures. c, UMAP scoring the individual organoid phenotype signatures to a human PDAC data set37. d, Schematic representation of the in vivo orthotopic transplantation and the subsequent analysis, including histopathological analysis, whole-tissue clearing and IF staining, and organoid line isolation/characterization; image created with BioRender.com. e, H&E staining of orthotopically transplanted organoids. Scale bars, 60 µm. f–h, 3D in vivo growth patterns of PDAC organoids. f, 3D views of PDAC organoid grafts stained for pan-Keratin and Vimentin. All scale bars, 100 μm. g, High magnifications of pan-Keratin from the PDAC grafts in f, demonstrating different growth patterns of the various organoid lines. All scale bars, 20 μm. h, 3D segmentations of coherent tumour cell strands from different organoid grafts. All scale bars, 30 μm. i, Manual phenotype analysis of organoids post implantation (n = 41 lines, n = 1,171 organoids from the epithelial lines and n = 633 organoids from the mesenchymal lines). Bar plot represents the mean ± s.e.m. of the average number of organoid phenotypes (%). j, Truncated violin plots of the total number of metastatic nodules in the liver from epithelial (left) and mesenchymal (right) transplanted organoid phenotypes. k, Truncated violin plots of the total number of metastatic nodules in the lung from epithelial (left) and mesenchymal (right) transplanted organoid phenotypes. Br. mesenchymal, branched mesenchymal; sign., signature.
