Fig. 4: Spatial phenotypes interrogated for immune determinants and evasive pathways.

a Heatmap showing scaled average frequencies of immune cells based on Cibersort deconvolution (red: high, blue: low, immune cell subsets with significant differences among spatial phenotypes are indicated in bold); corresponding boxplots show median with 25th–75th percentile and range (outliers are displayed as dots) of immune cell subsets with differential abundances among spatial phenotypes (n = 101 LNN TNBC, of which n = 24 excluded, n = 33 ignored, and n = 44 inflamed). b Heatmap showing scaled average expression of gene-sets related to T cell evasion (differential gene-sets are indicated in bold). c Volcano plot of differential gene expressions between excluded and inflamed (upper), and ignored and inflamed phenotypes (lower); top DE genes related to T cell evasion are shown in bold. d IPA analyses of cells, molecules, and pathways associated with spatial phenotypes (red: upregulated, blue:downregulated); and lists of major characteristics per spatial phenotype (bottom). e Correlations between expressions of COL10A1 and TGFB- or VEGF-signaling in the excluded phenotype. f Correlations between expressions of CD163 and WNT targets or negative regulators of PPAR genes in the ignored phenotype. g Correlations between the presence of activated dendritic cells (according to BATF3 expression) and expressions of chemokines or type-I IFN genes in the inflamed phenotype. h Correlations between expressions of CD8A and various T cell evasive genes/gene-sets (all phenotypes) (all correlations show regression coefiicients and p values). Significant differences are: ***p < 0.001; **p < 0.01; *p < 0.05, NS, p > 0.05 (Kruskal–Wallis, one-sided). Source data are provided as the source data file.