Rattus norvegicus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA266534 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Betaine (trimethylglycine) is a non-toxic, highly water-soluble organic osmolyte widely used in skin care due to its assumed moisturizing and protective properties, but only few studies have addressed its specific effects in skin. Here, the cellular and molecular targets of betaine were analyzed by genome-wide expression analysis in organotypic cultures of rat epidermal keratinocytes (REK). In this model, we also examined whether betaine modifies the impacts of acute UVB exposure. The expression of several genes relevant to epidermal biology, proliferation/differentiation or malignancy as well as solute transport were verified by independent methods (qRT-PCR, western blotting). The data concerning changes in calcium metabolism after UVB exposure has been published separately (Bart et al., Br. J. Dermatol. 171:376-387, 2014). Organotypic cultures of rat epidermal keratinocytes (REK) were prepared by plating cells on a collagen-coated insert (submerged in medium), lifting the confluent cell layer to the air-liquid interface 3 days after plating. These 3D cultures were divided in four treatment groups with three replicates in each: control, betaine (10 mM), UVB (30 mJ/cm2) and betaine + UVB. Betaine was added to the cultures for 11 days, starting from day 4 until sample collection. UVB exposure was performed 24 h prior to sample collection for 2-week-old 3D cultures with a well-formed epidermal layer. For further details on the experimental set-up and characteristics of the UV source, please refer to Bart et al. (Br. J. Dermatol. 171:376-387, 2014) and Rauhala et al. (J. Biol. Chem. 288:17999-18012, 2013).
2015-10-26 | E-GEOD-63004 | biostudies-arrayexpress
Project description:Betaine (trimethylglycine) is a non-toxic, highly water-soluble organic osmolyte widely used in skin care due to its assumed moisturizing and protective properties, but only few studies have addressed its specific effects in skin. Here, the cellular and molecular targets of betaine were analyzed by genome-wide expression analysis in organotypic cultures of rat epidermal keratinocytes (REK). In this model, we also examined whether betaine modifies the impacts of acute UVB exposure. The expression of several genes relevant to epidermal biology, proliferation/differentiation or malignancy as well as solute transport were verified by independent methods (qRT-PCR, western blotting). The data concerning changes in calcium metabolism after UVB exposure has been published separately (Bart et al., Br. J. Dermatol. 171:376-387, 2014).
2015-10-26 | GSE63004 | GEO
Project description:Genome-wide 10k SNP profiling of FOXM1B-transduced N/TERT and primary normal human epidermal keratinocytes (NHEK). The aim of this study was to study the cancer initiation role of UVB and FOXM1B upregulation in NHEK. Upregulation of FOXM1B alone (without UVB) was found to directly induce genomic instability in the form of copy number aberration (CNA) and low levels of loss of heterozygosity (LOH) in primary NHEK. The FOXM1B-induced CNA was found to be retained and accumulated in subsequent cell culture passages. UVB-exposure resulted in significant chromosomal LOH and CNA in N/TERT cells expressing FOXM1B but not in EGFP-expressing cells. This indicates that UVB corroborated with FOXM1B to recruit LOH and CNA which may predispose cell to malignant transformation. Collectively, these results indicate that aberrant upregulation of FOXM1B in skin keratinocytes following UVB exposure may be an early mechanism whereby cells acquire genomic changes required for oncogenesis. Keywords: Genome-wide SNP profiling for loss of heterozygosity (LOH) and copy number aberration (CNA), FOXM1, UVB, Keratinocytes, Basal cell carcinoma, genomic instability, carcinogenesis, squamous cell carcinoma.
