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Discovery of genes regulated by the metastasis suppressor gene, RhoGDI2

ABSTRACT: A number of studies find that metastasis suppressor proteins, including RhoGDI2, may function in part though controlling expression of genes regulating metastasis (reviewed in Smith and Theodorescu, Nature Reviews Cancer, 2009, PMID: 19242414). To uncover systematically gene expression patterns dependent on RhoGDI2 expression, we profiled gene expression in stably transfected control (GFP empty vector) UM-UC-3 bladder carcinoma cells (which have lost endogenous expression of RhoGDI2, as occurs commonly in the progression of bladder cancer PMID: 15173088), as well as stably transfected GFP-tagged RhoGDI2 expressing UM-UC-3 cells. References: Moissoglu K, McRoberts KS, Meier JA, Theodorescu D et al. Rho GDP dissociation inhibitor 2 suppresses metastasis via unconventional regulation of RhoGTPases. Cancer Res 2009 Apr 1;69(7):2838-44. PMID: 19276387 Wu Y, Moissoglu K, Wang H, Wang X et al. Src phosphorylation of RhoGDI2 regulates its metastasis suppressor function. Proc Natl Acad Sci U S A 2009 Apr 7;106(14):5807-12. PMID: 19321744 Smith SC, Theodorescu D. Learning therapeutic lessons from metastasis suppressor proteins. Nat Rev Cancer 2009 Apr;9(4):253-64. PMID: 19242414 Theodorescu D, Sapinoso LM, Conaway MR, Oxford G et al. Reduced expression of metastasis suppressor RhoGDI2 is associated with decreased survival for patients with bladder cancer. Clin Cancer Res 2004 Jun 1;10(11):3800-6. PMID: 15173088

ORGANISM(S): Homo sapiens

PROVIDER: GSE35014 | GEO | 2012/04/15

SECONDARY ACCESSION(S): PRJNA151163

REPOSITORIES: GEO

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Discovery of genes regulated by the metastasis suppressor gene, RhoGDI2

Project description:A number of studies find that metastasis suppressor proteins, including RhoGDI2, may function in part though controlling expression of genes regulating metastasis (reviewed in Smith and Theodorescu, Nature Reviews Cancer, 2009, PMID: 19242414). To uncover systematically gene expression patterns dependent on RhoGDI2 expression, we profiled gene expression in stably transfected control (GFP empty vector) UM-UC-3 bladder carcinoma cells (which have lost endogenous expression of RhoGDI2, as occurs commonly in the progression of bladder cancer PMID: 15173088), as well as stably transfected GFP-tagged RhoGDI2 expressing UM-UC-3 cells. References: Moissoglu K, McRoberts KS, Meier JA, Theodorescu D et al. Rho GDP dissociation inhibitor 2 suppresses metastasis via unconventional regulation of RhoGTPases. Cancer Res 2009 Apr 1;69(7):2838-44. PMID: 19276387 Wu Y, Moissoglu K, Wang H, Wang X et al. Src phosphorylation of RhoGDI2 regulates its metastasis suppressor function. Proc Natl Acad Sci U S A 2009 Apr 7;106(14):5807-12. PMID: 19321744 Smith SC, Theodorescu D. Learning therapeutic lessons from metastasis suppressor proteins. Nat Rev Cancer 2009 Apr;9(4):253-64. PMID: 19242414 Theodorescu D, Sapinoso LM, Conaway MR, Oxford G et al. Reduced expression of metastasis suppressor RhoGDI2 is associated with decreased survival for patients with bladder cancer. Clin Cancer Res 2004 Jun 1;10(11):3800-6. PMID: 15173088 Two paired biological replicates of GFP (control) and GFP-RhoGDI2 (experimental) UM-UC-3 cells were prepared at different times, isolated during log phase growth, and subjected to gene expression profiling using the Affymetrix HG-U133 Plus 2.0 oligonucleotide microarray platform.

2012-04-14 | E-GEOD-35014 | biostudies-arrayexpress

Role of the mRNA-binding protein HuR in the global transcriptomic status of cells stimulated with electrophiles and oxidants

Project description:HuR has been implicated as a stress-responsive protein: cytoplasmic translocation of HuR is promoted by several small-molecule stressors, e.g., H2O2, arsenite, and the cyclopentenone prostaglandin A2 (PGA2), a Michael acceptor RES (Wang et al., 2000; Yang et al., 2004). Treatment with PGA2 also increases the affinity of HuR for p21 mRNA (Wang et al., 2000). Intrigued by these reports, we launched HuR-dependent gene-expression profiling studies in the presence and absence of small-molecule stress signals. HNE—a native RES with a reactive core chemically similar to that of PGA2—was selected as a representative bioactive RES (Jacobs and Marnett, 2009; Schopfer et al., 2011) and H2O2 was selected as a representative ROS. shHuR and shControl HEK293T cells were first generated and then treated with HNE or H2O2 under the conditions where cell viability is largely unaffected. We subsequently sequenced their RNA post ribosomal RNA (rRNA) depletion (see details below). Significant differential expression was evaluated with CuffDiff (Trapnell et al., 2013).

