RPPA survey of cancer hotspot panel proteins and cell markers in matched tumor-normal human breast and kidney samples reveals a weak correlation between proteins expression and public transcriptome repositories

Abstract

Despite the tremendous global effort in discovering and cataloguing somatic mutations in cancer-related genes and the impact they exert on human cancers, the effects of these mutations on the levels of protein expression are inadequately addressed. Here, we semi-quantitated the expression of 48 (out of 50) proteins represented by the most widely used cancer hotspot panel, the Ion AmpliSeq Cancer Hotspot Panel v2, and 14 cell markers commonly used as house-keeping proteins, using reverse phase protein array (RPPA) technology in 586 human breast- and 192 kidney matched tumor-normal samples. We further correlated our RPPA data with gene chip data from the Gene Expression Omnibus repository fetched through the TNMplot portal. Nearly half of proteins expression exhibited a negative correlation from their gene expression, while several of the remaining were only moderately correlated. Our data complement the vast information obtained elsewhere by transcriptomic analysis of the respective genes and gene products, potentially assisting in harmonizing proteomic with NGS outputs.