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Effect of Pnpla6 gene silencing in D3 mouse embryonic stem cells

ABSTRACT: Pnpla6 gene was silenced in D3 mouse embryonic stem cells and the cells were allowed to spontaneously differentiate. Transcription of the whole genome was analyzed 96 days afterwards and compared against control cells differentiated during the same time without previous silencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE33974 | GEO | 2013/11/04

SECONDARY ACCESSION(S): PRJNA150509

REPOSITORIES: GEO

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Effect of Pnpla6 gene silencing in D3 mouse embryonic stem cells

Project description:Pnpla6 gene was silenced in D3 mouse embryonic stem cells and the cells were allowed to spontaneously differentiate. Transcription of the whole genome was analyzed 96 days afterwards and compared against control cells differentiated during the same time without previous silencing. Comparimg two experimental conditions: control differentiated cells versus Pnpla6 silenced differentiated cells.

2013-11-04 | E-GEOD-33974 | biostudies-arrayexpress

SILENCING OF PNPLA6, THE NEUROPATHY TARGET ESTERASE (NTE) CODIFYING GENE, ALTERS HUMAN NEURODIFFERENTIATION IN VITRO

Project description:Neuropathy Target Esterase (NTE) is a protein involved in the development of a polyneuropathy caused by exposure to certain organophosphorus compounds. In vivo and in vitro studies have also associated NTE with embryonic development since NTE null mice embryos are non-viable, and silencing the NTE-codifying gene (Pnpla6) in mouse embryonic stem cells strongly alters the differentiation of vascular and nervous systems. In this paper, human embryonal carcinoma stem cells (hNT2) are used as in vitro neurodifferentiation model to determine whether PNPLA6 gene silencing is able to alter the differentiation into a neuronal phenotype. In controls, the PNPLA6 mRNA levels increased in parallel with other neuroectodermal markers during the neurodifferentiation. PNPLA6 gene silencing with specific interference RNA led to a 97% maximum decrease in gene expression by day 3 after transfection, with a maximum of 50% reduction in NTE enzymatic activity by day 4. Microarray analyses of the PNPLA6-silenced cells showed alterations in several developmental processes, mainly neurogenesis and epithelium tube morphogenesis. PNPLA6 silencing also led to a reduction in electrical activity and an altered neuronal phenotype. This work is the first proof supporting the hypothesis that NTE protein plays a critical role in human early neurodevelopment using a human cell differentiation model. PNPA6 gene silencing in undifferentiatied hNT2 cells was performed, together with a Control (non-gene silencing cells) and a Negative Control (non-specific RNA silencer). Three biological replicates.

2014-10-06 | E-GEOD-55761 | biostudies-arrayexpress

SILENCING OF PNPLA6, THE NEUROPATHY TARGET ESTERASE (NTE) CODIFYING GENE, ALTERS HUMAN NEURODIFFERENTIATION IN VITRO

2014-10-06 | GSE55761 | GEO

Vibrio sp. D3 strain:D3

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Pseudomonas sp. D3 strain:D3

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Williamsia sp. D3 strain:D3

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RNA-sequencing of mRNAs from control and CAP-D3 deficient Salmonella infected HT-29 cells

Project description:BACKGROUND & AIMS- More frequent interaction of bacteria with the colonic epithelium is associated with ulcerative colitis (UC). The identities of all proteins which promote bacterial clearance in colonic epithelial cells are unknown. Previously, we discovered that dCAP-D3 (Chromosome Associated Protein-D3), regulates responses to bacterial infection. We examined whether CAP-D3 promotes bacterial clearance in human colonic epithelium. METHODS- Clearance of Salmonella or adherent-invasive Escherichia coli LF82 was assessed by gentamycin protection assays in HT-29 and Caco-2 cells expressing CAP-D3 shRNA. CAP-D3 levels in colonic epithelial cells from healthy and UC patient tissues were analyzed by immunoblot. RNA-sequencing identified bacterially-induced CAP-D3 target genes. The role of CAP-D3 target genes in bacterial clearance was analyzed by gentamycin protection assays, immunofluorescent staining, and by using pharmacologic inhibitors. RESULTS- CAP-D3 expression was reduced in colonic epithelial cells from UC patients with active disease. Reduction of CAP-D3 expression inhibited autophagy and decreased intracellular bacterial clearance. The components of the heterodimeric SLC7A5/SLC3A2 amino acid transporter were identified as CAP-D3 target genes; their levels increased in infected, CAP-D3 deficient cell lines and in cells from UC patients. In HT-29 cells, this resulted in earlier SLC7A5 recruitment to Salmonella-containing vacuoles, increased mTOR activity, and enhanced bacterial survival. Inhibition of SLC7A5/SLC3A2 or mTOR activity rescued the bacterial clearance defect in CAP-D3 deficient cells. CONCLUSIONS- CAP-D3 attenuates amino acid transporter transcription to promote bacterial autophagy in colon epithelial cells. CAP-D3 protein levels are decreased in patients with active UC, suggesting that CAP-D3 is a potential therapeutic target to restore mucosal homeostasis in UC patients.

2015-09-15 | GSE62520 | GEO

Transcriptome profiling of gingival fibroblasts treated by vitamin D3

Project description:In humans, vitamin D3 is a secosteroid, a prohormonal precursor of biologically active hydroxyforms. Vitamin D3 is related to periodontitis. The third American Health and Nutrition Survey found that plasma 25(OH)D3 levels are negatively correlated with attachment loss in people aged >50 years. The relationship between vitamin D3 and periodontitis remains to be investigated. We sent human gingival fibroblasts treated by vitamin D3 for transcriptome sequencing.

2022-09-09 | GSE212728 | GEO

Comparative gene expression profile of 1,25-dihydroxyvitamin D3-treated human monocyte-derived dendritic cells

Project description:We have carried out global gene expression analysis to clarify the interrelationship between 1,25-dihydroxyvitamin D3 and differentiation-driven gene expression patterns in developing human monocyte-derived dendritic cells. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. This design allows one to identify genes regulated by differentiation and/or 1,25-dihydroxyvitamin D3 in human monocyte-derived dendritic cells.

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