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E-GEOD-30491 - The use of the glycoarray chip to investigate VHL-dependent protein glycosylation changes in renal cancer Renal cell carcinoma (RCC)

Status
Released on 8 July 2011, last updated on 19 July 2011
Organism
Homo sapiens
Samples (18)
Array (1)
Protocols (6)
Description
Renal cell carcinoma (RCC) accounts for around 2-3% of all adult neoplasms and its incidence is increasing. RCC is largely resistant to standard cancer treatment regimens including chemotherapy and radiation therapy, whilst immunotherapy modestly provides benefit to only a small subset of patients. As a result, prognosis for RCC patients with advanced disease is very poor, with a 5-year survival rate of less than 10%. An early event in the development of familial and up to 90% of sporadic RCC is the loss and/or mutation/methylation of the von Hippel-Lindau (VHL) tumour suppressor gene. The tumor suppressor role of VHL relies primarily on its ability to target members of the hypoxia-inducible factors (HIF) for proteosomal degradation, however it has also been implicated in other biological processes linked to oncogenesis, such as the extracellular matrix assembly and the regulation of actin cytoskeleton, that are less clearly defined. Targeting the VHL/HIF pathway may dramatically improve RCC treatment, as demonstrated by an increasing number of novel agents that have shown promising activity in recent clinical trials6. Identification of other possible proteins regulated by VHL that may be involved in tumour suppression will improve our understanding of RCC pathobiology and also provide novel disease biomarkers or potential targets. A number of our studies have identified changes in glycosylation in RCC, at least some of which appear to alter as a result of changes in the VHL gene. Lectin binding immunohistochemistry shows altered reactivity with a number of lectins in the malignant tissue compared with the normal tissue. Comparison of plasma membrane protein enriched fractions from human RCC cells stably transfected with control vector or with wild type VHL led to the identification of VHL-associated changes in the forms of several plasma membrane proteins which we beelive to be due to differential glycosylation. For one of these we have now shown that it is differentially O-glycosylated and this has been confimed in cell lysates and patient tissue by Western blotting. A parallel approach using 2D-PAGE analysis of RCC cell line conditioned medium (CM) has also identified a tumour-specific glycoform of a secretory protein that appears to undergo differential N-glycosylation in RCC and this has been confirmed in analysis of some matched primary tumour/normal pairs. These findings are potentially very interesting, as these proteins could serve as prognostic or diagnostic markers, or even as targets for improving RCC therapy. We are therefore keen to explore the underlying mechanism of differential glycosylation that may be associated to VHL dependent gene expression. As there are an immense number of enzymes involved in the conjugation of N- and particularly O-glycans to proteins, the glyco-microarray is an ideal tool to elucidate this further. For chip analyses we have three cell lines generated from human RCC cells (RCC4, 786-0 and UMRC2) that have been stably transfected with control vector or with wild type VHL i.e. 6 cell lines in total. Whole RNA was extracted from each cell line in 3 replicates per line.
Experiment type
transcription profiling by array 
Contacts
Steven Head <shead@scripps.edu>, Roz Banks, Steven R Head
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-30491.idf.txt
Sample and data relationshipE-GEOD-30491.sdrf.txt
Raw data (1)E-GEOD-30491.raw.1.zip
Processed data (1)E-GEOD-30491.processed.1.zip
Array designA-GEOD-11095.adf.txt
R ExpressionSetE-GEOD-30491.eSet.r
Links