Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA93057 | ENA |
REPOSITORIES: ENA
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Project description:We used splicing-sensitive microarrays to detect differences in alternative splicing between two breast cancer cell lines MCF7 (estrogen receptor positive) and MDA-MB-231 (estrogen receptor negative), as well as cultured human mammary epithelial cells (HMEC). Several splicing alterations in genes, including CD44, FAS, RBM9, HnRNPA/B, APLP2, and MYL6, were detected by the microarray, and verified by RT-PCR. We also compared splicing in these breast cancer cells cultured in either two-dimensional flat dishes (2-D) or in three-dimensional Matrigel (3-D) conditions. Only a subset of the splicing differences that distinguish MCF7 cells from MDA-MB-231 cells under 2-D culture condition is retained under 3-D conditions, suggesting that alternative splicing events are influenced by the geometry of the culture conditions of these cells. Keywords: Splicing-sensitive microarray
2005-12-30 | GSE3042 | GEO
Project description:Protein arginine methyltransferase-6 (PRMT6) regulates steroid-dependent transcription and alternative splicing, and is implicated in endocrine system development and function, cell death, cell cycle, gene expression and cancer. Despite its role in these processes, little is known about its function and cellular targets in breast cancer. To identify novel gene targets regulated by PRMT6 in breast cancer cells, we used a combination of small interfering RNA (siRNA) and exon-specific microarray profiling in vitro, coupled to in vivo validation in normal breast and primary human breast tumours. This approach, which allows the examination of genome-wide changes in individual exon usage and total transcript levels, demonstrated PRMT6 knockdown significantly affected: (i) the transcription of 159 genes, and (ii) alternate splicing of 449 genes. Importantly, the levels of PRMT6 itself were significantly decreased in breast cancer, relative to normal breast tissue. The PRMT6 dependent transcriptional and alternative splicing targets identified in vitro, were validated in human breast tumours. Notably, expression of PRMT6 and the corresponding gene signature, correlated with decreased probability of relapse-free or distant metastasis free survival in ER+ breast cancer. These results suggest that dysregulation of PRMT6 dependent transcription and alternative splicing may be involved in breast cancer pathophysiology and the molecular consequences identifying a unique and informative biomarker profile. Total RNA obtained from MCF7 breast cancer cells transfected with siRNA directed against PRMT6 or negative control siRNA (Ambion Silencer Select negative control).
2012-08-01 | E-GEOD-36542 | biostudies-arrayexpress
Project description:Regulation of cell-cell junction formation and regulation of cell migration were enriched among EMT (Epithelial-Mesenchymal Transition)-associated alternatively splicing events. Our analysis suggested that most EMT-associated alternative splicing events are regulated by one or more members of the RBFOX, MBNL, CELF, hnRNP or ESRP classes of splicing factors. The EMT alternative splicing signature was confirmed in human breast cancer cell lines, which could be classified into basal and luminal subtypes based exclusively on their EMTassociated splicing pattern. Expression of EMT-associated alternative mRNA transcripts was also observed in primary breast cancer samples, indicating that EMT-dependent splicing changes occur commonly in human tumors. The functional significance of EMT-associated alternative splicing was tested by expression of the epithelial-specific splicing factor ESRP1 or depletion of RBFOX2 in mesenchymal cells, both of which elicited significant changes in cell morphology and motility towards an epithelial phenotype, suggesting that splicing regulation alone can drive critical aspects of EMT-associated phenotypic changes. The molecular description obtained here may aid in the development of new diagnostic and prognostic markers for analysis of breast cancer progression. Examination of transcriptomes of HMLE/Twist-ER before and after induction of EMT by tamoxifen
2011-07-15 | E-GEOD-30290 | biostudies-arrayexpress
Project description:Protein arginine methyltransferase-6 (PRMT6) regulates steroid-dependent transcription and alternative splicing, and is implicated in endocrine system development and function, cell death, cell cycle, gene expression and cancer. Despite its role in these processes, little is known about its function and cellular targets in breast cancer. To identify novel gene targets regulated by PRMT6 in breast cancer cells, we used a combination of small interfering RNA (siRNA) and exon-specific microarray profiling in vitro, coupled to in vivo validation in normal breast and primary human breast tumours. This approach, which allows the examination of genome-wide changes in individual exon usage and total transcript levels, demonstrated PRMT6 knockdown significantly affected: (i) the transcription of 159 genes, and (ii) alternate splicing of 449 genes. Importantly, the levels of PRMT6 itself were significantly decreased in breast cancer, relative to normal breast tissue. The PRMT6 dependent transcriptional and alternative splicing targets identified in vitro, were validated in human breast tumours. Notably, expression of PRMT6 and the corresponding gene signature, correlated with decreased probability of relapse-free or distant metastasis free survival in ER+ breast cancer. These results suggest that dysregulation of PRMT6 dependent transcription and alternative splicing may be involved in breast cancer pathophysiology and the molecular consequences identifying a unique and informative biomarker profile.
2012-08-02 | GSE36542 | GEO
Project description:Regulation of cell-cell junction formation and regulation of cell migration were enriched among EMT (Epithelial-Mesenchymal Transition)-associated alternatively splicing events. Our analysis suggested that most EMT-associated alternative splicing events are regulated by one or more members of the RBFOX, MBNL, CELF, hnRNP or ESRP classes of splicing factors. The EMT alternative splicing signature was confirmed in human breast cancer cell lines, which could be classified into basal and luminal subtypes based exclusively on their EMTassociated splicing pattern. Expression of EMT-associated alternative mRNA transcripts was also observed in primary breast cancer samples, indicating that EMT-dependent splicing changes occur commonly in human tumors. The functional significance of EMT-associated alternative splicing was tested by expression of the epithelial-specific splicing factor ESRP1 or depletion of RBFOX2 in mesenchymal cells, both of which elicited significant changes in cell morphology and motility towards an epithelial phenotype, suggesting that splicing regulation alone can drive critical aspects of EMT-associated phenotypic changes. The molecular description obtained here may aid in the development of new diagnostic and prognostic markers for analysis of breast cancer progression.
2011-07-15 | GSE30290 | GEO
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Project description:We assessed alternative splicing in breast cancer through global profiling of transcriptomes of basal and luminal subtype cell lines using Affymetrix Human Junction Array.
2010-06-15 | E-MTAB-183 | biostudies-arrayexpress