Gene expression analysis of collecting duct carcinoma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA644615 | ENA |
REPOSITORIES: ENA
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Project description:We performed a transcriptomic analysis in a cohort of 6 Collecting Duct Carcinoma, 5 Clear Cell Renal Cell Carcinoma and 4 non-matched normal renal tissues to unravel the underlying biological and molecular determinants and to identifiy specific genes and pathways of this rare tumor type.
2021-07-13 | GSE153965 | GEO
Project description:The genetic landscape and molecular features of collecting duct carcinoma (CDC) of the kidney remain largely unknown. Herein, we performed whole exome sequencing (WES) and transcriptome sequencing (RNASeq) on 7 CDC samples (CDC1 -7). Among the 7 samples, 4 samples with matched non-tumor tissue were used for copy number analysis by SNP array data. No recurrent somatic SNVs were observed except for MLL, which was found to be mutated (p.V297I and p.F407C) in 2 samples. We identified somatic SNVs in 14 other cancer census genes including: ATM, CREBBP, PRDM1, CBFB, FBXW7, IKZF1, KDR, KRAS, NACA, NF2, NUP98, SS18, TP53, and ZNF521. SNP array data identified a CDKN2A homozygous deletion in 3 samples and SNV analysis showed a non-sense mutation of the CDKN2A gene with unknown somatic status. To estimate the recurrent rate of CDKN2A abnormalities, we performed FISH screening of additional samples and confirmed the frequent loss (62.5%) of CDKN2A expression. Since cisplatin based therapy is the common treatment option for CDC, we investigated the expression of solute carrier (SLC) family transporters and found 45% alteration. In addition, SLC7A11 (cystine transporter, xCT), a cisplatin resistance associated gene, was found to be overexpressed in 4 out of 5 (80%) cases of CDC tumors tested, as compared to matched non-tumor tissue. In summary, our study provides a comprehensive genomic analysis of CDC and identifies potential pathways suitable for targeted therapies.
2016-10-25 | GSE89122 | GEO
Project description:Analysis of expression changes in renal collecting duct epithelial cells by adenoviral mediated Krüppel like transcription factor 5 (KLF5) overexpression. KLF5 is a key regulator of static and inflammatory stage in renal collecting duct epithelial cells. We thought these results provide insights into downstream genes of KLF5 in renal collecting duct epithelial cells.
2011-05-17 | GSE29323 | GEO
Project description:We would like to know the gene expression pattern in absence of transcription factor GATA2 in adult renal collecting duct We used Gata2 flox::Pax8-rtTA::Tet-Cre to make a doxycycline induced Gata2 renal tubule cell specific knockout mice We performed microarray analyses using DBA-lectin and magnetic beads purifed collecting duct cells from WT (n=3) or Gata2 CKO mice (n=3) at 4-weeks after doxycycline induction
2013-11-19 | E-GEOD-52448 | biostudies-arrayexpress
Project description:Analysis of expression changes in renal collecting duct epithelial cells by adenoviral mediated Krüppel like transcription factor 5 (KLF5) overexpression. KLF5 is a key regulator of static and inflammatory stage in renal collecting duct epithelial cells. We thought these results provide insights into downstream genes of KLF5 in renal collecting duct epithelial cells. Total RNAs were isolated from adenovirally-mediated KLF5 over expressed cultured mIMCD-3 cells or control adenovirus infected mIMCD-3. We analyzed these two gene expression profiles after 24 hours after infection.
2011-05-17 | E-GEOD-29323 | biostudies-arrayexpress
Project description:Here, establishing expansion cultures of hiPSC-derived ureteric bud tip cells, an embryonic precursor that gives rise to collecting ducts, we succeeded in advancing the developmental stage of collecting duct organoids and showed that all collecting duct organoids derived from PKD1-/- hiPSCs spontaneously develop multiple cysts, clarifying the initiation mechanisms of cystogenesis.
2023-11-30 | GSE215875 | GEO
Project description:Identification of gene expressed in the enriched inner medullary collecting duct cells in rat. Experiment Overall Design: Rat inner medullary collecting duct (IMCD) cells were isolated from 7 male Sprage-Dawley rats by collagenase and hyaluronidase digestion and follow by low speed centrifugation. The non-IMCD cells were collected by centrifugation of supernatant of enriched IMCD samples. Experiment Overall Design: Total RNA about 3 ug were used per microarray (Rat 230 2.0 Genechip array). Experiment Overall Design: The experiments were repeat 3 times (3 pairs of IMCD VS non-IMCD)
2008-06-15 | E-GEOD-7891 | biostudies-arrayexpress
Project description:Identification of gene expressed in the enriched inner medullary collecting duct cells in rat. Keywords: gene expression comparision between cell type
2007-12-21 | GSE7891 | GEO
Project description:Transcriptional profiling of new born mouse kidney collecting duct (CD) cells comparing the infuence of gestational high salt stress on gene expression remolding of BdkrB2 receptor knockout CD cells with that of BdkrB2 receptor wild type CD cells. The BdkrB2 receptor has been shown to be playing a role in renal vascular tone, kidney secretion and reabsorption function, normal kidney development, while impaired BdkrB2 receptor in kidney shown being associated with renal agenesis and renal dysplasia. Goal was to determine the effects of BdkrB2 receptor knockout together with gestational high salt stress on collecting duct gene expression pattern.
2013-08-08 | GSE49616 | GEO
Project description:Phosphorylation of the aquaporin-2 (AQP2) water channel at four COOH-terminal serines plays a central role in the regulation of water permeability of the renal collecting duct. The level of phosphorylation at these sites is determined by a balance between phosphorylation by protein kinases and dephosphorylation by phosphatases. The phosphatases that dephosphorylate AQP2 have not been identified. Here, we use large-scale data integration techniques to identify serine-threonine phosphatases likely to interact with AQP2 in renal collecting duct principal cells. As a first step, we have created a comprehensive list of 38 S/T phosphatase catalytic subunits present in the mammalian genome. Then we used Bayes’ theorem to integrate available information from large-scale data sets from proteomic and transcriptomic studies in order to rank the known S/T phosphatases with regard to the likelihood that they interact with AQP2 in renal collecting duct cells. To broaden the analysis, we have generated new proteomic data (LC-MS/MS) identifying 4538 distinct proteins including 22 S/T phosphatases in cytoplasmic fractions from native inner medullary collecting duct cells from rats. The official gene symbols corresponding to the top-ranked phosphatases (common names in parentheses) were: Ppp1cb (PP1-beta), Ppm1g (PP2C), Ppp1ca (PP1-alpha), Ppp3ca (PP2-B or calcineurin), Ppp2ca (PP2A-alpha), Ppp1cc (PP1-gamma), Ppp2cb (PP2A-beta), Ppp6c (PP6C) and Ppp5c (PP5). This ranking correlates well with results of prior reductionist studies of ion and water channels in renal collecting duct cells.
2018-10-26 | PXD005488 | Pride