Fig. 4.
FGFR3 plays an important role in the T-cell-depleted immune contexture of UTUC. a UTUC is T-cell depleted. Supervised consensus clustering of WCM UTUC, BCM-MDA UTUC, and TCGA UCB tumors according to a 170-immune gene signature classifies tumors into T-cell depleted (with lower expression of classifier genes), and T-cell inflamed (with higher expression of classifier genes) clusters (Fisher’s exact test P = 9 × 10-5). b FGFR3 is an expression outlier in UTUC tumors. WCM UTUC and BCM-MDA UTUC tumors are represented on the x-axis, and normalized z-scores of gene’s expression represented on the y-axis. c Boxplots of mean expression of FGFR3 and PPARG genes [in Fragments Per Kilobase of transcript per Million mapped reads (FPKM)] within the T-cell-depleted versus T-cell inflamed clusters (FGFR3: Wilcoxon test P = 1.3 × 10−6; PPARG: Wilcoxon test P = 1.1 × 10−5). The horizontal lines within the boxplots indicate the mean, boundaries of the boxes indicate the 25th-percentile and 75th-percentile, and the whiskers indicate the highest and lowest values of the results. d Interferon gamma (IFNG)-response genes are upregulated in response to FGFR3 knockdown. Volcano plot of differential fold expression of genes (logFC < 0 vs. logFC > 0; t-test adjusted P < 0.05) in FGFR3 shRNA + Doxycycline compared to control + Doxycycline UCB RT-112 cells (BST2: P < 0.001; GBP2: P = 0.038; IRF9: P = 0.005; MX2: P = 0.003). e Enrichment map of cancer-related pathways with significant positive and negative enrichment in FGFR3 shRNA UCB RT-112 cells. Node size corresponds to the number of genes within each gene set. The up-regulated nodes were represented in red while the down-regulated clusters were represented in blue. Overall, 476/3534 gene sets were upregulated, and 651/3534 gene sets were downregulated (t-test P < 0.05; false discovery rate (FDR) < 0.25). Several IFNG response gene sets were enriched after FGFR3 blockade (t-test P < 0.001; FDR = 0.062). f Pharmacologic inhibition of FGFR3 upregulates IFNG-response gene BST2 using two different primer pairs (BST2 #1, BST2 #2). Barplots showing relative fold increase (mean ± SD) of mRNA levels of BST2 (BST2 #1 and BST2 #2) after treatment with erdafitinib at 1 and 5 nM compared to DMSO vehicle in RT-112, RT-4, and SW780 cells. No statistically significant differences were observed in the expression of BST2 between the 1 and 5 nM erdafitinib conditions in any of the tested cell lines (statistical significance level is denoted by asterisks *t-test P < 0.05, **P < 0.01, ***P < 0.001, n.s: non-significant). Error bars show standard deviation (S.D.) for each condition