Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE58882
PROVIDER: PRJNA253804 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1481510.fastq.gz | Fastqsanger.gz | |||
| SRR1481520.fastq.gz | Fastqsanger.gz | |||
| SRR1481501.fastq.gz | Fastqsanger.gz | |||
| SRR1481511.fastq.gz | Fastqsanger.gz | |||
| SRR1481521.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
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Project description:Coordinated epigenetic remodelling occurs during early breast carcinogenesis [Expression profiling]
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Project description:Coordinated epigenetic remodelling occurs during early breast carcinogenesis [ChIP-seq & MBD-Seq]
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Project description:Coordinated epigenetic remodelling occurs during early breast carcinogenesis [Human promoter ChIP-chip]
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Project description:This work offers a dynamic picture of epigenetic switches in carcinogenesis and contributes to an overall understanding of coordinated regulation of gene expression in cancer. Our data indicate an H3K4me3/H3K27me3 epigenetic signature of prostate carcinogenesis.
2009-02-12 | E-TABM-635 | biostudies-arrayexpress
Project description:Subpopulations of primary Human Mammary Epithelial Cells (HMEC) have the unique ability to escape a period of growth arrest and continue to proliferate. These cells, called post-selection or variant cells (vHMEC), share features with premalignant breast cancer lesions, including p16INK4A promoter hypermethylation. Epigenetic silencing of tumour suppressor genes through DNA methylation and histone modification is an early event in tumorigenesis. One of the main challenges is to find genes or gene pathways that are commonly silenced to provide early epigenetic diagnostic and therapeutic cancer targets. To identify very early epigenetic events that occur in breast cancer, we used microarrays to screen for gene pathways that were suppressed in post-selection HMECs, but reactivated after treatment with the demethylation agent 5-Aza-2â-deoxycytidine (5-Aza-dC). We found several members of the Transforming Growth Factor Beta (TGFb) signalling pathway (THBS1, TGFb2, TGFb R1 & TGFb R2) were consistently down-regulated in the post-selection HMEC population. Gene suppression was not associated with DNA methylation but was associated with chromatin remodelling, involving a decrease in histone H3 lysine 27 (H3K27) tri-methylation and an increase in histone H3 lysine 9 (H3K9) di-methylation and H3K9 de-acetylation. Similar epigenetic repression was also identified MDAMB453 breast cancer cells and in breast tumour samples. These results demonstrate for the first time that TGFb2, its receptors TGFb R1 & TGFb R2 and activator THBS1 are concordantly suppressed early in breast carcinogenesis by repressive histone modifications and indicate that the TGFb signalling pathway is a novel target for gene activation by epigenetic therapy. Keywords: cell differentiation, breast cancer, gene silencing, epigenetics Two-colour reference design was used. Two biological replicates were included in the study - Bre60 and Bre-80. Each cell line was sampled at pre-selection stage, post-selection stage and post AZA treatment. The post-selection stage was chosen as the reference sample, and a control post-post hybridisation included to assess variability across the assay.
2010-05-26 | E-GEOD-8007 | biostudies-arrayexpress
Project description:To characterize early epigenetic events in breast carcinogenesis, we analyzed DNA methylation state of different stages of HMECs from pre-stasis to cancer cell lines using human promoter microarray
2009-01-01 | E-MEXP-1889 | biostudies-arrayexpress
Project description:Subpopulations of primary Human Mammary Epithelial Cells (HMEC) have the unique ability to escape a period of growth arrest and continue to proliferate. These cells, called post-selection or variant cells (vHMEC), share features with premalignant breast cancer lesions, including p16INK4A promoter hypermethylation. Epigenetic silencing of tumour suppressor genes through DNA methylation and histone modification is an early event in tumorigenesis. One of the main challenges is to find genes or gene pathways that are commonly silenced to provide early epigenetic diagnostic and therapeutic cancer targets. To identify very early epigenetic events that occur in breast cancer, we used microarrays to screen for gene pathways that were suppressed in post-selection HMECs, but reactivated after treatment with the demethylation agent 5-Aza-2’-deoxycytidine (5-Aza-dC). We found several members of the Transforming Growth Factor Beta (TGFb) signalling pathway (THBS1, TGFb2, TGFb R1 & TGFb R2) were consistently down-regulated in the post-selection HMEC population. Gene suppression was not associated with DNA methylation but was associated with chromatin remodelling, involving a decrease in histone H3 lysine 27 (H3K27) tri-methylation and an increase in histone H3 lysine 9 (H3K9) di-methylation and H3K9 de-acetylation. Similar epigenetic repression was also identified MDAMB453 breast cancer cells and in breast tumour samples. These results demonstrate for the first time that TGFb2, its receptors TGFb R1 & TGFb R2 and activator THBS1 are concordantly suppressed early in breast carcinogenesis by repressive histone modifications and indicate that the TGFb signalling pathway is a novel target for gene activation by epigenetic therapy. Keywords: cell differentiation, breast cancer, gene silencing, epigenetics
2008-06-05 | GSE8007 | GEO
Project description:The epithelial to mesenchymal transition (EMT) has been well recognized for many decades as an essential early step in the progression of primary tumors towards metastases. Widespread epigenetic reprogramming of DNA and histone modifications tightly regulates gene expression and cellular activity during carcinogenesis, and epigenetic therapy has been developed to design efficient strategies for cancer treatment. As the first oral agent approved for the clinical treatment of cancer, sorafenib has significant inhibitory effects on tumor growth and EMT. However, a detailed understanding of the underlying epigenetic mechanism remains elusive. In this manuscript, we performed a ChIP-Seq assay to evaluate the activity of sorafenib on the genome-wide profiling of histone modifications. We demonstrate that sorafenib largely reverses the changes in histone modifications that occur during EMT in A549 alveolar epithelial cells. Sorafenib also significantly reduces the coordinated epigenetic switching of critical EMT-associated genes in accordance with their expression levels. Furthermore, we show that sorafenib potentiates histone acetylation by regulating the expression levels of histone-modifying enzymes. Collectively, these findings provide the first evidence that sorafenib inhibits the EMT process through an epigenetic mechanism, which holds enormous promise for identifying novel epigenetic candidate diagnostic markers and drug targets for the treatment of human malignancies. To further explore the underlying epigenetic mechanisms of EMT regulation by sorafenib, we chose conventional markers of active euchromatin such as H3K9ac and H3K4me3, and contrasted their architecture with the repressive structures associated with H3K27me3 and H3K9me3. The profiling of these four selected histone modifications was performed using ChIP-seq on control, TGF-M-NM-21-treated and sorafenib-treated cells. We further performed pair-wise comparisons among the three treatment conditions to assess the changes in the histone modifications within specific genomic regions during EMT.
2012-10-11 | E-GEOD-41479 | biostudies-arrayexpress
Project description:We investigated, in a spontaneous mouse model of breast carcinogenesis (MMTV/NeuT), the modifications in the level of circulating miRNAs during different stages of disease, from early dysplastic stage to overt carcinoma, and their correlation with the pathological stage of the primary mammary lesions.
2019-12-03 | GSE117000 | GEO
Project description:Because gastric cancer cells already had genetic and epigenetic alterations which can affect the gastric carcinogenesis, we tried to characterize genetic and epigenetic changes during gastric carcinogenesis. To do this, we performed MBD sequencing and RRBS sequencing. MBD and RRBS sequencing of gastric mucosa, intestinal metaplasia, and gastric cancer cells from one patient were generated by NGS using Illumina GAII.
2015-09-01 | E-GEOD-55159 | biostudies-arrayexpress