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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Calcineurin signaling regulates neural induction through antagonizing the BMP pathway

ABSTRACT: Calcineurin activity is required for neural differentiation of embryonic stem cells (ESC). We assessed gene expression changes at several time points of in vitro ESC to neural differentiation when calcineurin activity is inhibitied by its antagonist FK506 and Cyclosporin(CsA). d4, d6, d8, and d12 EBs of FK506/CsA treatment group (d3-8) and its non-treated control group were harvested from three independent experiments of in vitro differentiation of 46C mouse ESCs. Total RNA of each sample was extracted, reverse transcribed, labeled and hybridized to Affymetric Mouse Gene ST 1.0 Arrays.

ORGANISM(S): Mus musculus

SUBMITTER: Ahryon Cho

PROVIDER: E-GEOD-54217 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Calcineurin signaling regulates neural induction through antagonizing the BMP pathway

Project description:Calcineurin activity is required for neural differentiation of embryonic stem cells (ESC). We assessed gene expression changes at several time points of in vitro ESC to neural differentiation when calcineurin activity is inhibitied by its antagonist FK506 and Cyclosporin(CsA).

2014-04-01 | GSE54217 | GEO

Musashi2 is required for the self-renewal and pluripotency of embryonic stem cells

Project description:Recent studies have shown that the RNA binding protein Musashi 2 (Msi2) plays prominent roles during development and leukemia. Additionally, in embryonic stem cells (ESC) undergoing the early stages of differentiation, Msi2 has been shown to associate with Sox2, which is required for the self-renewal of ESC. These findings led us to examine the effects of Msi2 on the behavior of ESC. Using an shRNA sequence that targets Msi2 and a scrambled shRNA sequence, we determined that knockdown of Msi2 disrupts the self-renewal of ESC and promotes their differentiation. Collectively, our findings argue that Msi2 is required to support the self-renewal and pluripotency of ESC. We used microarrays to better understand global changes in ESC gene expression following the knockdown of the RNA-binding protein Msi2 as compared to control ESC expressing a scrambled shRNA. Mouse embryonic stem cells (D3) were treated with lentivirus engineered for the expression of a Msi2 targeting shRNA sequence or scrambled (control) shRNA sequence. Following selection for infected cells with puromycin, cells were subcultured at low density and allowed to grow for 4 days (see treatment protocol) before RNA was extracted. RNA was collected and analyzed one time for each of the two samples.

2012-08-25 | E-GEOD-33882 | biostudies-arrayexpress

Identification of calcineurin- and Crz1-dependent targets in Candida glabrata

Project description:In order to identify calcineurin pathway-regulated genes, we compared the genome-wide expression profile of wild-type with FK506-treated wild-type, cna1, and crz1 mutants. We expect that FK506-treated wild-type will have similar expression profile with that of the cna1 mutant. In response to calcineurin inhibitor FK506, the up- and down-regulated by FK506 were 113 and 87 genes, respectively (cutoff q < 0.001). The genes regulated by FK506 are largely overlapped (90%, 180/200) with those of cna1 mutant. Interestingly, FK506 induced 20 distinct genes other than that of the cna1 mutant. These genes encode proteins involved in plasma membrane ATP-bindding cassette (ABC) multidrug transporters (PDR15, PDR5, and YOR1), amino acid transporters (ALP1 and YBT1), and transcription factors (CUP2 and INO2). We also identified 34 genes regulated by calcineurin and Crz1. These genes encode proteins involved in cell wall biosynthesis (YPS5, YPS1, YSR3, YPC1, PIR1, HOR7, and NTE1), heat shock protein responses (SBA1 and GRE2), regulator of calcineurin (RCN2), and other functions.

2011-09-01 | GSE31167 | GEO

Genome-wide analysis of gene expression regulated by calcineurin-NFAT signaling in mouse embryonic stem cells

Project description:Self-renewal and pluripotency are hallmarks of embryonic stem cells (ESCs). However, signaling pathways triggering their transition from self-renewal to differentiation are not well defined. Here, we report that the calcineurin-NFAT signaling pathway is both necessary and sufficient to switch ESCs from an undifferentiated state to early differentiation.To gain an insight into the function of calcinerin-NFAT signaling in ESC lineage commitment, we examined the repertoire of genes changed after LIF withdrawal alone, LIF withdrawal in the presence of cyclosporine A (CsA), a specific inhibitor of calcinerin and forced expression of active forms of calcineurin (deltaCnA) in the presence of LIF,and identified distinct classes of up and down regulated genes by calcineurin-NFAT signaling in mouse embryonic stem cells. Total RNA obtained from CGR8 ES cells under the following conditions: withdrawal of LIF for 0, 1 and 3 days; withdrawal of LIF for 0, 1 and 3 days in the presence of CsA, and induced expression of deltaCnA by withdrawal of Tc for 0, 1 and 4 days in ideltaCnAES cells.Hybridized to Illumina Sentrix Mouse-6 v1.1 Beadhips