2010-06-28 | GSE16937 | GEO
Project description:Genome-wide 10k SNP profiling of FOXM1B-transduced N/TERT and primary normal human epidermal keratinocytes (NHEK). The aim of this study was to study the cancer initiation role of UVB and FOXM1B upregulation in NHEK. Upregulation of FOXM1B alone (without UVB) was found to directly induce genomic instability in the form of copy number aberration (CNA) and low levels of loss of heterozygosity (LOH) in primary NHEK. The FOXM1B-induced CNA was found to be retained and accumulated in subsequent cell culture passages. UVB-exposure resulted in significant chromosomal LOH and CNA in N/TERT cells expressing FOXM1B but not in EGFP-expressing cells. This indicates that UVB corroborated with FOXM1B to recruit LOH and CNA which may predispose cell to malignant transformation. Collectively, these results indicate that aberrant upregulation of FOXM1B in skin keratinocytes following UVB exposure may be an early mechanism whereby cells acquire genomic changes required for oncogenesis. Keywords: Genome-wide SNP profiling for loss of heterozygosity (LOH) and copy number aberration (CNA), FOXM1, UVB, Keratinocytes, Basal cell carcinoma, genomic instability, carcinogenesis, squamous cell carcinoma. 1) Three individual normal primary NHEK cultures were retrovirally transduced (with either EGFP or EGFP-FOXM1B) and left to grow for 4 days prior to SNP array analysis. 2) EGFP or EGFP-FOXM1B-tansduced NHEK cells were harvested at passage 1, 2 and 3 for SNP array analysis to investigate if genomic instability is maintained and accumulated in subsequent passages. 3) N/TERT cells transduced with either EGFP or EFOX were UVB-irradiated and left to grow for 50 days in culture prior to SNP array analysis.
2010-07-29 | E-GEOD-16937 | biostudies-arrayexpress
Project description:Betaine critically contributes to the control of hepatocellular hydration and provides protection of the liver from different kinds of stress. This study investigates to what extent hepatocellular hydration changes affect the expression levels of enzymes involved in the metabolism of betaine and related organic osmolytes by using qRT-PCR gene expression studies in rat hepatoma cells as well as metabolic and gene expression profiling in 5,10 - methylene tetrahydrofolate reductase (MTHFR) deficient primary hepatocytes. The results demonstrate a coordinated regulation of betaine degradation and synthesis under anisoosmotic conditions. Expression of betaine degrading enzymes is downregulated by hyperosmolarity and strongly induced by hypoosmolarity. In contrast, synthesis of glycerophosphocholine from phosphoethanolamine and conversion of choline to betaine are both induced by hyperosmolarity but decreased under hypoosmotic conditions. In addition we evaluated the flux of choline and its derivates in liver and plasma of methylene tetrahydrofolate reductase knockout (Mthfr-/-) mice by tandem mass spectrometry. Analyses of system-wide alterations of osmolyte metabolism with microarray studies revealed expression changes similar to those after hypoosmotic exposure in this betaine depletion model. In conclusion, regulation of betaine synthesis and degradation and concomitant changes in intracellular osmolyte concentrations contribute to long-term adaptation to anisoosmotic exposure of the liver. Expression of 280 genes were analyzed in wild type and mthr-/- mice (n=7) with spotted oligonucleotides.
2013-04-01 | E-GEOD-42275 | biostudies-arrayexpress
Project description:Betaine critically contributes to the control of hepatocellular hydration and provides protection of the liver from different kinds of stress. This study investigates to what extent hepatocellular hydration changes affect the expression levels of enzymes involved in the metabolism of betaine and related organic osmolytes by using qRT-PCR gene expression studies in rat hepatoma cells as well as metabolic and gene expression profiling in 5,10 - methylene tetrahydrofolate reductase (MTHFR) deficient primary hepatocytes. The results demonstrate a coordinated regulation of betaine degradation and synthesis under anisoosmotic conditions. Expression of betaine degrading enzymes is downregulated by hyperosmolarity and strongly induced by hypoosmolarity. In contrast, synthesis of glycerophosphocholine from phosphoethanolamine and conversion of choline to betaine are both induced by hyperosmolarity but decreased under hypoosmotic conditions. In addition we evaluated the flux of choline and its derivates in liver and plasma of methylene tetrahydrofolate reductase knockout (Mthfr-/-) mice by tandem mass spectrometry. Analyses of system-wide alterations of osmolyte metabolism with microarray studies revealed expression changes similar to those after hypoosmotic exposure in this betaine depletion model. In conclusion, regulation of betaine synthesis and degradation and concomitant changes in intracellular osmolyte concentrations contribute to long-term adaptation to anisoosmotic exposure of the liver.
