Extended Data Fig. 5: Activated signalling in inflammatory ccRCC cells.
From: Epigenetic remodelling shapes inflammatory renal cancer and neutrophil-dependent metastasis
a, Scatter plot of individual genes expressed in OSPa and OS5K-3 cells. The dots represent 258 upregulated (red) and 220 downregulated (blue) genes in OS5K-3 cells (fold-change > 2). The data presented were from the RNA-sequencing analysis shown in Fig. 3. b, c, Promoter and enhancer analysis of cultured OS-RC-2 derivatives. The data presented were from the ChIP-sequencing analysis (H3K27ac) shown in Fig. 3. b, Volcano plot showing the fold-changes of individual H3K27ac peak intensity between OSPa and OS5K-3 cells. The dots represent 944 increased (red) and 437 decreased (blue) peaks in OS5K-3 cells (fold-change > 10, adjusted p-value < 0.05). Statistical analysis was performed in HOMER software. c, Heat map showing correlations between the H3K27ac peak intensities among the average value of each indicated OS-RC-2 derivative. Pearson’s r. d, GSEA (hallmark gene sets) showing genes related to ‘hallmark_hypoxia’. The data presented were from the RNA-sequencing analysis shown in Fig. 3. Genes were screened following the criteria; RPKM ≥ 3 in either OSPa or OS5K-3 cells. Statistical analysis was performed by the GSEA algorithm. e, Immunoblotting for p65, α-tubulin, and HDAC1 in 786-O derivatives. f, Immunoblotting for C/EBPβ, C/EBPδ, and α-tubulin protein expression in 786-O derivatives. g, Re-analysis of TCGA KIRC cohort data showing expression of the indicated genes. n = 267 (stage I), n = 57 (stage II), n = 123 (stage III), and n = 83 (stage IV) patients. The bars represent means ± S.D. One-way ANOVA and Tukey’s test. h, Re-analysis of TCGA KIRC cohort data showing relationships between the expression of each indicated gene and overall patient survival. All patient samples were divided, based on expression of the indicated genes. n =266 patients/group. Log-rank test. Hazard ratio with 95% confidence interval was also indicated.
