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Gene expression regulated by AGN193109 and 4-diehtylaminobenzaldehyde (DEAB) in mIMCD-3 cells

ABSTRACT: All-trans retinoic acid (tRA) is the bioactive derivative of vitamin A that regulates gene expression by activating RA receptors (RAR). By using a reporter mouse model, we recently showed that endogenous tRA/RAR signaling was present in kidney collecting duct cells, and in mouse inner medullary collecting duct cell line (mIMCD-3). In order to unveil target genes of endogenous tRA/RAR signaling in kidney collecting duct cells, whole genome microarray analysis was performed on mIMCD-3 cells treated with AGN193109, a pan-RAR antagonist, and 4-diethylaminobenzaldehyde (DEAB), an inhibitor of tRA synthesizing enzyme. Specificity of gene expression regulation was confirmed by determining the reversibility of the regulation by simultaneous addition of exogenous tRA.

ORGANISM(S): Mus musculus

PROVIDER: GSE33955 | GEO | 2011/11/26

SECONDARY ACCESSION(S): PRJNA150549

REPOSITORIES: GEO

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Gene expression regulated by AGN193109 and 4-diehtylaminobenzaldehyde (DEAB) in mIMCD-3 cells

Project description:Retinoic acid (RA) is the bioactive derivative of vitamin A that regulates gene expression by activating RA receptors (RAR). By using a reporter mouse model, we recently showed that endogenous RA/RAR signaling was present in kidney collecting duct cells, and in mouse inner medullary collecting duct cell line (mIMCD-3). In order to unveil target genes of endogenous RA/RAR signaling in kidney collecting duct cells, whole genome microarray analysis was performed on mIMCD-3 cells treated with AGN193109, a pan-RAR antagonist, and 4-diethylaminobenzaldehyde (DEAB), an inhibitor of RA synthesizing enzyme. Specificity of gene expression regulation was confirmed by determining the reversibility of the regulation by simultaneous addtion of exogenous tRA. In the first set of experiment, mIMCD-3 cells were treated with either vehicle (0.1% ethanol and 0.1% DMSO) or 1 μM AGN193109 or 1 μM AGN193109+0.2 μM tRA. Three independent biological experiments were performed. In the second set of experiment, mIMCD-3 cells were treated with either vehicle (0.1% ethanol and 0.1% DMSO) or 25 μM DEAB or 25 μM DEAB+0. 01 μM tRA. Three independent biological experiments were performed. Treatment period for both sets of experiments were 24 hours.

2011-11-26 | E-GEOD-33955 | biostudies-arrayexpress

Characterization of the miRNA Landscape in an Inner Medullary Collecting Duct Cell Line

Project description:The affect of aldosterone on the miRNA landscape in mIMCD-3 cells was determined In the study presented here, the affect of aldosterone was examined on the miRNA content in a murine inner medullary collecting duct cell line

2014-05-31 | E-GEOD-47901 | biostudies-arrayexpress

Effects of KLF5 overexpression on renal collecting duct epithelial cell line (mIMCD-3)

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

MicroRNA (miRNA) expression of IMCD tubule suspension

2014-06-21 | GSE58693 | GEO

Effect of potassium-depleted diet on kidney

Project description:Libraries obtained from microdissected kidney outer medullary collecting duct from C57Bl6/J mice control or after 3 days potassium-depleted diet. Keywords: other

2004-05-30 | E-GEOD-1445 | biostudies-arrayexpress

Effect of potassium-depleted diet on kidney

Project description:Libraries obtained from microdissected kidney outer medullary collecting duct from C57Bl6/J mice control or after 3 days potassium-depleted diet. Keywords: other

2004-05-30 | GSE1445 | GEO

MicroRNA (miRNA) expression of IMCD tubule suspension

Project description:miRNA plays a role as post-transcriptional regulator. However, miRNAs in the kidney collecting duct cell have not been well understood. So we aimed to profile miRNAs in the kidney inner medullary collecting duct (IMCD) cells, and to identify the vasopressin-responsive miRNAs in the kidney IMCD cells. The microarray assay revealed that relative expression of miRNAs in the kidney IMCD cells was changed by desmopressin (dDAVP) stimulation. Fresh IMCD tubules were prepared from rat kidney and incubated in the medium in the absence or presence of dDAVP (1 nM, 2 h). Total RNA purified from IMCD tubules was used to analyze miRNA expression by GeneChipM-BM-. miRNA 3.0 Array (Affymetrix).

