Original articleDifferential gene expression identifies subgroups of renal cell carcinoma
Section snippets
Tissue samples
Tissue from 16 ccRCC samples, 21 cases of normal kidney, and 518 samples from 16 different types of tissues, including 22 normal adipose tissue; 25 reparative bone samples from degenerative joint disease, 5 samples of normal bone, and 25 normal cervix; 41 normal colon; 22 normal liver; 36 normal lung; 20 normal skeletal muscle; 90 normal myometrium; 59 normal ovary; 12 normal skin; 28 normal small intestine; 7 normal stomach, 63 normal thymus; 59 tonsils with lymphoid hyperplasia; and 4 thyroid
Results
Quantification of gene expression using the Affymetrix GeneChip U_133 microarray set was performed on all samples. About 6800 of the ∼40,000 gene fragments examined were present in all 16 samples in the set of ccRCC. This number did not vary greatly if 6 or more samples of the set were included in the analysis (Fig 1, top panel). In an attempt to identify genes that are overexpressed in ccRCC compared with other tissues, a fold change analysis was performed comparing the set of ccRCC samples
Discussion
In this study, the authors examined the expression of ∼40,000 genes/ESTs in ccRCC and a variety of other tissues. The results confirmed and extended the findings of an earlier report23 with a larger number of ccRCC and normal tissue samples and the newer Affymetrix U_133 microarray set. Many genes were found to be differentially expressed in ccRCC compared with normal kidney. As the most promising potential targets of therapy would be expected to be overexpressed in ccRCC compared with not only
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2011, European UrologyCitation Excerpt :Two other studies were also predominantly geared towards identifying the inherent subgroups and underlying biologic differences of ccRCC [51,52], and they too observed two types of ccRCC. In one study, RCC with more highly overexpressed metabolic genes or more highly overexpressed extracellular matrix/cell adhesion genes was described [52]. In a bioinformatic technique called unsupervised consensus, clustering was used on 48 tumours to identify two subtypes of ccRCC, ccA and ccB, distinguished by <120 probes [51].
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Supported in part by the Clinical Cooperation Group, “Immunotherapy of Urological Tumors” and the “Deutsche Krebshilfe” (106141).