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Identification of the tumor suppressor gene at chromosome 5q21

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE29227: aCGH profiling of prostate tumors GSE29228: 5q21 tiling array on prostate tumors GSE33531: Gene expression profiling of prostate cells with CHD1 knockdown Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Stephanie Huang

PROVIDER: E-GEOD-29229 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness.

Huang S S Gulzar Z G ZG Salari K K Lapointe J J Brooks J D JD Pollack J R JR

Oncogene 20111219 37

Though prostate cancer is often indolent, it is nonetheless a leading cause of cancer death. Defining the underlying molecular genetic alterations may lead to new strategies for prevention or treatment. Towards this goal, we performed array-based comparative genomic hybridization (CGH) on 86 primary prostate tumors. Among the most frequent alterations not associated with a known cancer gene, we identified focal deletions within 5q21 in 15 out of 86 (17%) cases. By high-resolution tiling array CG ...[more]

PMID: 22179824

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Gene expression profiling of prostate cells with CHD1 knockdown

Project description:Gene expression profiling of prostate tumor cells comparing cells that have CHD1 knockdown by shRNA (RWPE-1, OPCN2) or siRNA (LNCaP) with cells treated with non-targeted control. Prostate cell lines had CHD1 knockdown via shRNA or siRNA were hybridized against cells that were targeted with non-targeting control. OPCN2 and RWPE-1 RNA were dye-swapped in replicate experiments.

2011-12-19 | E-GEOD-33531 | biostudies-arrayexpress

aCGH profiling of prostate tumors

Project description:This experiment was an aCGH study on 86 prostate tumors samples. The samples were profiled on Agilent Human Genome 44karrays to identify recurrent regions of deletion and amplification, thus revealing potential new tumor suppressor genes and/or oncogenes involved in prostate cancer. The CGH profile on the 44k arrays revealed a deletion at 5q21 in 17% of samples. CGH analysis of 86 prostate tumor samples.

2011-12-19 | E-GEOD-29227 | biostudies-arrayexpress

5q21 tiling array on prostate tumors

Project description:CGH profiles of prostate tumors on custom designed high resolution arrays tiling chromosome 5q21 A custom high-density Agilent 15k CGH array tiling 5q21 was designed to narrow down the region of deletion at 5q21 to a few genes that could be followed up with functional studies. 8 critical prostate tumors samples with the most focal regions of deletion were chosen to be profiled on the 5q21 tiling array.

2011-12-19 | E-GEOD-29228 | biostudies-arrayexpress

The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-04-15 | E-GEOD-52349 | biostudies-arrayexpress

Identification of target genes of tumor suppressor microRNAs in human cancer

Project description:To identify target genes of tumor suppressive microRNAs in human cancer, several cell lines (bladder cancer, prostate cancer, renal cell carcinoma, and head and neck squamous cell carcinoma) were subjected to Agilent whole genome microarrays. miR-517a, miR-218, miR-145, miR-1 and miR-874 function as tumor suppressors. Human cancer cell lines (BOY, T24, A498, PC3, DU145, FaDu, SAS, HSC3, IMC3) were transfected with miRNAs (miR-517a, miR-218, miR-145, miR-1, miR-874). The miRNA-transfected human cancer cell lines were compared to control cell lines.

