Fig. 3

vCAF and mCAF marker genes can be used to trace back subpopulations in tissue sections. a Violin plots of selected vCAF differentially expressed genes in log₂(RPKM + 1). Violin colors represent mean expression of each population. Genes were sorted based on gene ontology terms. b Immunohistochemistry (IHC) staining of desmin on MMTV-PyMT tumor sections (6 µm). Images were acquired from the leading edge and the tumor center. Yellow boxes (left) indicate 2× magnified area (right). c IF staining of Nidogen-2 (green) and CD31 (magenta) or PDGFRα (red) on MMTV-PyMT tumor sections (5 µm) from mice of age 8 weeks, 12 weeks, and 15 weeks (top to bottom). Nuclei were counterstained with DAPI. d Immunofluorescence (IF) staining of Nidogen-2 on human tumor tissue (5 µm). Nuclei were counterstained with DAPI. e Violin plots of selected mCAF differentially expressed genes in log₂(RPKM + 1). f IHC staining of fibulin-1 and PDGFRα in MMTV-PyMT tumor sections (6 µm). Images were acquired from the leading edge and the tumor center. IHC staining of fibulin-1 (g) and PDGFRα (h) in human tumor tissue sections (6 µm). FACS-sort of MMTV-PyMT tumor (i) and mammary gland (j) tissue. Gating on single, living CD45⁻CD31⁻NG2⁻EPCAM⁻ cells followed by gating on PDGFRα⁺ cells (blue box) or PDGFRα^- cells (red box). k Violin plots of cell cycle gene expression in log₂(RPKM + 1). l IF staining for Nidogen-2 (red) and Ki-67 (grey) on sections (5 µm) from PDGFRα-EGFP (green) reporter mice. Arrows indicate Nid2⁺Ki67⁺ cCAF. Scale bar: 50 µm