Fig. 1

Genomic characteristics and the identification of a druggable target of a chemo-refractory metastatic muscle-invasive urothelial bladder cancer (MIUBC). a Overall workflow. Abbreviations: BCG, Bacillus Calmette–Guerin; WES, whole exome sequencing; WTS, whole transcriptome sequencing. b Clinical course of the patient investigated in the present study. c The mRNA expression-based molecular subtype of MIUBC identified by Pearson’s correlation coefficients between the bulk RNA sequencing samples and pre-defined Cancer Genome Atlas Urothelial Bladder Carcinoma (TCGA-BLCA) samples. *P < 0.05. d Immunohistochemistry staining of cytokeratin (CK)13, CD5/6, and CK14 performed on tumor sections to validate the molecular subtype of each sample. Abbreviation: H&E, hematoxylin and eosin. Scale bar, 100 μm. e Scatter plots showing mRNA expression levels versus variant allele frequencies (VAFs) for nonsynonymous mutation genes. Gray lines indicate cutoff of potential treatment target (VAF > 0.2 and gene expression > 6). Potential treatment target genes are marked as colored dots. Immunohistochemistry staining of HRASQ61R (insets) demonstrates protein expression. Scale bar, 100 μm. f The activation scores of core cancer-related pathways are plotted for BC159-T#1, #2, #3, and TCGA-BLCA samples. The RAS pathway was activated in all BC159-T samples compared with TCGA-BLCA samples. Each box shows the median and IQR (interquartile range, 25th to 75th percentiles), and whiskers indicate the highest and lowest value within 1.5 times the IQR. g The in-depth validation at single-cell level. T-distributed stochastic neighbor embedding (tSNE) plot of 2075 cells in BC159-T#3 sample, color-coded by their graphic-based clusters; basal tumor cell cluster is marked as a circle (left panel). HRAS gene is overexpressed in basal tumor cells (middle panel). Epithelial cells were identified by the average expression of epithelial-related genes (right panel)