Extended Data Fig. 8: Capturing heterogeneous branching in PDO phenotypes.
a Representative organoid morphologies of established PDAC lines: DANG, MiaPaCa2, Panc1, PatuS, PatuT, PSN-1 and BxPC3 (from left to right) grown inside floating collagen gels in two different media culture conditions: the established media conditions containing 10% FBS (top) and the Basal Branching PDO Media (bottom) (n = 113 organoids in the 10% FBS Media and 106 organoids in the Basal Branching PDO Media). All scale bars= 500 μm except from the PatuS and BxPC3 organoids where the scale bars= 200 μm. b-f Analyses of the following PDO line IDs: B211, B250, B320. b Heatmap of bulk RNA sequencing for different pathways associated with the extracellular matrix organization and rearrangement. c Individual PDO line morphological heterogeneity in Full PDO Media as visualized by density overlays superimposed on the imaged-derived clusters. The overlays indicate which cell lines correspond to which cluster. d Individual PDO line morphological heterogeneity in Base PDO Media as visualized by density overlays superimposed on the imaged-derived clusters. The overlays indicate which cell lines correspond to which cluster. e Major morphologies found in PDOs cultured in Basal Branching PDO Media. Color coding implies the hierarchical relation of the super families and manual morphological clustering of the total number of organoids, n = 916 organoids. Scale bars= 200 μm. f Transcriptional correlation scoring of PDOs growing in Basal Branching PDO Media to murine organoid phenotype signatures. g Characteristic PDO organoid morphologies of additional PDO lines (n = 3 patients, PDO line IDs: B379, B403, B535) cultured in different conditions: Full PDO Media (top), Base PDO Media (middle), Basal Branching PDO Media (bottom) and HEs of the corresponding PDAC tissues. All organoid scale bars= 100 μm, HEs of the PDAC tissues scale bars= 200 μm. h K-means clustering of the image-derived features of an additional unseen data set from the PDO line IDs: B379, B403, B535 (n = 531) organoids integrated with the original data from Fig. 8h reveals 2 distinct morphological clusters when PDOs are cultured in Full PDO Media. i K-means clustering of the image-derived features of an additional unseen data set from the PDO line IDs: B379, B403, B535 (n = 349 organoids) integrated with the original data from Fig. 8i reveals 2 distinct morphological clusters when PDOs are cultured in Base PDO Media. j K-means clustering of the image-derived features of an additional unseen data set from the PDO line IDs: B379, B403, B535 (n = 783 organoids) integrated with the original data set from the Fig. 8j reveals 6 distinct morphological clusters when PDOs are cultured in Basal Branching PDO Media. k Individual PDO line (ID: B379-left, ID: B403-middle, ID: B535-right) morphological heterogeneity in Basal Branching PDO Media as visualised by density overlays superimposed on the imaged-derived clusters (Extended Data Fig. 8j). The overlays indicate which cell lines correspond to which cluster.