2011-01-01 | E-GEOD-21378 | biostudies-arrayexpress

Identification of calcineurin- and Crz1-dependent targets in Candida glabrata

2011-08-31 | E-GEOD-31167 | biostudies-arrayexpress

Renal Cyclosporin-A (CsA) toxicity

Project description:The calcineurin inhibitor immunosuppressant cyclosporin A (CsA) soon gained clinical application, and became a standard of care in organ transplantation, as well as an important treatment option in a variety of autoimmune diseases. The immunosuppressive effect of CsA is mainly attributed to inhibiting calcineurin phosphatase activity, consequently favouring the inactive phosphorylated form of nuclear factor of activated T cells (NFAT). Renal toxicity is a serious adverse effect of CsA, but the underlying mechanisms are insufficiently understood. CsA has also been shown to induce episodic hypoxia (Fähling et al, 2017; doi: 10.1111/apha.12811). Here, we sought to identify molecular mechanisms of CsA nephrotoxicity.

2021-02-22 | GSE111516 | GEO

Patients with Chronic Kidney Disease with Acute Exercise Before and After Kidney Transplant

Project description:The post kidney transplant period is associated with insulin resistance partly due to corticosteroids. Patients on minimal corticosteroid therapy receiving tacrolimus (FK506) for immunosuppression also are affected. FK506 inhibits calcineurin in immune cells. Skeletal muscle calcineurin, which also might be inhibited, mediates exercise-induced transcription leading to more insulin-sensitive muscle. This study was performed to determine if gene transcription responses to exercise are lower in patients awaiting kidney transplant or 3 months post-transplant on a low-steroid, FK506 protocol.

2015-09-30 | GSE68585 | GEO

Characterization of A Novel CRAC Inhibitor that Potently Blocks Human T cell Activation and Effector Functions

Project description:Store operated calcium entry (SOCE) downstream of T cell receptor (TCR) activation in T lymphocytes has been shown to be mediated mainly through the Calcium Release Activated Calcium (CRAC) channel. Here, we compared the effects of a novel, potent and selective CRAC inhibitor, 2,6-Difluoro-N-{5-[4-methyl-1-(5-methyl-thiazol-2-yl)-1,2,5,6-tetrahydro-pyridin-3-yl]-pyrazin-2-yl}-benzamide (RO2959), on T cell effector functions with that of a previously reported CRAC channel inhibitor, YM-58483, and a calcineurin inhibitor Cyclosporin A (CsA). Using both electrophysiological and calcium-based fluorescence measurements, we showed that RO2959 is a potent SOCE inhibitor that blocked an IP3-dependent current in CRAC-expressing RBL-2H3 cells and CHO cells stably expressing human Orai1 and Stim1, as well as SOCE in human primary CD4+ T cells triggered by either TCR stimulation or thapsigargin treatment. Furthermore, we demonstrated that RO2959 completely inhibited cytokine production as well as T cell proliferation mediated by TCR stimulation or MLR (Mixed Lymphocyte Reaction). Lastly, we showed by gene expression array analysis that RO2959 potently blocked TCR triggered gene expression and T cell functional pathways similar to CsA and FK506. Thus, both from a functional and transcriptional level, our data provide evidence that RO2959 is a novel and selective CRAC inhibitor that potently inhibits human T cell functions. PBMC from healthy donors (n=4) were stimulated with anti-CD3/CD28 in the presence or absence of CRAC inhibitor, CsA or FK506 for 24 hrs

2013-01-31 | E-GEOD-43210 | biostudies-arrayexpress

Genome-wide analysis of gene expression regulated by calcineurin-NFAT signaling in mouse embryonic stem cells

2011-01-01 | GSE21378 | GEO

Dynamics of calcineurin-regulated gene expression in the absence of Hog1 in S. cerevisiae

Project description:Gene expression was quantified in crz1 hog1 delete S. cerevisae cells over a time course following calcineurin activation by CaCl2. Cells were pretreated with buffer or the calcineurin inhibitor FK506 to allow the identification of calcineurin-regulated genes. We show that calcineurin-dependent downregulation of G1/S genes is partly dependent on the osmostress-activated kinase Hog1.

2020-01-14 | GSE115014 | GEO

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