Kidney protein profiling of Wilms' tumor patients by analysis of formalin-fixed paraffin-embedded tissue samples

Wilms' tumor (nephroblastoma, WT) is the most frequent renal cancer in children. However, molecular details leading to WT have not been characterized sufficiently yet. Proteomic studies might provide new insights but are hampered by limited availability of fresh frozen tissue specimen. Therefore, we tested formalin-fixed paraffin-embedded (FFPE) tissue sections routinely collected for pathological inspection for their use in in-depth-proteomic analyses of WT samples in comparison to fresh frozen specimen. The overlap of the proteins identified was over 65%. Thus we used FFPE material from 7 patients for tandem mass spectrometry based comparison of the proteomes of WT and healthy renal tissues. We detected 262 proteins, which were differentially expressed in tumor compared to healthy renal tissue. The majority of these proteins displayed lower levels in the tumor tissue and only 30% higher levels. For selected candidates data were confirmed by immunohistochemical staining. Correlation analysis of blastemal proportions in WT and protein intensities revealed candidates for tumor stratification. This proof of principle proteomic study of FFPE tissue sections from WT patients demonstrates that these archived tissues constitute a valuable resource for larger in-depth proteomic studies to identify markers to follow chemotherapy efficiency or for stratification of tumor subtypes. •Comparative protein profiling of kidney from fresh frozen and FFPE specimen•FFPE from sample collections can be used for the study of rare diseases.•Wilms' tumor tissue displays increased levels of acute phase response proteins.•Biomarker candidates were identified for stratification of Wilms' tumor.•Protein levels of SH3BGRL reflect abundance of blastemal components in WT.