TK expression in MIBC patient tumor samples and BCa cell lines.

(A) Heat maps of relative mRNA expression levels in 408 tumor samples from patients with MIBC [22] (RNA Seq V2, left) and absolute mRNA copy number in 15 BCa cell lines (right) of 31 TKs (gene symbols listed vertically, middle). MIBC patient tumor samples are grouped on the horizontal axis by mRNA subtype classifications as previously defined [22] indicated at the top (from left to right): neuronal (N, green); basal squamous (BS, red); luminal (L, gray); luminal infiltrating (LI, gold); luminal papillary (LP, purple). TK genes are clustered hierarchically; colored vertical bars at indicate group 1 TKs (black) above group 2 TKs (orange). Highest expression is shown in yellow, moderate expression in blue and lowest expression in black; ND for cell line data indicates transcript was undetectable. (B) Cladogram of 34 receptor TKs (RTKs) most closely related to Met based on TK domain amino acid sequence identity, constructed using the EMBL-EBI ClustalW2 Phylogeny tool (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny). RTK symbol colors identify established subfamilies. Values for cabozantinib doses calculated to provide 50% TK inhibition (IC₅₀, nM) in a cell-free assay, listed at right, were derived from a minimum of 3 x 10-dose binding curves with regression (R) values > 0.98 unless indicated by NC (not calculated), where values were >3 micromolar. Values considered clinically relevant (< 150 nM) are shown in red. TKs for which IC₅₀ values could not be determined are denoted by a single dash. (C) Oncoprint showing alterations for 19 genes encoding ctRTKs (identified previously and/or by cell-free kinase inhibition assay) among 408 MIBC samples [22]. Gene symbols and percentage of samples altered (%) for each are listed at left (Oncoprint generated using visualization tools at the cBioPortal for Cancer Genomics, Memorial Sloan Kettering Cancer Center, https://www.cbioportal.org/ [37]). (D) Linear regression analysis of AXL (left) and MET (right) mRNA abundance (y-axis) vs. protein content (x-axis) for 15 BCa-derived cell lines shows significant direct correlation (AXL: Spearman r = 0.638, p = 0.040; MET: Spearman r = 0.7902, p = 0.003).