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IFNgamma and 1a,25(OH)2D3 dependent gene expression in bone marrow derived macrophages

ABSTRACT: Gene expression profiling of macrophages derived from WT and Vdr deficient mice after stimulation with IFNgamma and/or 1alpha,25(OH)2D3 Keywords = macrophages Keywords = VDR Keywords = activated vitamin D3 Keywords = IFNgamma Keywords = KO mice Keywords: dose response

ORGANISM(S): Mus musculus

PROVIDER: GSE2421 | GEO | 2005/04/21

SECONDARY ACCESSION(S): PRJNA91135

REPOSITORIES: GEO

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Transcription profiling of macrophages derived from WT and Vdr dificient mice after stimulation with IFNgamma and/or 1alpha,25(OH)2D3 to study molecular mechanisms of macrophage activation

Project description:Gene expression profiling of macrophages derived from WT and Vdr deficient mice after stimulation with IFNgamma and/or 1alpha,25(OH)2D3

2007-08-31 | E-GEOD-2421 | biostudies-arrayexpress

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Project description:B10.PL mice with severe (stage 2.5-3) experimental autoimmune encephalomyelitis were treated with placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA was extracted for microarray analysis. Naive mice serve as controls. Individual samples were hybridized to individual microarrays. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Keywords: repeat sample

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Naive, EAE placebo-treated and EAE 1,25(OH)2D3-treated groups

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Genomic and epigenomic 1α,25(OH)2D3 responses in human colonic organoids

Project description:Background & Aims: Active vitamin D, 1α,25(OH)2D3, is a nuclear hormone with roles in colonic homeostasis and carcinogenesis, yet mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. Here, we utilize human colonic organoids to measure 1α,25(OH)2D3 responses on genome-wide gene expression and chromatin accessibilityover time. Methods: Human colonic organoids were cultured and treated in triplicate with either 100nM 1α,25(OH)2D3 or vehicle control for 4 and 18 hours (h) for chromatin accessibility, and 6 and 24hfor gene expression. DNA and RNA were extracted for ATAC- and RNA-sequencing, respectively. Differentially accessible peaks were analyzed using DiffBind and EdgeR; differentially expressed genes were analyzed using DESeq2. Motif enrichment was determined using HOMER. Results: At 6h and 24h, 2870 and 2721 differentially expressed genes, respectively (FDR<5%) were identified with overall stronger responses with 1α,25(OH)2D3. Similarly, 1α,25(OH)2D3 treatment led to stronger chromatin accessibility especially at 4h. The vitamin D receptor (VDR) motif was strongly enriched among open chromatin peaks with 1α,25(OH)2D3 treatment accounting for 30.5% and 11% of target sequences at 4h and 18h, respectively (FDR<1%). A number of genes such as CYP24A1, FGF19, MYC, FOS and TGFBR2 showed significant transcriptional and chromatin accessibility responses to 1α,25(OH)2D3 treatment with open chromatin located distant from promoters for some gene regions. Conclusions: Assessment of chromatin accessibility and transcriptional responses to 1α,25(OH)2D3 yielded new observations about vitamin D genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study host-environment interactions between individuals and populations in future.

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1,25(OH)2D3 upregulated lncRNA

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Differential and overlapping effects of 20.23(OH)2D3 and 1,25(OH)2D3 on gene expression in human epidermal keratinocytes

Project description:Neonatal keratinocytes from African American donors of passage 2 or 3 were treated with 20,23(OH)2D3, 1,25(OH)2D3 or 0.1% ethanol (control) for 6 and 24 hours. The cells were harvested separately, RNA isolated and submitted for microarray analysis at the Molecular Resources Center at the UTHSC.

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Target gene profiles of 1,25(OH)2D3 and 25(OH)D3 in Cyp27b1 knockout mDCT cells.

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