Gene expression profiles of primary cultured ovarian cells and ovarian cancer cell lines in the presence and absence of a DNA methyltransferase inhibitor
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PROVIDER: PRJNA133783 | ENA |
REPOSITORIES: ENA
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Project description:This SuperSeries is composed of the following subset Series: GSE25427: Gene expression profiles of primary cultured ovarian cells in the presence and absence of a DNA methyltransferase inhibitor GSE25428: Gene expression profiles of ovarian cancer cell lines in the presence and absence of a DNA methyltransferase inhibitor Refer to individual Series
2010-11-17 | E-GEOD-25429 | biostudies-arrayexpress
Project description:Epithelial ovarian cancer is the leading cause of death among gynecologic malignancies. Diagnosis usually occurs after metastatic spread, largely reflecting vague symptoms of early disease combined with lack of an effective screening strategy. Epigenetic mechanisms of gene regulation, including DNA methylation, are fundamental to normal cellular function and also play a major role in carcinogenesis. To elucidate the biological and clinical relevance of DNA methylation in ovarian cancer, we conducted expression microarray analysis of 43 cell lines and 17 primary culture specimens grown in the presence or absence of DNA methyltransferase (DNMT) inhibitors. Two parameters, induction of expression and standard deviation among untreated samples, identified 378 candidate methylated genes, many relevant to TGF-beta signaling. We analyzed 43 of these genes and they all exhibited methylation. Treatment with DNMT inhibitors increased TGF-beta pathway activity. Hierarchical clustering of ovarian cancers using the 378 genes reproducibly generated a distinct gene cluster strongly correlated with TGF-beta pathway activity that discriminates patients based on age. These data suggest that accumulation of age-related epigenetic modifications leads to suppression of TGF-beta signaling and contributes to ovarian carcinogenesis. Seventeen primary cultures of ovarian cells (two pooled normal ovarian surface epithelium, two serous borderline tumors, one endometrioid and twelve serous epithelial ovarian cancers) were mock treated or treated with 5 µM 5-AzaC for 72 hours, followed by gene expression microarray analysis to enable identification of genes differentially expressed as a result of inhibition of DNA methyltransferase activity.
2010-11-17 | E-GEOD-25427 | biostudies-arrayexpress
Project description:Epithelial ovarian cancer is the leading cause of death among gynecologic malignancies. Diagnosis usually occurs after metastatic spread, largely reflecting vague symptoms of early disease combined with lack of an effective screening strategy. Epigenetic mechanisms of gene regulation, including DNA methylation, are fundamental to normal cellular function and also play a major role in carcinogenesis. To elucidate the biological and clinical relevance of DNA methylation in ovarian cancer, we conducted expression microarray analysis of 39 cell lines and 17 primary culture specimens grown in the presence or absence of DNA methyltransferase (DNMT) inhibitors. Two parameters, induction of expression and standard deviation among untreated samples, identified 378 candidate methylated genes, many relevant to TGF-beta signaling. We analyzed 43 of these genes and they all exhibited methylation. Treatment with DNMT inhibitors increased TGF-beta pathway activity. Hierarchical clustering of ovarian cancers using the 378 genes reproducibly generated a distinct gene cluster strongly correlated with TGF-beta pathway activity that discriminates patients based on age. These data suggest that accumulation of age-related epigenetic modifications leads to suppression of TGF-beta signaling and contributes to ovarian carcinogenesis.