2020-02-10 | GSE127444 | GEO

Comparison of Labeling Methods for gene expression analysis on the NimbleGen platform

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2009-11-25 | GSE15816 | GEO

APR-246 enhances colorectal cancer sensitivity to radiotherapy

Project description:p53 mutation is common and highly related to radiotherapy resistance in rectal cancer. APR-246, as a small molecule, can restore the tumor-suppressor function to mutant p53. There is no study on combining APR-246 with radiation in rectal cancer; therefore, we examined whether APR-246 sensitized colorectal cancer cells with different p53 status to radiation. The combination treatment had synergistic effects on HCT116p53-R248W/-(p53Mut) cells, followed by HCT116p53+/+(p53WT) cells, and exhibited an additive effect on HCT116p53-/-(p53Null) cells through inhibiting proliferation, enhancing reactive oxygen species, and apoptosis. The results were confirmed in zebrafish xenografts. Comparison of the transcriptome in colorectal cancer cells with different p53 status 72hrs post-treatment with APR-246, irradiation, or the combination of APR-246 with irradiation was carried out. p53Mut and p53WT cells shared more activated pathways and differentially expressed genes following the combination treatment, compared to p53Null cells, although the combination treatment regulated individual pathways in the different cell lines. APR-246 mediated radio-sensitization effects through p53-dependent and -independent ways.

2023-05-12 | GSE232305 | GEO

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Project description:Pulmonary exposure to multiwalled carbon nanotubes (MWCNT) induces an inflammatory and rapid fibrotic response, although the long-term signaling mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in mice blood to identify non-invasive blood based biomarkers for medical and occupational surveillance. The pathological results in this 1-year MWCNT post-exposure study was previously published in Snyder-Talkington et al. J Toxicol Environ Health A. 2016;79(8):352-66. doi: 10.1080/15287394.2016.1159635. Epub 2016 Apr 19. PMID: 27092743

2019-07-26 | GSE126959 | GEO

Down-regulation of SFRP1 in a mammary epithelial cell line

Project description:Microarray data to accompany Gauger et al. (2009) Cancer Cell International paper

2009-06-30 | GSE15948 | GEO

Alterations in the gene expression profile in SKOV3 cells exposed to elaiophylin

Project description:Elaiophylin was screened and identified as a novel autophagy inhibitor, with significant antitumor efficacy as a single agent. To explore the mechanisms by which elaiophylin kills cancer cells, NimbleGen 12x135K microarrays were used to find the gene expression changes in SKOV3 cells treated with elaiophylin for indicated time points. The gene expression microarray data were also analyzed and described in our previous study. Zhao, X., Fang, Y., Yang, Y., Qin, Y., Wu, P., Wang, T., Lai, H., Meng, L., Wang, D., Zheng, Z., Lu, X., Zhang, H., Gao, Q., Zhou, J., & Ma, D. (2015). Elaiophylin, a novel autophagy inhibitor, exerts antitumor activity as a single agent in ovarian cancer cells. Autophagy, 11(10), 1849–1863 (PMID: 25893854).

2022-06-07 | GSE205529 | GEO

Notch2 over expression in urinary bladder RT4V6 cell line

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2014-08-21 | E-GEOD-60564 | biostudies-arrayexpress

d630294d-2c12-413f-b1b5-c0b9946c8385 - samples

Project description:The dataset includes 144 BAM files of WGS, WES, and RNA-seq data from primary and PDOX samples analyzed in Smith et al, Acta Neuropathologica, 2020 (PMID: 32519082).

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Project description:Bladder cancer is one of the most common genitourinary malignancies worldwide. It is a heterogeneous disease at the clinical, pathological, and genetic levels. In an exome-sequencing study of bladder cancer, we identified genes mutated in bladder cancer coding for proteins involved in chromatin modification, cell division, and DNA repair. STAG2, a constituent of the cohesin complex, was commonly mutated or lost, mainly in tumors of low stage or grade. Loss of STAG2 expression was often observed in genomically stable tumors, suggesting that STAG2 may act as a tumor suppressor through mechanisms other than chromosome segregation (Balbás-Martínez et al. 2013). In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and organization of the genome into Topologically Associating Domains (TADs). Two variant cohesin complexes that contain either STAG1 or STAG2 are present in all cell type. Here we addressed their genome wide binding in bladder cancer cells.

2021-03-15 | GSE111913 | GEO

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