Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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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Publications

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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Project description:Copy number variant (CNV) analysis was performed on renal cell carcinoma (RCC) specimens (chromophobe, clear cell, oncocytoma, papillary type 1, papillary type 2) using high resolution arrays (1.85 million probes). RCC samples exhibited diverse genomic changes within and across tumor types ranging from 106 CNV segments in a clear cell specimen to 2238 CNV segments in a papillary type 2 specimen. Despite the genomic heterogeneity, distinct CNV segments were common within each of 4 tumor classifications: chromophobe (7 segments), clear cell (3 segments), oncocytoma (9 segments), and papillary type 2 (2 segments). Shared segments ranged from a 6.1 Kb deletion among oncocytomas to a 208.3 Kb deletion common to chromophobes. Among common tumor type-specific variations, chromophobe, clear cell and oncocytomas comprised exclusively non-coding DNA. No CNV regions were common to papillary type 1 specimens although there were 12 amplifications and 12 deletions in 5 of 6 samples. Three microRNAs and 12 mRNA genes had M-bM-^IM-% 98% of their coding region contained within CNV regions including multiple gene families (chromophobe: amylase 1A, 1B, 1C; oncocytoma: general transcription factor 2H2, 2B, 2C, 2D). Gene deletions involved in histone modification and chromatin remodeling affected individual subtypes (clear cell: SFMBT, SETD2; papillary type 2: BAZ1A) as well as the collective RCC group (KDM4C). The genomic amplifications/deletions identified in each renal tumor type represent potential diagnostic and/or prognostic biomarkers. Tissue samples were obtained from the University of Pittsburgh Health Sciences Tissue Bank (HSTB) using an honest broker system and according to IRB approved protocol #970480. Samples were acquired as surgical specimens, flash-frozen in a 1.8 ml cryotube (NalgeNunc, Inc., Rochester, NY) followed by immediate storage at -80C. Each tumor sample (n=27) was classified into one of 5 renal cancer subtypes (chromophobe: n=5, clear cell: n=5, oncocytoma: n=5, papillary type 1: n=6, papillary type 2: n=6) by consensus evaluation of correlative hematoxylin and eosin stained slides performed independently by 3 anatomical pathologists. The three pathologists also confirmed the absence of pathological features in adjacent normal renal samples (n=9) and this normal reference group was expanded by inclusion of 14 normal thyroid samples and 8 normal lung specimens. DNA from each of these specimens was analyzed using genotyping microarrays (SNP 6.0, Affymetrix, Sunnyvale, CA).

Dataset Information

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

Publications

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

Similar Datasets

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