Fig. 3: Charting the CAF landscape in the PDAC tumor microenvironment.

A UMAP overview of the mesenchymal compartment. CAF cancer-associated fibroblast, iCAF inflammatory CAF, myCAF myofibroblastic CAF, UMAP uniform manifold approximation and projection. B Heatmap of the five most differentially expressed genes within each cluster. Colors correspond to the cluster colors in panel (A, C). iCAF, myCAF, and apCAF signatures from Elyada et al.¹⁹ overlaid on the UMAP embedding of our mesenchymal compartment. The iCAF and myCAF signatures are derived from human fibroblasts; the apCAF signature is derived from KPC mouse fibroblasts. apCAF antigen-presenting CAF. D Assessment of correlation (two-sided Pearson correlation) between myCAF/iCAF composition and basal/classical composition among our samples (n = 16). Samples are plotted as a function of the percentage of their CAF cells that are myCAFs and the percentage of their malignant epithelial cells that are basal. Samples with fewer than 40 total CAF cells were excluded; all but one of these samples were biopsies, which were not expected to pick up many mesenchymal cells. E Selected gene set enrichment analysis results from a comparison between the cells in the iCAF and myCAF compartments. ECM extracellular matrix.