Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell Renal Cell Carcinoma
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE47032 | GEO | 2013/09/06
SECONDARY ACCESSION(S): PRJNA203314
REPOSITORIES: GEO
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Project description:In this study we performed a genome wide analysis of the entire complement of mRNAs in clear cell renal cell carcinomas (ccRCC) by means of the Affymetrix Exon Array platform. The analyses were performed both at gene and exon level. Under our parameters over 2,000 genes resulted differentially expressed, and about 250 genes resulted alternative spliced showing differential inclusion of specific cassette exons comparing tumor and non tumoral tissues. 20 total samples were used for exon array analysis: 10 ccRCC tumor sample (T) and their matched non-tumor (NT) kidney tissues samples. All exon array data were analyzed using Partek Genomic Suite 6.4 software (Partek). The robust multi-array average (RMA) algorithm was used for the gene- and exon-level intensity analyses. Data were M-oM-,M-^Altered to consider only those probe sets included in the M-bM-^@M-^\Core Meta-ProbesetM-bM-^@M-^]. Lists of genes and exons with significant variation of the expression levels were generated by using a 0.01 FDR criterion as a significant cutoff. Partek list of significant exon-level probesets (FDR corrected p-value < 0.01) and exon level ANOVA test list were used to create - by an ad hoc Python script - a database of significant probesets from Exon Array experiments. To make more stringent the analysis criteria we excluded from the final exon lists all those cases in which Exon Array revealed a significant change at gene-level. This database we created has been used to explore simple exon skipping events using as reference ASPicDB single exon skipping splicing events after mapping Affymetrix probesets on ASPicDB .gtf files. A single exon from the Partek list was defined significantly skipped only if its adjacent exons were not, by using 0.01 and 0.05 p-value criterions as a significant cutoff for the M-bM-^@M-^\skippedM-bM-^@M-^] and adjacent exons, respectively.
2013-09-06 | E-GEOD-47032 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs), non-coding RNAs regulating gene expression, are frequently aberrantly expressed in human cancers. Next-generation deep sequencing technology enables genome-wide expression profiling of known miRNAs and discovery of novel miRNAs at unprecedented quantitative and qualitative accuracy. Deep sequencing was performed on 22 fresh frozen clear cell renal cell carcinoma (ccRCC), 11 non-tumoral renal cortex (NRC) samples and 2 ccRCC cell lines (n=35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. Those without disease recurrence, with recurrence and with metastatic disease at diagnosis Deep sequencing was performed on 22 fresh frozen clear cell renal cell carcinoma (ccRCC), 11 non-tumoral renal cortex (NRC) samples and 2 ccRCC cell lines (n=35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. Those without disease recurrence, with recurrence and with metastatic disease at diagnosis.
2012-06-21 | E-GEOD-37616 | biostudies-arrayexpress
Project description:To determine the biological mechanisms underlying the oncogenic properties of YAP in ccRCC the human ccRCC cell line MZ1774 was transduced with lentivirus containing a shRNA-cassette targeting YAP-mRNA. Expression profiles of MZ1774 YAP knockdown cells were compared to mock-transduced control cells.
2014-12-23 | GSE50053 | GEO
Project description:To determine the biological mechanisms underlying the oncogenic properties of YAP in ccRCC the human ccRCC cell line MZ1774 was transduced with lentivirus containing a shRNA-cassette targeting YAP-mRNA. Expression profiles of MZ1774 YAP knockdown cells were compared to mock-transduced control cells. Total RNA from MZ1774 cells stably expressing shRNA directed against YAP compared to mock-transduced MZ1174 cells
2014-12-23 | E-GEOD-50053 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs), non-coding RNAs regulating gene expression, are frequently aberrantly expressed in human cancers. Next-generation deep sequencing technology enables genome-wide expression profiling of known miRNAs and discovery of novel miRNAs at unprecedented quantitative and qualitative accuracy. Deep sequencing was performed on 22 fresh frozen clear cell renal cell carcinoma (ccRCC), 11 non-tumoral renal cortex (NRC) samples and 2 ccRCC cell lines (n=35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. Those without disease recurrence, with recurrence and with metastatic disease at diagnosis
2012-06-21 | GSE37616 | GEO
Project description:Most human transcripts are alternatively spliced, and many disease-causing mutations affect RNA splicing. Towards better modeling the sequence determinants of alternative splicing, we measured the splicing patterns of nearly 2 million (M) synthetic mini-genes, which include degenerate subsequences totaling to nearly 100M bases of variation. The massive size of these training data allowed us to improve upon current models of splicing as well as to gain new mechanistic insights. Our results show that a vast majority of hexamer sequence motifs measurably influence splice site selection when positioned within alternative exons, with multiple motifs acting additively rather than cooperatively. Intriguingly, motifs that enhance (suppress) exon inclusion in alternative 5’ splicing also enhance (suppress) exon inclusion in alternative 3’ or cassette exon splicing, suggesting a universal mechanism for alternative exon recognition. Finally, our empirically trained models are highly predictive of the effects of naturally occurring variants on alternative splicing in vivo.
