Extended Data Fig. 4: ContactTracing inference of cell-cell interactions from single cell data.

a, Illustrative histogram showing log-transformed expression of the Mrc1 receptor in Macrophages (target cell type) for the receptor-null (white) and receptor-expressing (gray) subsets. b, Volcano plot showing genes differentially expressed in Mrc1-expressing vs. Mrc1-null macrophages (target cell type). Nodes are scaled by the absolute value of the transcriptional response score; top up- and down-regulated genes are labeled. c, Visual summary of MAST results from the CIN-dependent interaction test (see Methods); shown here for Mrc1 receptor expression in macrophage target cells. Each node represents a highly variable gene. The x-axis shows the log2-fold change estimate in receptor-expressing vs. receptor-null target cells in the CIN^low condition. The y-axis shows the same parameter estimate, but computed in the CIN^high condition. Node size is proportional to the significance of the interaction effect, and the node color represents the magnitude of the interaction effect, which here shows CIN-dependent amplification of the transcriptional response. d, Each node represents a receptor/cell type combination, on the x-axis is the number of genes with significant transcriptional response (FDR < 0.05) in the CIN^high/CIN^low dataset; on the y-axis is the same value for the CIN^high Sting1^WT/Sting1^KD data set. e, As in d, except the number of genes with significant conditionally-dependent interaction effect (FDR < 0.05) is shown. f, UMAP projection based on STING-dependent interaction effects in CIN^high tumors. The effect matrix has a row for each receptor/cell-type combination with at least one significant interaction effect (FDR q-value < 0.05), and a column for every gene. Each entry in the matrix is −log₁₀(p-value)*interaction_coef. Node color reflects the cell type in which the ligand effect is measured and node size reflects the number of significant condition-specific interaction effects in target cells expressing the receptor. g, Transcriptional response states are mapped to individual cell clusters by taking the dot-product between the transcriptional response score for a given gene (given by x-axis) and its log2(expression fold change), here shown for one tumor subcluster vs. all other tumor cells (y-axis) and visualized using a clustered heatmap based on the average Euclidean distance metric. Red: positive dot-product, blue: negative dot-product, white: any value with abs(dot product) < 0.5. The log2(expression fold change) was set to zero if it was not significant (FDR q-value > 0.15) prior to computing the dot product. h, ContactTracing network plot corresponding to data in Fig. 4a. Here, nodes represent cell subtypes; node size is scaled by their relative fraction in the TME, and color reflects their average CIN-dependent differential abundance. Directed arrows represent interactions between cell subtypes (emanating from ligand-producing, donor cell subtype to receptor-expressing, target cell subtype), with arrow thickness encoding the total number of CIN-dependent interactions predicted between each pair of subtypes, and arrow darkness reflecting the number of STING-dependent interactions.