Fig. 4: Differential signature analysis and delineated macrophage states in TME.

a Differential MeC signature testing for enriched cell states comparing pre- and post- immunotherapy conditions in basal cell carcinoma (BCC) with two-sided t-test. X-axis: Difference of mean signature scores between post- and pre-immunotherapy conditions. Y-axis: -log(p-value) from two-sided t-test. The significant cluster-wise differential signature is marked as “EnrichedMeC@ClusterName”; when the enriched MeC is the same as cluster name, the signature is marked “ClusterName”. Red dots, differentially increased signature; size of the dots is proportionally to the mean signature score of cells from the post-immunotherapy condition in the cluster. Blue dots, differentially repressed signature; size of the dots is proportionally to the mean signature score of cells from the pre-immunotherapy condition in the cluster. b Differential signature testing for enriched cell states comparing non-responders and responders from pre-treatment condition in bladder carcinoma (BLCA) with two-sided t-test. Red dots, differentially increased signature; size of the dots is proportionally to the mean signature score of cells from the responder condition in the cluster. Blue dots, differentially repressed signature; size of the dots is proportionally to the mean signature score of cells from the non-responder condition in the cluster. c Model of monocytes and macrophage states in tumor and their metabolic differences. d Top pathways enriched in different macrophage MeCs, with adjusted hypergeometric tested p-value from Enrichr. BCC basal cell carcinoma, BLCA bladder carcinoma. Source data are provided as a Source Data file.