Fig. 6: IMC reveals cellular neighborhoods, cytokine milieus and tertiary lymphoid structures.
a Heat map indicating significant pairwise cell type interaction/avoidance in individual images from the Protein Panel dataset (n = 77 images, 1000 permutations each). Significance is indicated by square color (p < 0.01, two-sided permutation tests), corrected for relative cell type frequency. Highlighted interactions indicate (1) fibroblast-endothelial interactions, (2) myeloid auto-interactions, (3) tumor compartment, (4) hypoxic/apoptotic tumor cell to immune cell interactions, (5) tumor to T cell subtype interactions, (6) main immune compartment, and (7) migDC-PD-1high T cell interaction. b Single-cell masks for selected IMC images (top: mature TLS image, bottom: immature TLS image). Only a subsection of each image is shown. c Paired boxplot comparing the percentage of PD-1high T cells versus PD-1low T cells that have at least one migDC as a direct neighbor. Each pair of dots represents a separate sample (n = 14 independent patient samples; two-sided paired Wilcoxon rank sum test). Boxplot centers indicate group median, bodies show IQR, and whiskers extend to the largest and the smallest value lying within 1.5 times the IQR above the 75th percentile and below the 25th percentile, respectively. d Heatmap displaying the average relative proportion of each indicated cell type among the 10 nearest neighbors for each T cell subtype across non-TLS images (left) and TLS-images (mature and immature, right). e Heatmap indicating significant relative enrichment or depletion of each cell type in the different cytokine milieus in all images of the RNA Panel dataset (Fisher’s exact test; n = 77 images; for each individual combination, only images containing the respective community and cell type were included). f Single-cell masks for selected representative IMC images with cell outline colored by the indicated cytokine community and cell body colored by cell type. The selected images are representative of cellular patterns seen across the dataset (n total = 77 images). g Stacked barplots indicating the slide-wide TLS status for 13 IE1 samples and 12 IE2 samples. h Stacked barplots showing the proportions of CXCL13+ T cells that are part of a CXCL13-cytokine-cluster for images with the indicated TLS status.
