Expression data from ccRCC specimens
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Kentaro Jingushi
PROVIDER: E-GEOD-55138 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To identify a therapeutic candidate target molecule for ccRCC, we analyzed the microRNA (miRNA) expression signatures in ccRCC clinical specimens.
2014-02-20 | GSE55138 | GEO
Project description:We aimed to assess differences in miRNA expression profiles in transcriptomic molecular subtypes of ccRCC (Beuselinck et al, Clinical Cancer Research 2015) and to correlate miRNAs with overal survival since diagnosis of ccRCC. Sequencing was done for 129 primary ccRCC (formalin-fixed paraffin-embedded surgical resection specimens, previously untreated) and 16 normal kidney specimens. Normal kidney was obtained from the nephrectomy specimens at time of ccRCC removal, in tissue blocks containing only normal kidney (so nót the normal kidney immediately adjacent to ccRCC). The samples were sequenced in 2 major batches (2014 and 2017).
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Project description:This SuperSeries is composed of the following subset Series: GSE34979: Array-based CGH analysis of ccRCC derived cell lines GSE34981: miRNA transcript levels in ccRCC-derived cell lines and proximal tubular epithelial cell samples Refer to individual Series
2012-11-01 | E-GEOD-34985 | biostudies-arrayexpress
Project description:Metastatic clear cell renal cell carcinoma (ccRCC) has a poor prognosis and unpredictable course and there are no molecular markers that reliably predict ccRCC metastasis. In this study, specimens from 84 patients with ccRCC were directly cultured in vitro. The primary cultures from 38 of 94 specimens contained more than 90% tumor cells at 4th passages. After identified by immunostaining, the primary cultures of metastatic- and nonmetastatic ccRCC specimens from the age-, gender-matched patients were subjected to cDNA microrray assays. A total of 842 differentially expressed genes with FDR (false discovery rate) = 4.79% were identified by using SAM (Significance Analysis of Microarray) software. Pathway enrichment and co-occurrence with “cancer”, “metastasis” and “invasion” in the literature annotations enriched the functions of the 842 genes and indicated the reliability of our microarray assays. Novel genes associated with metastasis were selected based on intra-molecular interaction between 205 differentially expressed genes co-occurred with “metastasis” and those not appeared with “metastasis” on Medline, as well as co-expression analysis between 205 differentially expressed genes co-occurred with “metastasis” and those not appeared on Medline in 12 microarray data. FSTL1, AV722783, SLC15A1, DDX17, ORC2L and PKMYT1 were proved to be potential ccRCC metastasis-associated novel genes, based on its expression patterns in the cultures and tumor tissues. Interestingly, the up-regulated genes (CAV1, PKMYT1 and ORC2L) were up-regulated and the down-regulated genes (FSTL1, GSTM3, CYR61, SLC15A1 and AV722783) were down-regulated, in the primary ccRCC specimens as compared with its adjacent normal kidney in 37 patients (determined by semi-quantitative RT-PCR). This study provides potential biomarkers and novel molecular targets for the early diagnosis and treatment of ccRCC metastasis. Keywords: Homo sapiens Because of limited cell number of primary cultures, total RNA of the primary cultures from 2 age and gender matched patients was pooled for each microarray assay. Each assay was technically repeated once. Cy3-labeled 1st cDNA synthesized from total RNA of the metastatic ccRCC pool was mixed with Cy5-labeled 1st cDNA synthesized from total RNA of the non-metastatic ccRCC pool, and hybridized to 16K cDNA chips (GEO Platform ID: GPL6259; SBC-R-HC-100-22, National Engineering Center for Biochip, Shanghai, China) that included 14784 unigenes, 241 negative controls and 527 positive controls. In our study we used a co-expression analysis for the relationship between genes; three gastric cancer Samples were only introduced to this analysis methods.
2008-08-27 | E-GEOD-11072 | biostudies-arrayexpress
Project description:Metastatic clear cell renal cell carcinoma (ccRCC) has a poor prognosis and unpredictable course and there are no molecular markers that reliably predict ccRCC metastasis. In this study, specimens from 84 patients with ccRCC were directly cultured in vitro. The primary cultures from 38 of 94 specimens contained more than 90% tumor cells at 4th passages. After identified by immunostaining, the primary cultures of metastatic- and nonmetastatic ccRCC specimens from the age-, gender-matched patients were subjected to cDNA microrray assays. A total of 842 differentially expressed genes with FDR (false discovery rate) = 4.79% were identified by using SAM (Significance Analysis of Microarray) software. Pathway enrichment and co-occurrence with “cancer”, “metastasis” and “invasion” in the literature annotations enriched the functions of the 842 genes and indicated the reliability of our microarray assays. Novel genes associated with metastasis were selected based on intra-molecular interaction between 205 differentially expressed genes co-occurred with “metastasis” and those not appeared with “metastasis” on Medline, as well as co-expression analysis between 205 differentially expressed genes co-occurred with “metastasis” and those not appeared on Medline in 12 microarray data. FSTL1, AV722783, SLC15A1, DDX17, ORC2L and PKMYT1 were proved to be potential ccRCC metastasis-associated novel genes, based on its expression patterns in the cultures and tumor tissues. Interestingly, the up-regulated genes (CAV1, PKMYT1 and ORC2L) were up-regulated and the down-regulated genes (FSTL1, GSTM3, CYR61, SLC15A1 and AV722783) were down-regulated, in the primary ccRCC specimens as compared with its adjacent normal kidney in 37 patients (determined by semi-quantitative RT-PCR). This study provides potential biomarkers and novel molecular targets for the early diagnosis and treatment of ccRCC metastasis. Keywords: Homo sapiens
2008-08-27 | GSE11072 | GEO
Project description:Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal cancer. Identification of ccRCC likely to progress, despite an apparent low risk at the time of surgery, represents a key clinical issue. Methods: From a cohort of adult ccRCC patients (n=443), we selected low-risk tumors progressing within a 5-years average follow-up (progressors: P, n=8) and non-progressing (NP) tumors (n=16). Transcriptome sequencing, miRNA sequencing and proteomics were performed on tissues obtained at surgery. Our work suggests that LXR, FXR and macrophage activation pathways could be critically involved in the inhibition of the progression of low-risk ccRCC. Furthermore, a 10-component classifier could support an early identification of apparently low-risk ccRCC patients.
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Project description:Patients with polycystic kidney disease (PKD) encounter a high risk of clear cell renal cell carcinoma (ccRCC), a malignant tumor with dysregulated lipid metabolism. SET domain–containing 2 (SETD2) has been identified as an important tumor suppressor gene in ccRCC. However, the role of SETD2 in tumorigenesis during the transition from PKD to ccRCC remains largely unexplored. Herein, we performed metabolomics, lipidomics, transcriptomics and proteomics with SETD2 loss induced PKD-ccRCC transition mouse model. To characterize biological responses triggered by SETD2 deletion during PKD-ccRCC transition at the protein level, we conducted global proteomics studies.
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Project description:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues.
2015-10-26 | GSE61441 | GEO