Fig. 6: Tumor immune microenvironments and macroenvironments across organ sites.
a, Unsupervised clustering of 12 pan-cancer immune archetypes in the RAM tumor (n = 93), AN (n = 68) and NAN (n = 67) tissue compartments, across RAM cases/patients, organ sites and treatment histories. Each sample’s enrichment scores of immune archetypes were used to generate heat maps. b, The composition of immune archetypes in the tumor, AN and NAN compartments across multiple organ sites. c, Absolute enrichment scores (CIBERSORTx) of anti-tumorigenic (named M1 by CIBERSORTx) or pro-tumorigenic (M2) TAMs, eosinophils, resting mast cells and neutrophils in the tumor, AN and NAN compartments of indicated organ sites, compared against the TCGA–SKCM cohort (labeled ‘skin’ as the organ site) (n = 344 BRAFMUT or NRASMUT melanoma). Comparisons among organs by the Krustal–Wallis test. Central line of each box, median; top and bottom edges of each box, first and third quartiles; whiskers extend 1.5× the interquartile range beyond box edges. Tumor compartment (brain, n = 6; cardio, n = 4; liver, n = 18; lung, n = 17; lymph node, n = 13; spleen, n = 5; soft tissue, n = 10; skin, n = 344). AN (brain, n = 21; cardio, n = 5; liver, n = 17; lung, n = 6; lymph node, n = 6; spleen, n = 5; soft tissue, n = 7). NAN (brain, n = 20; cardio, n = 5; liver, n = 15; lung, n = 5; lymph node, n = 6; spleen, n = 5; soft tissue, n = 10). d, Quantifications by multiplex immunofluorescence of the ratios of pro-tumorigenic (CD68+CD163+CD206+/−) to anti-tumorigenic (CD68+iNOS+/−CD206–CD163−) TAMs in metastatic tumors to visceral organs (n = 4; RAM19003: liver, omentum; RAM19006: lung and LN) relative to ratios in tumors to the brain (n = 2) in two RAM cases. Box plot as defined in c. e, As in c, except enrichment scores of T cell exhaustion and type 2 immunity signatures in the tumor, AN and NAN compartments across organ sites.
