Fig. 4: Multiparametric imaging of indolent and aggressive lesions reveals spatially heterogeneous tumor and immune niches.

a–d All images shown are pseudo-colored channels from a single mammary tissue section bearing indolent and aggressive lesions stained using a cocktail of antibodies and visualized using imaging mass cytometry. Lesions were stained for collagen IV (basement membrane), α-SMA (smooth muscle actin, myoepithelial marker), cytokeratin 8 (luminal epithelial marker), cytokeratin 5 (basal epithelial marker), vimentin (mesenchymal marker), and pS6 (S235/S236, mTOR signaling). Combinations of markers were selected to evaluate indolent and aggressive lesions for membrane integrity (a), epithelial identity and mixed epithelial lineage (b), mixed epithelial/mesenchymal lineage (c), and metabolic activity (d). Representative images on the left panel show low-magnification view of adjacent indolent and aggressive lesions. Boxes in left panel correspond by color to high magnification images, shown in middle (blue, indolent), and right (yellow, aggressive) panels. Arrows of the same color point to the same cell in each image. Quantification of indolent or aggressive tumor cells co-expressing CK5 and CK8 (e), vimentin (f), and pS6 (g). P value was calculated using two-tailed Welch’s t-test (e, t = 5.588, degrees of freedom (df) = 3.012; f, t = 10.50, df = 3.075) or two-sided Wilcoxon rank-sum test (g, U = 0); error bars indicate standard error of the mean (SEM). Each dot represents quantification from one region. See also Supplementary Fig. 4. Source data are provided as a Source Data file.