Gene expression profile of cancerous and non-cancerous renal tissues
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PROVIDER: PRJNA714233 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation profile of cancerous and non-cancerous renal tissues
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Project description:Clear cell renal cell carcinoma (ccRCC), is the most common subtype of kidney tumors and characterised by the highest mortality rates among the genitourinary cancers. The currently used models for predicting patient outcome, are based on clinicopathological features only, however patients with similar measures can still have divergent outcomes. This study aimed at identification of novel prognostic DNA methylation biomarkers to aid in predicting patient survival. As DNA methylation in the most cases is related to alteration of gene expression, firstly, SurePrint G3 Human GE 8×60K Microarrays were used for gene expression profiling in 4 ccRCC tissues and paired non-cancerous renal tissue (NRT) samples. The DNA methylation status of four down-regulated genes were evaluated in 123 ccRCC and 45 NRT samples by means of methylation specific PCR (MSP). Microarray-based transcriptome comparison of 4 ccRCC and 4 NRT samples identified 3942 genes, that were significantly deregulated (P < 0.050) with absolute fold change (FC) value of ≥2. A half of these genes (N = 1958) were down-regulated and four of such genes with moderate-to-high alteration were selected for the further DNA methylation analysis. DNA hypermethylation of all selected genes were cancer specific (P<0.050) with the frequency in tumour tissues ranging from 18 to 42%. The methylated status of at lest one gene showed significant associations with larger tumor size, higher Fuhrman and WHO/ISUP grades as well as the presence of tumor intravascular invasion and necrosis. Moreover, the methylated status of the panel of tree genes was highly predictive for poorer overall survival and outperformed the prognostic value of tumor stage and tumor necrosis. In conclusion, the three-gene DNA methylation biomarker panel predicts outcome of patients with ccRCC and might be used to improve current prognostic models.
2021-03-14 | GSE168845 | GEO
Project description:Renal cell carcinoma (RCC), particularly clear cell RCC (ccRCC), is the most common type of kidney tumors characterized by the highest mortality rate of the genitourinary cancers. Lack of symptoms leads to late detection of the disease using conventional imagining procedures. There is an urgent need for new diagnostic biomarkers with the potential for early detection and prediction of high risk of progression. In the present study, based on microarray profiling of DNA methylation in 11 pairs of ccRCC and noncancerous renal tissues (NRT), the methylation at regulatory regions of six putative ccRCC biomarkers was further analyzed in 123 ccRCC and 45 NRT samples by means of methylation specific PCR (MSP). Thereafter, the quantitative MSP was applied for the methylation analysis in the urine samples of 123 ccRCC patients and 93 asymptomatic controls (ASC). The comparison of ccRCC and NRT samples revealed significant methylation differences in 1319 genes, of which 191 were hypermethylated and 1128 were hypomethylated. DNA methylation of selected genes were validated by means of MSP and significantly higher methylation frequencies for all genes was found in ccRCC tissues compared to NRT (33-60% vs. 0-11%). Methylated status of at least one gene was significantly related with various adverse clinical-pathological parameters of the patients, including larger tumor size, higher tumor pathological stage, grade, intravascular and fat invasion as welll as tumor necrosis. The multivariate Cox regression model revealed the methylation in a panel of selected three genes as independent prognostic biomarker of ccRCC. Moreover, five genes were characterised by higher methylation intensity in the urine samples of ccRCC patients, as compared to ASC, and various combination of these biomarkers revealed moderate-to-high sensitivity and specificity values for the diagnosis of ccRCC.
2021-02-15 | GSE166734 | GEO
Project description:To identify the the functional roles and the pathophysiological contributions of the mRNA m6A modification in human colorectal carcinogenesis, we analysed the profile the landscape of the mRNA m6A modification in colorectal cancer tissues and the corresponding non-cancerous tissues.
2024-05-01 | GSE247632 | GEO
Project description:To identifythe the functional roles of circRNAs in human colorectal cancer, we analysed the differenial expression of circRNAs in 5 colorectal cancer tissues and the corresponding non-cancerous tissues. We used microarrays to detail the global programme of circRNA expression in human colorectal cancer tissues and correponding non-cancerous tissues.
2020-01-03 | GSE142837 | GEO
Project description:To identifythe the functional roles and the pathophysiological contributions of coding genes and noncoding RNAs in human hepatic carcinogenesis, we analysed the differenial expression of genes and noncoding RNAs in hepatocellular carcinoma tissues and the corresponding non-cancerous tissues. We used microarrays to detail the global programme of gene expression in human hepatocellular carcinomas and correponding non-cancerous tissues.
2017-09-14 | GSE84402 | GEO
Project description:We investigated the involvement of microRNAs (miRNAs) in gastric cancers. MiRNA expression was profiled from 40 cancerous and 40 non-cancerous tissues obtained from the National Cancer Centre, Singapore, and Singhealth Tissue Repository, Singapore. We identified 80 differentially expressed miRNAs in tumors compared with normal tissues. Among these miRNAs, we identified hsa-mir-486-5p (mir-486) as a significantly downregulated miRNA in GC. Subsequent functional characterization revealed that mir-486 playing a tumor suppressor role. We also observed frequent genomic deletion of mir-486 in 20-30% of GCs. To our knowledge, mir-486 represents one of the first tumor suppressor miRNAs in GC inactivated through genomic deletion. MiRNA expression was profiled on Agilent Human miRNA Microarrays (V2) representing 723 human and 76 human viral miRNAs in 40 normal and 40 cancerous gastric tissues.
2011-08-01 | E-GEOD-23739 | biostudies-arrayexpress
Project description:We investigated the involvement of microRNAs (miRNAs) in gastric cancers. MiRNA expression was profiled from 40 cancerous and 40 non-cancerous tissues obtained from the National Cancer Centre, Singapore, and Singhealth Tissue Repository, Singapore. We identified 80 differentially expressed miRNAs in tumors compared with normal tissues. Among these miRNAs, we identified hsa-mir-486-5p (mir-486) as a significantly downregulated miRNA in GC. Subsequent functional characterization revealed that mir-486 playing a tumor suppressor role. We also observed frequent genomic deletion of mir-486 in 20-30% of GCs. To our knowledge, mir-486 represents one of the first tumor suppressor miRNAs in GC inactivated through genomic deletion.
2011-08-01 | GSE23739 | GEO
Project description:To identifythe the functional roles and the pathophysiological contributions of coding genes and noncoding RNAs in human lung squamous cell carcinoma, we analysed the differenial expression of genes and noncoding RNAs in 5 lung squamous cell carcinoma tissues and the corresponding non-cancerous tissues. We used microarrays to detail the global programme of gene expression in human lung squamous cell carcinoma and correponding non-cancerous tissues.
2019-06-20 | GSE126533 | GEO
Project description:Expression data from human colorectal cancer tissues and the corresponding non-cancerous tissues
| PRJNA1026532 | ENA