Project description:Label-free proteomics data matched tumor and normal-adjacent tissues from 84 patients with stage I to IV ccRCC, by using pooled samples.
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.
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. Bisulphite converted DNA from the 92 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip v1.2
Project description:Downregulation is a common feature of tumor suppressor gene (TSG), which can be caused by allele deletion, promoter hypermethylation, histone deacetylation and posttranscriptional silencing by microRNA. Therefore, comparison of expression profiles by cDNA microarray between tumor and non-tumor tissues and characterization of downregulated genes in tumor specimens is a useful strategy to identify TSGs. To identify deregulated genes during ESCC development, Affemetrix cDNA microarray was applied to compare differentially expressed genes between 4 pairs of ESCC tumors and corresponding adjacent non-tumor tissues (#301, #327, #351 and #363), and one pair of esophageal dysplasia tissue and adjacent normal tissue (#314).
Project description:We performed microarray expression profiling to analyze the differentially expressed genes between 19 human glioma tissues and corresponding adjacent non-tumor tissues.
Project description:We performed microarray expression profiling to analyze the differentially expressed genes between 5 human glioma tissues and corresponding adjacent non-tumor tissues.
Project description:To identify aberrantly expressed long intergenic noncoding RNAs (lincRNAs) in bladder cancer tissues compared with normal adjacent tissues, we have employed microarray expression profiling as a discovery platform to identify lincRNAs that may play important roles in bladder cancer origin and progression. Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were obtained during surgical resection, and total RNA was extracted for microarray analysis. Expression of six mRNAs and lincRNAs (E2F1, CCNE2, CCNB1, lincRNA:chr1:205404014-205407007, lincRNA:chr7:130723313-130727663, lincRNA:chr4:15669186-15683175) from this signature was quantified in the same RNA samples by real-time PCR, confirming good quality of the microarray analysis. Data in the matrix are log2 transformed. Three pairs of fresh frozen bladder cancer tissues and corresponding normal adjacent tissues were used in the microarray analysis.
Project description:Clear cell Renal Cell Carcinoma (ccRCC) is among the 10 most common cancers and causes more than 140,000 deaths worldwide every year. In order to elucidate the underlying molecular mechanisms orchestrated by phosphorylation modifications, we performed a comprehensive quantitative phosphoproteomics characterization of ccRCC tumor and normal adjacent tissues. Here, we identified 16,253 phosphopeptides, of which more than 9,000 were quantified. Our in-depth analysis revealed 1,336 phosphopeptides to be differentially regulated between tumor and normal tissues. Moreover, our data reveals that significantly up-regulated phosphoproteins are associated with cytoskeletal re-organization which suggests migratory and invasive behavior of renal tumors. This is supported by a pronounced mesenchymal profile of ccRCC phosphorylation events. Our rigorous characterization of the renal phosphoproteome also revealed that both EGFR and VEGFR are the most important mediators of phospho signaling in RCC pathogenesis. Furthermore, we determined the kinases PAK2, CDK1, Erk1 and Erk2 to be master kinases that are responsible for phosphorylations of many substrates associated with cell proliferation, inflammation and migration. These master kinases are targetable by inhibitory FDA-approved drugs such as fostamatinib and minocycline, which can serve as novel therapeutic agents for ccRCC treatment.
Project description:A multi-step approach combining microarray profile and bioinformatics analysis was adopted to identify the CRC specific miRNA-mRNA regulatory network. First, differentially expressed miRNAs and mRNAs were found out in CRC samples compared with normal epithelial tissues by miRNA and mRNA microarray respectively. Secondly the target mRNAs of dysregualted miRNA were identified by a combination of Pearson correlation coefficient between the expression level of miRNAs and mRNAs and online miRNA target predicting databases. Thirdly, the biological pathways which the miRNA-mRNA pairs involved in were identified by DAVID. Finally, some of the dysregualted miRNAs and mRNAs were validated by qRT-PCR RNA isolated from 8 colorectal cancer tissues and their corresponding adjacent normal tissues were analyzed.