2010-11-17 | GSE25427 | GEO
Project description:Epithelial ovarian cancer is the leading cause of death among gynecologic malignancies. Diagnosis usually occurs after metastatic spread, largely reflecting vague symptoms of early disease combined with lack of an effective screening strategy. Epigenetic mechanisms of gene regulation, including DNA methylation, are fundamental to normal cellular function and also play a major role in carcinogenesis. To elucidate the biological and clinical relevance of DNA methylation in ovarian cancer, we conducted expression microarray analysis of 43 cell lines and 17 primary culture specimens grown in the presence or absence of DNA methyltransferase (DNMT) inhibitors. Two parameters, induction of expression and standard deviation among untreated samples, identified 378 candidate methylated genes, many relevant to TGF-beta signaling. We analyzed 43 of these genes and they all exhibited methylation. Treatment with DNMT inhibitors increased TGF-beta pathway activity. Hierarchical clustering of ovarian cancers using the 378 genes reproducibly generated a distinct gene cluster strongly correlated with TGF-beta pathway activity that discriminates patients based on age. These data suggest that accumulation of age-related epigenetic modifications leads to suppression of TGF-beta signaling and contributes to ovarian carcinogenesis. The cancer stem cell hypothesis posits that malignant growth arises from a rare population of progenitor cells within a tumor that provide it with unlimited regenerative capacity. Such cells also possess increased resistance to chemotherapeutic agents. Resurgence of chemoresistant disease following primary therapy typifies epithelial ovarian cancer and may be attributable to residual cancer stem cells, or cancer initiating cells, that survive initial treatment. As the cell surface marker CD133 identifies cancer initiating cells in a number of other malignancies, we sought to determine the potential role of CD133+ cells in epithelial ovarian cancer. We detected CD133 on ovarian cancer cell lines, in primary cancers, and on purified epithelial cells from ascitic fluid of ovarian cancer patients. We found CD133+ ovarian cancer cells generate both CD133+ and CD133- daughter cells, whereas CD133- cells divide symmetrically. CD133+ cells exhibit enhanced resistance to platinum-based therapy, drugs commonly used as first line agents for treatment of ovarian cancer. Sorted CD133+ ovarian cancer cells also form more aggressive tumor xenografts at a lower inoculum than their CD133- progeny. Epigenetic changes may be integral to the behavior of cancer progenitor cells and their progeny. In this regard, we found that CD133 transcription is controlled by both histone modifications and promoter methylation. Sorted CD133- ovarian cancer cells treated with DNA methyltransferase and histone deacetylase inhibitors show a synergistic increase in cell surface CD133 expression. Moreover, DNA methylation at the ovarian tissue active P2 promoter is inversely correlated with CD133 transcription. We also found that promoter methylation increases in CD133- progeny of CD133+ cells, with CD133+ cells retaining a less methylated or unmethylated state. Taken together, our results show that CD133 expression in ovarian cancer is directly regulated by epigenetic modifications and support the idea that CD133 demarcates an ovarian cancer initiating cell population. The activity of these cells may be epigenetically detected and such cells might serve as pertinent chemotherapeutic targets for reducing disease recurrence. The objective of the study was to identify genes that are subject to DNA methylation through pharmacological inhibition of DNA methyltransferase activity in a panel of cancer cell lines. Cells were mock treated with culture media (mock treated) or treated with 5 µM decitabine for 72 hours. Resulting expression profiles were compared to identify genes with altered expression following decitabine treatment. These data represent two experiments: In the first, 43 established cell lines were mock treated or treated with decitabine to enable identification of genes differentially expressed as a result of inhibition of DNA methyltransferase activity. HEYA8-decitabine treated cells were run in replicate. In the second experiment, A2780 and PEO1 cells underwent flow activated cell sorting to separate CD133(+) from CD133(-) cells in each cell line; the sorted cell populations were cultured in the same manner as the first experiment and similarly mock treated or treated with decitabine. All specimens were arrayed in parallel and used for RMA normalization.
2010-11-17 | E-GEOD-25428 | biostudies-arrayexpress
Project description:Epithelial ovarian cancer is the leading cause of death among gynecologic malignancies. Diagnosis usually occurs after metastatic spread, largely reflecting vague symptoms of early disease combined with lack of an effective screening strategy. Epigenetic mechanisms of gene regulation, including DNA methylation, are fundamental to normal cellular function and also play a major role in carcinogenesis. To elucidate the biological and clinical relevance of DNA methylation in ovarian cancer, we conducted expression microarray analysis of 39 cell lines and 17 primary culture specimens grown in the presence or absence of DNA methyltransferase (DNMT) inhibitors. Two parameters, induction of expression and standard deviation among untreated samples, identified 378 candidate methylated genes, many relevant to TGF-beta signaling. We analyzed 43 of these genes and they all exhibited methylation. Treatment with DNMT inhibitors increased TGF-beta pathway activity. Hierarchical clustering of ovarian cancers using the 378 genes reproducibly generated a distinct gene cluster strongly correlated with TGF-beta pathway activity that discriminates patients based on age. These data suggest that accumulation of age-related epigenetic modifications leads to suppression of TGF-beta signaling and contributes to ovarian carcinogenesis. The cancer stem cell hypothesis posits that malignant growth arises from a rare population of progenitor cells within a tumor that provide it with unlimited regenerative capacity. Such cells also possess increased resistance to chemotherapeutic agents. Resurgence of chemoresistant disease following primary therapy typifies epithelial ovarian cancer and may be attributable to residual cancer stem cells, or cancer initiating cells, that survive initial treatment. As the cell surface marker CD133 identifies cancer initiating cells in a number of other malignancies, we sought to determine the potential role of CD133+ cells in epithelial ovarian cancer. We detected CD133 on ovarian cancer cell lines, in primary cancers, and on purified epithelial cells from ascitic fluid of ovarian cancer patients. We found CD133+ ovarian cancer cells generate both CD133+ and CD133- daughter cells, whereas CD133- cells divide symmetrically. CD133+ cells exhibit enhanced resistance to platinum-based therapy, drugs commonly used as first line agents for treatment of ovarian cancer. Sorted CD133+ ovarian cancer cells also form more aggressive tumor xenografts at a lower inoculum than their CD133- progeny. Epigenetic changes may be integral to the behavior of cancer progenitor cells and their progeny. In this regard, we found that CD133 transcription is controlled by both histone modifications and promoter methylation. Sorted CD133- ovarian cancer cells treated with DNA methyltransferase and histone deacetylase inhibitors show a synergistic increase in cell surface CD133 expression. Moreover, DNA methylation at the ovarian tissue active P2 promoter is inversely correlated with CD133 transcription. We also found that promoter methylation increases in CD133- progeny of CD133+ cells, with CD133+ cells retaining a less methylated or unmethylated state. Taken together, our results show that CD133 expression in ovarian cancer is directly regulated by epigenetic modifications and support the idea that CD133 demarcates an ovarian cancer initiating cell population. The activity of these cells may be epigenetically detected and such cells might serve as pertinent chemotherapeutic targets for reducing disease recurrence.
