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Fig. 5 | Journal of Experimental & Clinical Cancer Research

Fig. 5

From: Inhibition of HSP 90 is associated with potent anti-tumor activity in Papillary Renal Cell Carcinoma

Fig. 5

RNA sequencing of PRCC cells treated with SNX2112 (A) Venn diagram showing the number of differentially expressed genes in UOK345 and UOK342 following treatment with SNX2112. UOK345 and UOK342 cells were treated with SNX2112 (50 nM) and RNA was isolated after 48 h of treatment for the mRNA-Seq analysis. Of the 6,038 differentially expressed genes common in both cell lines, 2,902 genes were downregulated (fluorescent blue color), and 3,136 genes were upregulated (dark green color). Analysis used genes meeting an FDR value < 0.05; fold change > 1.5 threshold. B Heatmap showing the mRNA levels of the top 100 genes (50 up or downregulated) after SNX2112 (50 nM) treatment. The expression levels of each gene were normalized to the total mRNA abundance of each sample and compared with that of vehicle-treated controls. C The top ranked negatively, and positively enriched gene sets identified using Gene Set Enrichment Analysis (GSEA) in response to SNX2112. GSEA was performed with top common differentially expressed genes in UOK345 and UOK342 cells after SNX2112 treatment using 50 HALLMARK gene sets database in MSigDB. GSEA plots showing strong (D) negative enrichment of the E2F, G2M_checkpoint and MYC Targets v1 and (E) positive enrichment of protein secretion pathway in UOK345 and UOK342 cells in response to SNX2112. NES; Normalised Enrichment Score, FDR: false discovery rate (F) Kaplan–Meier estimate of overall survival based on expression of differentially expressed genes (TCGA PRCC Cohort). Relative high expression of CDC20, TPX2, CEP55, FOXM1, KIFC1, NUF2, BUB1B, BIRC5 and PLK1 genes and (G) low expression of RCAN1 gene was associated with poor overall survival in KIRP cohort. Log rank (Mantel-Cox) test was used for significance; p < 0.05 was considered significant. H Relative mRNA expression of selected E2F, G2M checkpoint and MYC regulated genes. The mRNA levels of CDC20, FOXM1, BUB1B, BIRC5 and PLK1 genes were evaluated by qRT-PCR 48 h after SNX2112 treatment (50 nM) in UOK345 and UOK342. Data are mean ± SEM of three independent experiments. **p < 0.001, Statistical significance was determined using the two tailed Student’s t test

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