Fig. 3: Comparison of mutation frequencies and RNA expression profiles.

Patient specimens that resulted in successful engraftment (PDX) vs those that did not (No PDX) were compared. a The rates of successful engraftment differed among tumors with putative driver mutations. The number of patient cases with mutation in the gene is shown in parenthesis. b Comparison of RNA-seq data from patient specimens that successfully engrafted (PDX, n = 8, salmon) vs those that did not (No PDX, n = 9, turquoise). 749 genes (428 upregulated and 321 downregulated) were differentially expressed between UTUC tumors that did and did not engraft based on the z-score of normalized gene reads from RNA-seq. c Single Sample Gene Set Enrichment Analysis (ssGSEA) scores of basal (P = 0.19) and luminal gene sets (P = 0.41) based on the BASE47 classifier and ssGSEA scores of tumor basal genes (expressed in cancer cells of a basal-like phenotype, indicated at the bottom of Fig. 1b, P = 0.04) plotted for the patient tumors resulting in PDX (n = 8) vs No PDX (n = 9). Error bars are mean standard error from bootstrap. The center line in the boxplots indicates the mean, the lower and upper hinges correspond to the first and third quartiles, the upper whisker is the maxima and the lower whisker the minima. P-value indicates two-sided two group t-test without adjustment. d GSEA plots comparing specimen that did and did not yield PDX. Enrichment of cell cycle/DNA replication pathways was observed in the PDX group, whereas extracellular matrix receptor interaction and focal-adhesion pathways were enriched in the No PDX group. Source data for b–d are provided as a Source Data file.