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Transcription profiling by array of human chromophobe renal cell carcinoma and oncocytoma

ABSTRACT: This study aims to compare gene expression profiles of chromophobe renal cell carcinoma (RCC) and benign oncocytoma, aiming at identifying differentially expressed genes. Experiment Overall Design: Nine cases each of chromophobe RCC and oncocytoma were analyzed by oligonucleotide microarray. Candidate genes that showed consistent differential expression were validated by RT-PCR using 25 fresh-frozen and 15 formalin-fixed paraffin-embedded tumor samples. Immunohistochemical analysis was also performed for two selected gene products, Claudin 8 and MAL2.

ORGANISM(S): Homo sapiens

SUBMITTER: Piali Mukherjee

PROVIDER: E-GEOD-12090 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genes.

Rohan Stephen S Tu Jiangling J JJ Kao Jean J Mukherjee Piali P Campagne Fabien F Zhou Xi K XK Hyjek Elizabeth E Alonso Miguel A MA Chen Yao-Tseng YT

Clinical cancer research : an official journal of the American Association for Cancer Research 20061201 23

<h4>Purpose</h4>To compare gene expression profiles of chromophobe renal cell carcinoma (RCC) and benign oncocytoma, aiming at identifying differentially expressed genes.<h4>Experimental design</h4>Nine cases each of chromophobe RCC and oncocytoma were analyzed by oligonucleotide microarray. Candidate genes that showed consistent differential expression were validated by reverse transcription-PCR using 25 fresh-frozen and 15 formalin-fixed, paraffin-embedded tumor samples. Immunohistochemical an ...[more]

PMID: 17145811

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microRNA profiling in renal cell carcinoma subtypes

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Gene expression discriminates chromophobe renal cell carcinoma and oncocytoma

Project description:[original title] Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma. Background : Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities. While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity. The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC. Methods : Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n=15) and oncocytoma specimens (n=15). Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes. Immunohistochemical validation was performed in an independent set of tumors. Results : A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel immunohistochemical markers effectively discriminating the two pathologic entities. Conclusion : Gene expression profiles and pathway analysis effectively distinguish chRCC from oncocytoma. We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability. We have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma.

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2010-07-08 | E-GEOD-19982 | biostudies-arrayexpress

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Renal Cell Neoplasms Contain Shared Tumor Type-Specific Copy Number Variations

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Microarray analaysis of adult and childhood renal tumors.

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Homo sapiens

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| PRJNA120139 | ENA