2013-04-01 | GSE42275 | GEO
Project description:The specific functional features of the epidermal keratinocytes are determined by the activity of many genes. The aim of the project was to characterize the role of HSPA2, a member of the HSPA chaperone family (HSP70), in human epidermal keratinocytes. The inactivation of the HSPA2 gene in the HaCaT line of spontaneously immortalized epidermal keratinocytes was performed by CRISPR/Cas9 gene editing system. Next, the effect of modifications on the transcriptomic profile of cells growing in a three-dimensional model of reconstructed human epidermis in vitro was investigated. The cells were grown at air-liquid interface culture on collagen-fibroblast matrix to achieve maximal level of HaCaT differentiation in RHE system.
2023-09-25 | E-MTAB-13166 | biostudies-arrayexpress
Project description:The UVB component of the sunlight (290-320 nm) plays an important role in carcinogenesis through generation of high levels of bipyrimidine DNA photoproducts, while UVA (320-400 nm) has been associated with photoaging and tumor progression through generation of low, but continuous levels of DNA damage and oxidative stress. However, the contribution of UVA light to epidermal cell fate in the context of photoaging remains poorly understood. Here, by using proteomic analyses and biochemical assays for validation, we show that UVA induces proteome remodeling and senescence in primary keratinocytes, eliciting potent antioxidant and pro-inflammatory responses. As a model of early skin tumorigenesis during aging, immortalized non-malignant keratinocytes, bearing potentially oncogenic mutations and dysfunctional components of the senescent machinery , are resilient to UVA-induced stress, but are sensitive to paracrine oxidative stress and immune system activation induced by senescent neighboring keratinocytes. These observations reveal a new cellular mechanism by which UVA induces photoaging in the epidermis.
2022-02-17 | PXD025191 | Pride
Project description:To address CPD-dependent UVB activities, a model system was established in which transfection of keratinocytes with pseudouridine-modified mRNA (M-NM-(-mRNA) encoding CPD-photolyase resulted in 90% reduction of CPDs within 6 and 24 hours after UVB exposure. Microarray analysis of this model system demonstrated that more than 50 % of the gene expression altered by UVB were changed in a CPD-dependent manner. The expression of most of the CPD-dependent genes was changed at 6 h after UVB as compared to 24 h likely due to the higher CPD levels. Nine genes (ATF3, CCNE1, CDKN2B, EGR1, ID2, PTGS2, RUNX1, SNAI1, SNAI2) regulated by CPDs were selected for further investigation (qPCR, Western blot) based on the microarray data. Gene expression modulated by UVB irradiation in HaCaT keratinocytes was measured at 6 and 24 hours after the exposure to dose of 20 mJ/cm2 UVB. Three independent experiments were performed at each time (6 or 24 hours) using different passages for each experiment.
2015-01-16 | E-GEOD-65034 | biostudies-arrayexpress
Project description:The specific functional features of the epidermal keratinocytes are determined by the activity of many genes. The aim of the project was to characterize the role of HSPA2, a member of the HSPA chaperone family (HSP70), in human epidermal keratinocytes. The inactivation of the HSPA2 gene in the HaCaT line of spontaneously immortalized epidermal keratinocytes was performed by CRISPR/Cas9 gene editing system. Next, the effect of modifications on the transcriptomic profile of cells growing in 2D monolayer culture was investigated. This study was supported by a Polish National Science Center grant number NCN 2017/25/B/NZ4/01550.
2023-11-29 | E-MTAB-13251 | biostudies-arrayexpress