Integration of genome wide molecular analysis and subcellular proteomics for renal cell carcinoma biomarker identification

Clear cell renal carcinomas (cRCC) is representing about 3% of all kidney cancers. No biomarkers for early diagnosis of cRCC in asymptomatic patients or for post-surgery monitoring are yet available. In the context of an italian research project aimed to the discovery of new markers for cRCC, the identification of differentially up-regulated genes associated to regions of increased DNA copy number was carried out, by genome-wide SNP copy number analysis (DNA) and transcriptomic profiling (RNA) using GeneChip Affymetrix technology on 30 cRCC patients tissues. In order to confirm the differential expression at protein level, methods of protein enrichment were developed, preparing subcellular fractions from tumor or cortex tissues from the same cRCC patients. We focused our study on a subset of membrane-associated proteins such as RGS1, CXCR4, CAV1, CAIX, located in the chromosome cytobands 1p31, 2p21, 7q31.1, 9p13 respectively, that were further investigated using a subcellular comparative proteomic approach. Results obtained by SDS-PAGE and western blotting with specific antibodies show a good concordance between genomic profling, gene expression and protein levels. Therefore, integration of DNA/RNA genome wide analysis with sucellular protein enrichment approach may provide the discovery of candidate tumour markers for cRCC.