Fig. 5: EMT markers spatially overlap with high tension matrix and associate with poor survival in patient tumors. | Nature Communications

Fig. 5: EMT markers spatially overlap with high tension matrix and associate with poor survival in patient tumors.

From: A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer

Fig. 5

a Pearson correlation between GSVA scores for collagen genes and hallmark pathway genes in the Nuvera dataset. b Scatterplot of GSVA scores for collagen genes and hallmark EMT genes. Each point represents one patient. N = 508 patients. Pearson r = 0.880. c FOVs for Twist1 staining within FFPE tumors (left). Scale bar, 50 μm. Inset scale bar, 10 μm. Scatterplots of STIFMap intensity vs stain intensity for each pixel shown in (i) indicating the 99th percentile of stain intensity for each STIFMap percentile (right). N = 22 imaged FOVs. d–f Violin plots of the Spearman correlation for each FOV comparing the 99th percentile of staining intensity versus percentiles of DAPI, predicted elasticity, or collagen stain intensity. Internal gray bars indicate a box-plot. N = 22 Twist1 FOVs, n = 5 ZEB1 FOVs, and n = 25 SLUG FOVs. g Representative whole slide image (WSI) and regions of interest (ROIs) of ZEB1 stain with STIFMap in HER2+ breast cancer cohort. Scale bar (WSI), 1 mm. Scale bar (ROIs), 100 μm. N = 21 patient tumor samples. h Spearman correlation for each whole tissue section comparing the 99th percentile of staining intensity versus percentiles of predicted elasticity and collagen stain intensity. N = 21 patient tumor samples. i Box and whiskers plots to show the association between metastatic recurrence and spatial autocorrelation (Moran’s I) for tissue markers and STIFMaps in the HER2+ breast cancer cohort (n = 84 breast tumors). Kaplan–Meier curves comparing survival between the upper and lower quartiles of EMT (j) and collagen (k) GSVA scores within the Nuvera cohort. N = 127 patients in each group. Boxes denote 25th to 75th percentile with median line. Whiskers mark the minima and the maxima excluding outliers. Statistical analyses were performed using two-sided Mann–Whitney U test (d–f, h, i) and logrank test (j, k), *P < 0.05, **P < 0.01, ***P < 0.001 ****P < 10−5. Source data are provided as a Source Data file.

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