2014-06-21 | E-GEOD-58693 | biostudies-arrayexpress

Transcription profiling of mouse inner medullary collecting duct cells treated with aldosterone to characterize early aldosterone-responsive genes.

Project description:Murine inner medullary collecting duct cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. The mineralocorticoid aldosterone is a major regulator of Na+ and acid-base balance and control of blood pressure. Although the long-term effects of aldosterone have been extensively studied, the early aldosterone-responsive genes remain largely unknown. Using DNA array technology, we have characterized changes in gene expression after 1 h of exposure to aldosterone in a mouse inner medullary collecting duct cell line, mIMCD-3. Results from three independent microarray experiments revealed that the expression of many transcripts was affected by aldosterone treatment. Northern blot analysis confirmed the upregulation of four distinct transcripts identified by the microarray analysis, namely, the serum and glucose-regulated kinase sgk, connective tissue growth factor, period homolog, and preproendothelin. Immunoblot analysis for preproendothelin demonstrated increased protein expression. Following the levels of the four transcripts over time showed that each had a unique pattern of expression, suggesting that the cellular response to aldosterone is complex. The results presented here represent a novel list of early aldosterone-responsive transcripts and provide new avenues for elucidating the mechanism of acute aldosterone action in the kidney.

2007-11-06 | E-GEOD-434 | biostudies-arrayexpress

Disentangaling the gene expression programs controlled by ciliary and cytosolic cAMP signaling

Project description:Primary cilia are tiny membrane protrusions emanating from the surface of almost all mammalian cell types. Recently, a picture has emerged of the primary cilium functioning as a cellular antenna that senses extracellular stimuli via receptors, locally processes the signal using cilia-specific signalling pathways, and transduces this information into a cellular response. Components of the cyclic AMP (cAMP) signalling cascade have been proposed to be part of the ciliary signalling pathways. We aimed to shed light on whether ciliary cAMP signaling controls gene expression, and if yes, which gene expression program is particularly targeted by ciliary cAMP signaling. To this end, we targeted an optogenetic tool to increase cAMP levels (bPAC) to the primary cilium in murine, kidney-derived inner medullary collecting duct (mIMCD-3) cells (mIMCD-3 cilia-bPAC cells). As controls, we used cells were bPAC is targeted to the cytosol (mIMCD-3 cyto-bPAC cells) and wild-type cells (mIMCD-3 WT cells). We increased cAMP levels by light stimulation and next analysed gene expression using bulk RNA-sequencing. As an additional control, we also included WT cells treated with the compound Forskolin, which targets endogeneous adenylyl cyclases and thus, in principle, is believed to increase cAMP levels in both compartments, cilium and cell soma.

2022-05-11 | GSE182339 | GEO

Cilia-APEX proteomics profiling of Arl6-/- vs wiltype reveal UbK63 retrieval adaptors

Project description:Ascrobate peroxidase (APEX) was expressed as a fusion protein and directed to primary cilia of mouse inner medullary collecting duct (mIMCD-3) cells, where it was used for proximity labeling to biotinylate proteins, which are subsequently enriched by streptavidin chromatography and identified by mass spectrometry. Cilia-APEX proteomics profiling compared the cilia proteomes of wild-type and Arl6-/- cilia (generated by CRISPR/Cas9-mediated genome editing) by spectral counting.

2022-11-02 | MSV000090633 | MassIVE

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