2012-02-09 | E-GEOD-24782 | biostudies-arrayexpress

Gene Expression in Castration-Resistant C4-2 Cells after AR Knockdown

Project description:Prostate cancer is the most common, lethal malignancy in men. Although androgen withdrawal therapies are used to treat advanced disease, progression to a castration-resistant, end-stage is the usual outcome. In this study, the tested hypothesis was that the androgen receptor remains essential for the growth and viability of castration-resistant disease. Knocking down the androgen receptor in well-established tumors grown in castrated mice caused growth arrest, decreased serum PSA, and frequently regression and total eradication of tumors. Growth control of castration-resistant tumors appeared to be linked to the extent of androgen receptor knockdown, which triggers upregulation of many genes involved in apoptosis, cell cycle arrest, and inhibition of tumorigenesis and protein synthesis. Our findings provide proof of principle that in vivo knockdown of the androgen receptor is a viable therapeutic strategy to control and possibly eradicate prostate cancers that have progressed to the lethal castration-resistant state. C4-2 human prostate cancer cells stably expressing a tetracycline-inducible AR-targeted short hairpin RNA (shRNA) or scrambled shRNA were generated. These two cell lines were incubated in the absence of androgens with or without doxycycline hyclase (DOX). Comparison analysis of the gene expression profiles of C4-2 cells stably expressing AR shRNA + DOX and control cells (AR shRNA - DOX and scrambled shRNA Â± DOX) was conducted to identify differentially regulated genes due to AR knockdown after normalization and data filtering. Genes were considered to be significantly different if the expression in the induced AR shRNA + DOX cells was at least 1.7-fold greater or 1.7-fold less than that seen in the control cells, with P< 0.05.

2010-06-23 | E-GEOD-13332 | biostudies-arrayexpress

Hepatic proteome analysis of Atlantic salmon (Salmo salar) after exposure to environmental concentrations of human pharmaceuticals

Project description:Pharmaceuticals are pseudo persistent aquatic pollutants with unknown effects at environmentally relevant concentrations. Atlantic salmon (Salmo salar) were exposed to Acetaminophen: 54.77 ± 34.67; Atenolol: 11.08 ± 7.98 and Carbamazepine: 7.85 ± 0.13 µg•L-1 for 5 days. After Acetaminophen treatment, 19 proteins were differently expressed, of which 11 were significant with respect to the control group (eight up-regulated and three down-regulated). After Atenolol treatment, 7 differently expressed proteins were obtained in comparison with the control, of which 6 could be identified (four up-regulated and 2 down-regulated). Carbamazepine exposure resulted in 15 differently expressed proteins compared with the control, with 10 of them identified (seven up-regulated and three down-regulated). Out of these, 3 features were common between Acetaminophen and Carbamazepine and one between Carbamazepine and Atenolol. One feature was common across all treatments. Principal component analysis and heat map clustering showed a clear grouping of the variability due to the applied treatments. The obtained data suggest (1) that exposure to environmentally relevant concentrations of the pharmaceuticals alters the hepatic protein expression profile of the Atlantic salmon; and (2) the existence of treatment specific processes that may be useful for biomarker development.

2014-11-18 | PXD001354 | Pride

Transcription profiling of human prostate cancer cell lines and normal prostate epithelial and stromal cells in primary culture

Project description:The primary goal of this study was to assess differences in gene expression between prostate cancer cell lines and normal prostate epithelial and stromal cells in primary culture. Experiment Overall Design: 9 samples were analyzed with 1 replicate each. Samples included 6 prostate cancer cell lines, 1 normal prostate epithelial cell system in primary culture, and 2 normal prostate stromal cell systems in primary culture.

2008-11-13 | E-GEOD-12348 | biostudies-arrayexpress

Transcriptome profiling of breast cancer cells with Insulin like growth factor binding protein 2 (IGFBP2) knockdown

Project description:The study was carried out to identify the genes regulated upon IGFBP2 modulation in breast cancer. This will help to understand the molecular targets and biological pathways targeted by IGFBP2 in breast cancer. C5 (Cy5) Vs. Vector(Cy3), C5 (Cy5) Vs. Vector(Cy3), C12 (Cy5) Vs. Vector(Cy3), C12 (Cy5) vs. Vector(Cy3)

2013-09-06 | E-GEOD-40682 | biostudies-arrayexpress

Expression data from androgen treated LNCaP cells

Project description:Androgens are required for the development of normal prostate, and they are also linked to the development of prostate cancer. We used microarrays to understand the role of androgen in an androgen dependent, androgen receptor (AR) positive human metastatic cell line, LNCaP. LNCaP cells were grown in RPMI medium and they were subjected to stay in phenol-red free, RPMI with charcoal stripped serum for 48h. Synthetic androgen R1881 was added and the cells were allowed to grow for 48h. Control cells were given with corresponding amount of ethanol as vehicle which is used for the solubilization of R1881. Cells were harvested and RNA was isolated for microarray analysis.

2009-12-29 | E-GEOD-17044 | biostudies-arrayexpress

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