2010-11-17 | GSE25428 | GEO
Project description:Expression data from TH17 cells cultured in the presence or absence of glutamine
| PRJNA700974 | ENA
Project description:The growth of the mammalian ovarian follicle requires the formation of a fluid filled antrum, and maturation and differentiation of the ovarian granulosa cells, largely under the control of Follicle Stimulating Hormone (FSH). Many follicles will regress and die by a process called atresia at this early antral stage. We therefore decided to analyse the gene expression profiles of granulosa cells cultured in the presence or absence of FSH and Tumour Necrosis Factor-alpha (TNFα), an apoptotic factor, to simulate the key influences. Different concentratons of FSH and TNFa in granulosa culture were used to determine effective conditions via estradiol and progesterone production, and cell number. RNA for the array experiments and quantitative real time PCR was extracted from cells cultured with FSH added at 0.33 and TNFα at 50 ng/ml.
2014-05-20 | GSE42535 | GEO
Project description:Next Generation Sequencing Analysis of S. aureus cultured in the presence/absence of V12CBD
| PRJNA476780 | ENA
Project description:The growth of the mammalian ovarian follicle requires the formation of a fluid filled antrum, and maturation and differentiation of the ovarian granulosa cells, largely under the control of Follicle Stimulating Hormone (FSH). Many follicles will regress and die by a process called atresia at this early antral stage. We therefore decided to analyse the gene expression profiles of granulosa cells cultured in the presence or absence of FSH and Tumour Necrosis Factor-alpha (TNF-alpha), an apoptotic factor, to simulate the key influences. Different concentratons of FSH and TNFa in granulosa culture were used to determine effective conditions via estradiol and progesterone production, and cell number. RNA for the array experiments and quantitative real time PCR was extracted from cells cultured with FSH added at 0.33 and TNF-alpha at 50 ng/ml. Four treatments of : (1) FSH alone, (2) TNF-alpha alone, (3) FSH + TNF-alpha and (4) control = neither drug, with replicates (n=4, except controls n=3 ) were used to generate RNA for the gene expression arrays (n=15)
2014-05-20 | E-GEOD-42535 | biostudies-arrayexpress
Project description:We profiled gene expression changes in differentiating i-Mixl1 ES cells(Willey, Ayuso-Sacido et al., 2006, Blood 107(8): 3122-3130) cultured in the presence or absence of Doxycycline (DOX, 0.1 ug/ml, 3 replicates per treatment/time point). Total RNA was isolated from EBs harvested at day 2, 3 and 4 (DOX added 1 day after plating of ES cells). RNA (1 ug) was subjected to one round of linear amplification (RiboAmp System) to yield 10 ug of RNA. The RNA was indirectly labeled using amino allyl-dUTP('t Hoen, de Kort et al., 2003, Nucleic Acids Res. 31: e20), then conjugated with Cy3 or Cy5. The labeled RNAs were used to screen a 15K mouse developmental cDNA microarray(Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132). Pairwise analysis of hybridization results for EBs cultured with or without DOX was performed for samples harvested on each day. Spotfire(R) software was used for data management and filtering. Gene expression ratios were normalized after filtering the data to remove low-intensity and poor quality spots. Data obtained for replicate samples were in excellent agreement. Six experiments total: three time points (day 2, day 3, day 4); for each time point mRNA was collected in the presence or absence of Doxycycline. Three biological replicas were collected for each of the six experiments
2015-09-01 | E-GEOD-40703 | biostudies-arrayexpress