Genomic characterization of Chinese clear cell renal cell carcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE126964 | GEO | 2020/02/22
REPOSITORIES: GEO
Similar Datasets
Project description:We analyze the clonal architectures of ccRCC patients from three different populations, including TCGA, Japanese and Chinese patients. We characterize the mutational signatures across different populations and evolution stages. The TCGA and Japanese data sets were downloaded from published studies and we also generated the whole genome sequencing data for more than 40 Chinese patients.
| EGAS00001003447 | EGA
Project description:Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKIs) is a challenge. Our aim was to identify molecular markers associated with outcome in m-ccRCC patients treated with sunitinib. A Cartes d’Identite des Tumeurs (CIT) study from the 'Institut Curie' and the french 'Ligue Nationale Contre le Cancer' (http://cit.ligue-cancer.net).
2015-01-27 | E-MTAB-3267 | biostudies-arrayexpress
Project description:A total of 164 ccRCC patient’s specimens were used for microarray (n=12, tumor and corresponding normal tissue) or pyrosequencing (PSQ) analyses (n=152). From The Cancer Genome Atlas (TCGA) portal, microarray methylation profiles composed of 312 subjects with ccRCC were utilized (159 for gene selection and 153 for prognostic relevance). Using the methylation profiles from our and TCGA, tumor-specific hypermethylated genes were selected, and prognostic relevance of candidate markers were examined with TCGA data set and pyrosequencing analysis data from our ccRCC patients samples.
2019-12-15 | GSE92482 | GEO
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net); Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKIs) is a challenge. Our aim was to identify molecular markers associated with outcome in m-ccRCC patients treated with sunitinib.
2015-01-27 | E-MTAB-3269 | biostudies-arrayexpress
Project description:Here we performed 3’ transcriptome single cell sequencing on 7 ccRCC patients’ tumor and matched 5 adjacent normal samples. We identified two different functional subgroups in ccRCC tumor epithelial cells and two different gene transcriptional programs that were associated with survival across a TCGA cohort. We found important transcriptional factor regulons that played roles in ccRCC progression. We identified macrophage and T cell clusters whose higher infiltration in tumor was associated with overall survival. We also discovered some potentially targetable inhibitory interactions among tumor epithelial cells, the infiltrating T cell and myeloid compartments. Collectively, our data provided cell clusters and gene sets for predict clinical outcome and potential targets for ccRCC therapy.
2021-08-31 | GSE156632 | GEO
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:A Cartes d'Identite des Tumeurs (CIT) project from the French Ligue Nationale Contre le Cancer (<a href=\\ttp://cit.ligue-cancer.net/\\ target=\\_blank\\>http://cit.ligue-cancer.net</a>). Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKIs) is a challenge. Our aim was to identify molecular markers associated with outcome in m-ccRCC patients treated with sunitinib.\
2016-02-26 | E-MTAB-3274 | biostudies-arrayexpress
Project description:By analyzing RNAseq data from TCGA in ccRCC and metabolomics data from CCLE, we identified the strong correlation of GPX8 with the lipid and glycogen metabolism, which are highly upregulated in ccRCC. We validated this observation by knocking out GPX8 in Caki1 (ccRCC cell line). Using transcript profiling, we confirmed the association of GPX8 with de novo lipogenesis and suppressed fatty acid oxidation. Mechanically, from RNA-seq data we also found the decrease of NNMT upon GPX8 KO, which functions as the downstream of GPX8 and regulates the lipid phenotype in ccRCC.
2022-08-01 | GSE193249 | GEO
Project description:Clear cell renal cell carcinoma is one of the most common diagnostic tumor, with nearly one third patients diagnosed as metastatic ccRCC. Although increasing number of studies have revealed that piwi-interacting RNAs were aberrantly expressed in diverse type of cancers, few of them explored the detailed molecular mechanism of piRNAs in carcinogenesis, particular in ccRCC. In this study, differentially expressed piRNAs associated with ccRCC was selected by using piRNA-sequencing combined with analyzing TCGA data, from which piR-57125 was identified. PiR-57125 was found remarkably downregulated in ccRCC samples. Functionally, knockdown of piR-57125 promoted migration and invasion of ccRCC, while overexpression of piR-57125 suppressed ccRCC metastasis. In vivo lung metastasis model also confirmed the same results. CCL3 was identified as the direct target of piR-57125 which could reverse the inhibition effect of piR-57125 in ccRCC metastasis. Further studies revealed that piR-57125 modulated ccRCC metastasis through AKT/ERK pathway. Those data indicate that piR-57125 restrains ccRCC metastasis through directly targeting CCL3 and inhibiting AKT/ERK pathway, and could be a potential therapeutic target for ccRCC.
2021-09-08 | GSE183496 | GEO
Project description:Purpose: In this study, we have undertaken the whole proteomic analysis and got a better understanding of biological processes involved in the development and progression of ccRCC. We hope promising biomarkers can be uncovered to facilitate early diagnosis, predict the prognosis and progression, more importantly, to be applied as potential therapeutic targets. Experimental design: Fresh frozen tissue samples were surgically resected from patients with local or locally advanced ccRCC. Trypsin digested proteins were analyzed using TMT-based LC-MS/MS proteomic approach, followed by bioinformatic analysis. A potential prognostic marker FMNL1, annotated with actin cytoskeleton assembly and cell migration, was chosen to be validated in TCGA_KIRC datasets(n=597), further validation sets(n=20) and expanded validation sets(n=97). Results: A total of 657 differentially expressed proteins were identified and quantified between ccRCC and adjacent normal tissues (p-value<0.05, FC>2 or<1/2), of which 186 proteins were up-regulated and 471 proteins were down-regulated. Bioinformatic analysis showed enriched metabolic biological processes and pathways including oxidative phosphorylation, valine, leucine and isoleucine degeneration, propanoate metabolism, fatty-acid degeneration, TCA cycle, glycolysis/gluconeogenesis, etc. Univariate and multivariate analysis defined FMNL1 as an independent negative prognostic marker in the TCGA datasets. High expression of FMNL1 correlated significantly with tumor stage, T stage, lymph node metastasis(P<0.05), and distant metastasis(P<0.05) both in the TCGA-KIRC datasets and expanded validation sets. And KM survival curve illustrated that patients with high FMNL1 protein level had shorter OS time in the expanded validation sets (p=0.0273) Conclusion and clinical relevance: The proteomic results uncovered sophisticated metabolic reprogramming of ccRCC and indicated that the upregulation of rate-limiting enzymes in glycolysis and mitochondrial impairment may be the cause of metabolic reprogramming in ccRCC. Moreover, FMNL1 has been identified as a diagnostic and prognostic marker, and may be implicated in the progression of ccRCC.
2022-02-16 | PXD022919 | Pride