Figure 4. Mapping cancer cell states and their interactions with the TME.

a. Scoring ST spots for module expression. Top: Schematic of spots colored by their annotation as ‘Malignant’, ‘Both’ and ‘Normal’; ‘Malignant’ spots are scored for expression of each module. Bottom: BRCA NYU2 sample with ‘Malignant’ spots colored by their expression of the indicated modules. Scale bar represents 1mm.

b. Characterizing spots by cell type neighborhood. Top: Schematic with grey spots indicating the presence of the cell type of interest, orange indicating ‘Malignant’ spots, and dashed lines indicating their surrounding spots. Bottom: BRCA NYU2 sample with ‘Malignant’ spots colored by neighborhood macrophage score. Scale bar represents 1mm.

c. Characterizing ST spots by cell type proximity. Top: Schematic colored as in b with arrows indicating the distance to the closest spot containing the cell type of interest. Bottom: BRCA NYU2 sample with ‘Malignant’ spots colored by macrophage proximity score. Scale bar represents 1mm.

d. Heatmap of correlations (Pearson) between module scores and cell type neighborhood for BRCA NYU2 ‘Malignant’ spots. Boxes indicate clusters.

e-f. Plot of the relationship between the interferon response module score and macrophage neighborhood score (e) or proximity score (f) in the BRCA NYU2 ‘Malignant’ spots. Line and grey area represent linear regression and standard error.

g. Boxplot of correlation scores (±log₁₀(p-value), Pearson) between module scores and macrophage neighborhood scores across 10 samples, colored as in Figure 1a. For each boxplot, the line indicates the median, the box indicates the 1st and 3rd quartile, the whiskers indicate the minimum and maximum values. Positive scores correspond to positive correlations. Dashed lines indicate p-value=0.05.

h-i. Map of correlations between module expression and cell type neighborhoods (h) and cell type proximity (i). Color represents the median ±log₁₀(p-value) of the correlation (Pearson). Point size represents the fraction of samples in which the correlation is of the same sign as the median correlation. Black outlines indicate relationships with (1) median ±log₁₀(p-value) greater than 0.75 and (2) fraction of samples greater than 0.5 - using both the neighborhood and proximity metrics.