Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA123871 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Multi-component epigenetic control of pro-invasive genes in cancer cells
| PRJNA121305 | ENA
Project description:Multi-component epigenetic control of pro-invasive genes in cancer cells (Illumina)
| PRJNA123867 | ENA
Project description:Multi-component epigenetic control of pro-invasive genes in cancer cells (ChIP-chip)
| PRJNA123869 | ENA
Project description:To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix. miRNA global profiling complements the ChIP-on-Chip experiment with U251 and MCF-7 cells. Two-condition experiment, MCF7 vs.U251 cells. 2 Biological replicates for each cell line
2010-01-05 | E-GEOD-18894 | biostudies-arrayexpress
Project description:To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix. Microarray probes were designed using eArray software (Agilent). Unique DNA probes specific to 486 human genes from the high density (HD) ChIP Database (Agilent) were included in each microarray. Microarray, 8x15K format, slides were custom manufactured by Agilent. Additional hybridization control probes (universal control grid LA577) were included in the arrays (Agilent). Each individual probe in the microarray was replicated 3-10 times. MCF7 vs.U251 cells
2010-05-16 | E-GEOD-18890 | biostudies-arrayexpress
Project description:To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix. miRNA global profiling complements the ChIP-on-Chip experiment with U251 and MCF-7 cells.
2010-01-05 | GSE18894 | GEO
Project description:Cervical cancer is a global public health subject as it affects women in the reproductive ages, and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50% mortality rate. Poor awareness and access to effective diagnosis have led to this enormous disease burden, calling for point-of-care, minimally invasive diagnosis methods. Here, an end-to-end quantitative approach for a new kind of diagnosis has been developed, comprising identification of optimal biomarkers, design of the sensor, and simulation of the diagnostic circuit. Using miRNA expression data in the public domain, we identified circulating miRNA biomarkers specific to cervical cancer using multi-tier screening. Synthetic riboregulators called toehold switches specific for the biomarker panel were then designed. To predict the dynamic range of toehold switches for use in genetic circuits as biosensors, we developed a generic grammar of these switches, and built a multivariate linear regression model using thermodynamic features derived from RNA secondary structure and interaction. The model yielded predictions of toehold efficacy with an adjusted R2 = 0.59. Reaction kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA biomarkers. Simulations showed a linear response between 10nM and 100nM before saturation. Our study demonstrates an end-to-end workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic signatures that would be increasingly important in today’s world. The approach has the potential to direct experimental efforts and minimise costs. All resources are provided open-source (https://github.com/igem2019) under GNU GPLv3 licence.
2022-05-05 | MODEL2107150001 | BioModels
Project description:Epigenetic regulators have emerged as critical factors governing the biology of cancer. Here, in the context of melanoma, we show that RNF2 is prognostic, exhibiting progression-correlated expression in human melanocytic neoplasms. Through a series of gain of function and loss of function studies, we establish that RNF2 is oncogenic and pro-metastatic. Mechanistically, RNF2-mediated invasive behavior is dependent on its ability to mono-ubiquitinate H2AK119 at the promoter of LTBP2, resulting in silencing of this negative regulator of TGFβ signaling. In contrast, RNF2's oncogenic activity did not require its catalytic activity nor derives from its canonical gene repression function, rather RNF2 drives proliferation through direct transcriptional up-regulation of the cell cycle regulator CCND2. In summary, RNF2 regulates distinct biological processes in the genesis and progression of melanoma via distinct molecular mechanisms, underscoring the complex and multi-faceted actions of epigenetic regulators in cancer. RNF2 is overexpressed in immortalized human melanocytes HMEL-BRAFV600E to address impact of RNF2 overexpression in melanoma. GFP was overexpressed in HMEL-BRAFV600E cells as a control cell line. Expression profiling using microarray was performed and compared between RNF2 overexpressing versus GFP overexpressing HMEL-BRAFV600E cells.
2016-07-03 | E-GEOD-51928 | biostudies-arrayexpress
Project description:To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix.
2010-01-05 | GSE18890 | GEO
Project description:To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix.
2010-01-05 | GSE18883 | GEO