Dataset Information

Proteomic analysis of clear cell renal cell carcinoma tissue versus matched normal kidney tissue

ABSTRACT: We analyzed 84 tumor/normal pairs (177 total) using standard shotgun proteomic techniques in order to characterize the molecular landscape of clear cell renal cell carcinoma (ccRCC) and interrogated changes in protein abundance and biological pathways with ccRCC grade. These tissues were distributed across stage 1 (n = 34), 2 (n = 40), 3 (n = 42), and 4 (n = 52), with 9 pairs also including samples from metastasized tumor. These data can be (and were) combined with a previously published transcriptomic data set from the same sample cohort (NCBI GEO: GSE53757).

INSTRUMENT(S): LTQ

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

DISEASE(S): Renal Clear Cell Carcinoma

SUBMITTER: Benjamin Neely

LAB HEAD: Richard R. Drake

PROVIDER: PXD003271 | Pride | 2016-04-18

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	1246A-Mar2011NewSamples.raw	Raw
	1246B-Mar2011NewSamples.raw	Raw
	1246C-Mar2011NewSamples.raw	Raw
	1272A-Mar2011NewSamples.raw	Raw
	1272B-Mar2011NewSamples.raw	Raw

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Publications

Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma.

Neely Benjamin A BA Wilkins Christopher E CE Marlow Laura A LA Malyarenko Dariya D Kim Yunee Y Ignatchenko Alexandr A Sasinowska Heather H Sasinowski Maciek M Nyalwidhe Julius O JO Kislinger Thomas T Copland John A JA Drake Richard R RR

PloS one 20160429 4

Renal cell carcinoma comprises 2 to 3% of malignancies in adults with the most prevalent subtype being clear-cell RCC (ccRCC). This type of cancer is well characterized at the genomic and transcriptomic level and is associated with a loss of VHL that results in stabilization of HIF1. The current study focused on evaluating ccRCC stage dependent changes at the proteome level to provide insight into the molecular pathogenesis of ccRCC progression. To accomplish this, label-free proteomics was used ...[more]

PMID: 27128972

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Project description:Patients with loss-of-function mutations of the von Hippel Lindau gene (“VHL-patients”) often develop clear cell renal cell carcinoma (ccRCC). Using archived, formalin-fixed, paraffin-embedded (FFPE) samples and a cohort of eight cases, 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, yielding comparable proteome profiles for the eight ccRCC cases. Limma statistics was used to identify significantly dysregulated proteins in ccRCC. Functional classification of these proteins highlighted a decrease in 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. 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 a strong increase 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 suppresses cellular proliferation and migration. These results suggest that XPNPEP-1 is rather an anti-target in VHL-driven ccRCC. Generally, we present one of the first proteomic profiling studies of ccRCC in VHL patients, comparing normal and tumor tissue, which are both deficient for the VHL tumor suppressor. Methodologically, our work further validates the robustness of using FFPE material for quantitative proteomics.