Fig. 2

Comparison of tumor immune microenvironment inKDM5-mutant and KDM5-non-mutant patients enrolled in TCGA cohort. (A) The differences of tumor mutation burden (TMB), silent mutation rate, and nonsilent mutation rate between KDM5-mutant and KDM5-non-mutant tumors examined by Wilcoxon test. Each dot represents one patient, box represents the median values and their interquartile ranges. Red, KDM5-mutant tumors; green, KDM5-non-mutant tumors. (B) The expression differences of 16 MHC-related antigen-presenting molecules and 25 co-stimulators between KDM5-mutant and KDM5-non-mutant tumors represented by heatmap. Red, the median expression values are higher in KDM5-mutant tumors; blue, the median expression values are lower in KDM5-mutant tumors. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ns, not significant. (C) The differences of leukocyte fractions, lymphocytes fraction and tumor-infiltrating lymphocyte fraction between KDM5-mutant and KDM5-non-mutant tumors. (D) Comparisons of the abundances of SNV/Indel neoantigens and the diversity of TCR/BCR. (E) Expression difference of PD-1, PD-L1, and CTLA-4 in KDM5-mutant and KDM5-non-mutant tumors. (F) The expression differences of 48 chemokines and their receptors between KDM5-mutant and KDM5-non-mutant tumors represented by heatmap. (G) The expression differences of 39 immune-stimulators between KDM5-mutant and KDM5-non-mutant tumors represented by heatmap. (H) The differences of 29 immune signatures estimated by ssGSEA between KDM5-mutant and KDM5-non-mutant tumors. BCR, B cell receptor; CTLA-4, cytotoxic T-lymphocyte-associated antigen 4; MHC, major histocompatibility complex; PD-1, programmed cell death protein 1; PD-L1, programmed cell death ligand 1; SNV, single nucleotide variants; TCGA, the cancer genome atlas; TCR, T cell receptor; TIL, tumor-infiltrating lymphocyte; TMB, tumor mutation burden