Fig. 6
Brain metastasis (BrM) lesions presented an immunosuppressive tumor microenvironment. a Gene Set Enrichment Analysis (GSEA) plots of 5 immune-related signaling pathways based on RNA sequencing data. The peak point of the top park in each plot represented the enrichment score (ES), whereas the bottom part showed where the rest of genes of each pathway were located according to the ranking. b, c Box plot representation of normalized MCP counter scores (b) and ESTIMATE scores (c) for paired primary lung cancers and BrMs. The p-value was determined by the pairwise t-test. d Protein set enriched analysis of 4 immune related signaling pathways based on proteomics data. The peak point of the top park in each plot represented the ES, whereas the bottom part showed where the rest of proteins of each pathway were located according to the ranking. e Representative multiplex immunofluorescence (mIF) staining of paired primary lung cancer and BrM lesions from the patient DHP18. mIF markers include DAPI (blue), CD3 (orange), CD68 (green), Ki-67 (red), pan-cytokeratin (white), PD-1 (Cyan), and PD-L1 (yellow). Scale = 50 μm. f, g Box plot representation of the count number of CD3+ (f) and CD68+ (g) cells per mm2 in paired primary lung cancer and BrM lesions (n = 50 patients). The p-value was determined by the pairwise two-sided Student’s t test (*, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001)