Fig. 5

EMT programs promoting metastatic behavior are highly elevated in metastatic ccRCC. A Joint embedding of tumor cells from ccRCC primary and ccRCC Bone Met samples. B Violin plots of genes expressed in the proximal tubule of the normal adjacent kidney tissue, ccRCC primary, and ccRCC Bone Met tumor cells. C InferCNV analysis showing CNV pattern of metastatic and primary tumor cells taking proximal tube cells as control. D Pairwise expression distances between samples are shown using MDS embeddings. Each dot is a sample, with colors and point shapes corresponding to the sample condition. E Volcano plot illustrate differential expressed genes comparing bone metastatic tumor cells compared with primary ccRCC tumor cells. The vertical dashed lines show the cut-off for gene filtering (log2FoldChange 1.5 and − 1.5), and the horizontal dashed line signifies an adjusted p value of 0.01 (see the “Methods” section). F Box plot comparing the EMT gene signature score across proximal tubule of the normal adjacent kidney tissue, ccRCC primary, and ccRCC Bone Met tumor cells. For box plots, center line represents the median and box limits represent upper and lower quartiles, and whiskers depict 1.5 × the interquartile range (IQR). G Heatmap showing representative EMT signature genes expression in proximal tubule of the normal adjacent kidney tissue, ccRCC primary, and ccRCC Bone Met tumor cells. Color represents scaled average gene expression