// Vanessa Drendel 1 , Bianca Heckelmann 1, * , Chia-Yi Chen 2, * , Juliane Weisser 2, 3, * , Guadalupe Espadas 4, 5 , Christoph Schell 1 , Eduard Sabido 4, 5 , Martin Werner 1, 6 , Cordula A. Jilg 6, 7 and Oliver Schilling 2, 6, 8 1 Department of Pathology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany 2 Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany 3 Present Address: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria 4 Proteomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain 5 Universitat Pompeu Fabra, Barcelona, Spain 6 German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany 7 Department of Urology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany 8 BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany * These authors have contributed equally to this work Correspondence to: Cordula A. Jilg, email: Cordula.Jilg@uniklinik-freiburg.de Oliver Schilling, email: oliver.schilling@mol-med.uni-freiburg.de Keywords: von Hippel-Lindau disease; clear cell renal cell carcinoma; formalin-fixation; paraffin embedment; proteomics Received: June 08, 2017 Accepted: August 08, 2017 Published: October 19, 2017 ABSTRACT Patients of the von Hippel-Lindau (VHL) disease frequently develop clear cell renal cell carcinoma (ccRCC). Using archived, formalin-fixed, paraffin-embedded (FFPE) samples, we sought to determine global proteome alterations that distinguish ccRCC tissue from adjacent, non-malignant kidney tissue in VHL-patients. Our quantitative proteomic analysis clearly discriminated tumor and non-malignant tissue. Significantly dysregulated proteins were distinguished using the linear models for microarray data algorithm. In the ccRCC tissue, we noticed a predominant under-representation of proteins involved in the tricarboxylic acid cycle and an increase in proteins involved in glycolysis. This profile possibly represents a proteomic fingerprint of the “Warburg effect”, which is a molecular hallmark of ccRCC. Furthermore, we observed an increase in proteins involved in extracellular matrix organization. We also noticed differential expression of many exoproteases in the ccRCC tissue. Of particular note were opposing alterations of Xaa-Pro Aminopeptidases-1 and -2 (XPNPEP-1 and -2): a strong decrease of XPNPEP-2 in ccRCC was accompanied by abundant presence of the related protease XPNPEP-1. In both cases, we corroborated the proteomic results by immunohistochemical analysis of ccRCC and adjacent, non-malignant kidney tissue of VHL patients. To functionally investigate the role of XPNPEP-1 in ccRCC, we performed small-hairpin RNA mediated XPNPEP-1 expression silencing in 786-O ccRCC cells harboring a mutated VHL gene. We found that XPNPEP-1 expression dampens cellular proliferation and migration. These results suggest that XPNPEP-1 is likely an anti-target in ccRCC. Methodologically, our work further validates the robustness of using FFPE material for quantitative proteomics.