Fig. 1: CAF compositions change between BRCA-WT and BRCA-mut PDAC tumors.
Formalin-fixed paraffin-embedded (FFPE) tumor sections from BRCA-mut and BRCA-WT PDAC patients were stained for hematoxylin and eosin (H&E), IHC, and MxIF. (a) IHC was performed for αSMA, CLU and HLA-DR (Scale bar, 200 μm). Representative images of a BRCA-WT tumor are shown (n = 2). (b–h) MxIF was performed using antibodies for the depicted proteins. DAPI was used to stain nuclei. Scale bar, 50 μm. Representative images are shown in (b). Images were analyzed using ImageJ software, CD45− CK− regions were defined as regions of interest (ROIs) and the area stained by each CAF marker was calculated, divided by the ROI and averaged for each patient sample (c–e). Mann-Whitney test was performed. The ratio of the different CAF subtypes is shown in (f–h) and was analyzed using Student’s t-test. Data are presented as Mean \(\pm\) SEM. ns marks p-values greater than 0.05. For IHC and H&E staining n = 2, and for MxIF staining n = 11 BRCA-mut and n = 15 BRCA-WT. (i–n) Single-cell RNA-seq data of fibroblasts and stellate cells from human PDAC tumors16 was reanalyzed using the Seurat R toolkit. (i) Uniform Manifold Approximation and Projection (UMAP) of 6,405 cells from16, color-coded for the indicated cell clusters defined by a local moving clustering algorithm. The clusters that differentially express ACTA2, CLU and HLA-DR are indicated. (j) Dot plot visualization of gene expression of the indicated CAF markers. (k–n) Single-cell expression level of CAF markers on the UMAP shown in (i). Marker genes of ACTA2 (k), CLUlow (l), CLUhigh (m), and HLA-DR (n) clusters are represented. Source data are provided as a Source Data file.