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Project description:Massively parallel exon inclusion assay
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Project description:Alternative splicing of SUZ12 exon 4 is predicted to generate two alternative isoforms differing by the inclusion or exclusion of 69 nucleotides in exon 4, which we named SUZ12-long (SUZ12-L) and SUZ12-short (SUZ12-S) respectively. At the protein level SUZ12 exon 4 encodes 23 amino acids (aa 129–152 in SUZ12-L) that partially overlap with the WD-binding domain 1 (WDB1, 110–145). To detect the existance of SUZ12-S at the protein levels we performed SUZ12 immunoprecipitation coupled with mass spectrometry (IP-MS) in the WT and ∆ex4 clones to identify SUZ12-S unique peptides. We identified a SUZ12-S specific peptide in both WT #2 and ∆ex4 #1. These observations were confirmed by SUZ12 IP followed by Western blot (WB) (size shift).
2024-03-18 | PXD046742 | Pride
Project description:Clear cell renal cell carcinomas (ccRCC) are characterized by arm-wide chromosomal alterations. Loss at 14q is associated with disease aggressiveness in ccRCC, which responds poorly to chemotherapeutics. The 14q locus contains one of the largest miRNA clusters in the human genome; however, little is known about the contribution of these miRNAs to ccRCC pathogenesis. In this regard, we investigated the expression pattern of selected miRNAs at the 14q32 locus in TCGA kidney tumors and in ccRCC cell lines. We validated that the miRNA cluster is downregulated in ccRCC (and cell lines) as well as in papillary kidney tumors relative to normal kidney tissues and primary renal proximal tubule epithelial (RPTEC) cells. We demonstrated that agents modulating expression of DNMT1 (e.g., 5-Aza-deoxycytidine) could modulate miRNA expression in ccRCC cell lines. Lysophosphatidic acid (LPA, a Lysophospholipid mediator elevated in ccRCC) not only increased labile iron content but also modulated expression of 14q32 miRNAs. Through an overexpression approach targeting a subset of 14q32 miRNAs (specifically at subcluster A: miR-431, miR-432, miR-127, and miR-433) in 769-P cells, we uncovered changes in cellular viability and claudin-1, a tight junction marker. A global proteomic approach was implemented using these miRNA overexpressing cell lines which uncovered ATXN2 as a highly downregulated target, which has a role in chronic kidney disease pathogenesis. Collectively, these findings support a contribution of miRNAs at 14q32 in ccRCC pathogenesis.
2023-05-10 | PXD036428 | Pride
Project description:MicroRNAs (miRNAs) are short single stranded RNAs that are associated with gene regulation at the transcriptional and translational level. Changes in their expression were found in a variety of human cancers. Because of the lack of corresponding data in clear renal cell carcinoma (ccRCC) we have performed genome-wide expression profiling of miRNAs using microarray analysis and quantification of specific miRNAs by TaqMan real-time RT-PCR. Matched malignant and non-malignant tissue samples from two independent 12 ccRCC sets were profiled. The microassay-based experiments identified 14 overexpressed and 20 downregultaed miRNAs in malignant samples. Expression in ccRCC tissue samples compared to matched non-malignant samples measured by RT-PCR was increased by 2.7 to 28fold for the hsa-mir-16, -452, -224, -155, and -210, but decreased by 6.2 to 96fold for hsa-mir-200b, -363, , -429, -200c, -514, and -141. No significant associations between these differentially expressed miRNAs and the clinico-pathological factors tumor stage, grade, and survival rate were found. Nevertheless, malignant and non-malignant tissue could clearly be differentiated by their miRNA profile . A combination of miR-141 and miR-155 resulted in a 96% overall correct classification of samples. The presented differential miRNA pattern provides a solid basis for further validation including functional studies. The study was performed with two independent sample sets. For each set 12 kidney tissue sample pairs were derived from adult patients undergoing radical nephrectomy at the University Hospital Charité. All tumor types were clear renal cell carcinoma. Tumor classification and stage were established according to the 2002 TNM System and the 2004 WHO Classification. Matched malignant (#NC (e.g. 2NC)) and non-malignant (#NN (e.g. 1NN)) tissue samples from two independent 12 ccRCC sets were profiled.
2010-06-25 | E-GEOD-12105 | biostudies-arrayexpress