Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma
Using only proteins that were differentially abundant at each stage, the glycolysis pathway was interrogated. Directionality of change is indicated by red (increased in tumor) or green (decreased in tumor) and the small bar graph next to each protein symbol in the pathway is protein fold-change (tumor/normal) at stage I, II, III, IV and then all stages (from left to right). Levels of two proteins, PFKP and PKM, were confirmed using IHC staining of stage I ccRCC tissue (other stages were not evaluated by IHC). A representative IHC image is shown for PFKP and PKM along with average staining intensity (H value) ± standard error of a stage I ccRCC TMA. For both PFKP and PKM the average log2 fold-change (FC) levels ± standard error for protein abundance (stage I-IV and metastasis tissue) and gene expression (stage I-IV) are displayed as bar graphs (‘*’ indicates significance, BH adjusted p < 0.05). Below each pair of bar graphs is a scatter plot of log2 normalized spectral counts (protein) versus RMA normalized array gene expression data from the 94 tissues with proteomic and transcriptomic data.