Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA97353 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have used microarray technology to identify the transcriptional targets of Rho subfamily GTPases. This analysis indicated that murine fibroblasts transformed by these proteins show similar transcriptomal profiles. Functional annotation of the regulated genes indicate that Rho subfamily GTPases target a wide spectrum of biological functions, although loci encoding proteins linked to proliferation and DNA synthesis/transcription are up-regulated preferentially. Rho proteins promote four main networks of interacting proteins nucleated around E2F, c-Jun, c-Myc, and p53. Of those, E2F, c-Jun and c-Myc are essential for the maintenance of cell transformation. Inhibition of Rock, one of the main Rho GTPase targets, leads to small changes in the transcriptome of Rho-transformed cells. Rock inhibition decreases c-myc gene expression without affecting the E2F and c-Jun pathways. Loss-of-function studies demonstrate that c-Myc is important for the blockage of cell-contact inhibition rather than for promoting the proliferation of Rho-transformed cells. However, c-Myc overexpression does not bypass the inhibition of cell transformation induced by Rock blockage, indicating that c-Myc is essential, but not sufficient, for Rock-dependent transformation. These results reveal the complexity of the genetic program orchestrated by the Rho subfamily and pinpoint protein networks that mediate different aspects of the malignant phenotype of Rho-transformed cells Keywords: Rho/Rac GTPases, microarray, oncogenesis, proliferation, gene expression, transcription, Rock, c-Myc
2007-01-03 | GSE5913 | GEO
Project description:Rho family small GTPases serve as molecular switches in the regulation of diverse cellular functions including actin cytoskeleton remodeling, cell migration, gene transcription, and cell proliferation. Importantly, Rho overexpression is frequently seen in many carcinomas. However, published studies have almost invariably utilized immortal or tumorigenic cell lines to study Rho GTPase functions and there are no studies on the potential of Rho small GTPase to overcome senescence checkpoints and induce preneoplastic transformation of human mammary epithelial cells (hMECs). We found that ectopic expression of wild-type RhoA as well as a constitutively-active RhoA mutant (G14V) in primary hMEC strains led to their immortalization and preneoplastic transformation. Significantly, RhoA-T37A mutant, known to be incapable of interacting with many well known Rho-effectors ,was also capable of immortalizing hMECs.Our results demonstrate that RhoA can induce the preneoplastic transformation of hMECs by altering multiple pathways linked cellular transformation and breast cancer. Through microarray analysis, we want to identify genes and pathways linked to RhoA induced hMECs immortalization. Experiment Overall Design: 4 samples, in triplicate analyses per sample.
2008-10-26 | E-GEOD-12917 | biostudies-arrayexpress
Project description:We have used microarray technology to identify the transcriptional targets of Rho subfamily GTPases. This analysis indicated that murine fibroblasts transformed by these proteins show similar transcriptomal profiles. Functional annotation of the regulated genes indicate that Rho subfamily GTPases target a wide spectrum of biological functions, although loci encoding proteins linked to proliferation and DNA synthesis/transcription are up-regulated preferentially. Rho proteins promote four main networks of interacting proteins nucleated around E2F, c-Jun, c-Myc, and p53. Of those, E2F, c-Jun and c-Myc are essential for the maintenance of cell transformation. Inhibition of Rock, one of the main Rho GTPase targets, leads to small changes in the transcriptome of Rho-transformed cells. Rock inhibition decreases c-myc gene expression without affecting the E2F and c-Jun pathways. Loss-of-function studies demonstrate that c-Myc is important for the blockage of cell-contact inhibition rather than for promoting the proliferation of Rho-transformed cells. However, c-Myc overexpression does not bypass the inhibition of cell transformation induced by Rock blockage, indicating that c-Myc is essential, but not sufficient, for Rock-dependent transformation. These results reveal the complexity of the genetic program orchestrated by the Rho subfamily and pinpoint protein networks that mediate different aspects of the malignant phenotype of Rho-transformed cells Experiment Overall Design: In order to generate the cell clones used in this study, we took advantage of the oncogenic properties of the constitutively active versions (Q63L mutants) of Rho subfamily proteins when overexpressed in rodent fibroblasts (Schuebel et al., 1998). Based on this property, we transfected NIH3T3 cells with plasmids encoding the indicated versions of Rho subfamily proteins to obtain foci of transformed cells. Selected foci were picked, pooled, and used for the subsequent microarray experiments. Experiment Overall Design: To avoid the activation of genetic programs related to serum withdrawal or contact inhibition that may confound the detection of Rho-specific transcriptomal changes (Coller et al., 2006), we cultured the chosen cell lines and the parental NIH3T3 cells in the presence of serum and maintained them at confluency levels lower than 70% prior to RNA extraction. In addition, we isolated total RNAs from eight (in the case of NIH3T3 cells), seven (in the case of RhoAQ63L-transformed cells) and six (in the case of RhoBQ63L- and RhoCQ63L-transformed cells) independent cell cultures in order to make it possible a robust statistical treatment of the data obtained. Experiment Overall Design: three 10-cm diameter plates containing exponentially growing cultures of IMB11-1P (expressing RhoAQ63L) IMB11-2P (expressing RhoBQ63L), or IMB11-3P (expressing RhoCQ63L) cells were washed with PBS and their total cellular RNAs isolated using the RNeasy kit (Qiagen) according to the supplierâs specifications. The quantity and quality of the total RNAs obtained was determined using 6000 Nano Chips (Agilent Technologies). Total RNA samples (4 ug) were then processed for hybridization on MGU75Av2 microarrays (Affymetrix) using standard Affymetrix protocols at the CIC Genomics and Proteomics Facility (www.cicancer.org). Normalization, filtering and analysis of the raw data obtained from the microarrays was carried out with the Bioconductor software (www.bioconductor.com) using de ReadAffy package and the RMA application. The RMA algorithm was selected over the standard Affymetrix software because it provides a better precision in signal detection to achieve adequate normalization of multiple microarray hybridizations, especially in cases of low levels of gene expression (Bolstad et al., 2004; Gautier et al., 2004; Gentleman et al., 2004; Parrish & Spencer, 2004). We considered a gene to be differentially expressed when exhibiting a signal ⥠100 and met the following criteria: in the case of the characterization of the transcriptome of Rho-transformed cells, we regarded a gene as common to all GTPases when: i) It showed a fold change ⥠1.5 in at least two of the cell lines used. ii) The fold change in the third cell line was ⥠1.0 and displayed a similar variation trend when compared to the other two cell lines (i.e., similar up-regulation or down-modulation in the three cell lines). iii) The fold change values in the three cell lines had always P values ⤠0.01. We regarded a gene as common to only two GTPases when: i) It showed a fold change ⥠1.5 in two the cell lines with P values ⤠0.01. ii) The fold change in the third cell line was non-existent or, alternatively, had P values ⥠0.01. We considered a gene as uniquely-regulated by a GTPase when: i) The fold change in the expression levels of is transcript in the cell line transformed by that GTPase was ⥠1.5 with P value ⤠0.01. ii) The fold change, if any, obtained in the other cell lines had P values ⥠0.01. Statistical analyses were performed using F-statistics.
2008-06-14 | E-GEOD-5913 | biostudies-arrayexpress
Project description:Rho family small GTPases serve as molecular switches in the regulation of diverse cellular functions including actin cytoskeleton remodeling, cell migration, gene transcription, and cell proliferation. Importantly, Rho overexpression is frequently seen in many carcinomas. However, published studies have almost invariably utilized immortal or tumorigenic cell lines to study Rho GTPase functions and there are no studies on the potential of Rho small GTPase to overcome senescence checkpoints and induce preneoplastic transformation of human mammary epithelial cells (hMECs). We found that ectopic expression of wild-type RhoA as well as a constitutively-active RhoA mutant (G14V) in primary hMEC strains led to their immortalization and preneoplastic transformation. Significantly, RhoA-T37A mutant, known to be incapable of interacting with many well known Rho-effectors ,was also capable of immortalizing hMECs.Our results demonstrate that RhoA can induce the preneoplastic transformation of hMECs by altering multiple pathways linked cellular transformation and breast cancer. Through microarray analysis, we want to identify genes and pathways linked to RhoA induced hMECs immortalization.
2008-09-26 | GSE12917 | GEO
Project description:RHO subfamily of small GTPases comprise highly conserved family members RHOA, RHOB, and RHOC which cycle between GTP-bound 'active' and GDP-bound 'inactive' states. In the active form, RHO proteins interact with a variety of downstream effector proteins, controlling their activity and function. Many of the RHO subfamily effector proteins such as ROCK, PKN, and mDIA, are key regulators of actin cytoskeleton and cell motility. To identify novel effector proteins for RHOA,we carried out a GST-pulldown from heavy or light SILAC labelled HeLa cells using GST tagged GTP-bound RHOA, or GST alone control, as bait. Pulldowns were performed in duplicates with switched labellings. Specific interactors were destinguished from the background on the basis of SILAC Heavy to Light ratios between GST-RHOA and GST alone pulldowns.
2016-11-01 | PXD004934 | Pride
Project description:The Rho family GTPases, Rac and Rho, play critical roles in transmitting mechanical information contained within the extracellular matrix (ECM) to the cell. Rac and Rho have well described roles in regulating stiffness-dependent actin remodeling, proliferation and motility. However, much less is known about the relative roles of these GTPases in stiffness-dependent transcription, particularly at the genome-wide level. Here, we selectively inhibited Rac and Rho in mouse embryonic fibroblasts cultured on deformable substrata and used RNA sequencing to elucidate and compare the contribution of these GTPases to the early transcriptional response to ECM stiffness. Surprisingly, we found that the stiffness-dependent activation of Rac is dominant over Rho in the initial transcriptional response to ECM stiffness. We also identified Activating Transcription Factor 3 (ATF3) as a major target of stiffness/Rac-mediated signaling and show that ATF3 repression by ECM stiffness helps to explain how the stiffness-dependent activation of Rac results in the induction of cyclin D1.
2023-10-04 | GSE236266 | GEO
Project description:This is a ordinary differential equation mathematical model describing the Rho GTPase cycle in which Rho GDP-dissociation inhibitors (RhoGDIs) inhibit the regulatory activities of guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) by interacting with them directly as well as by sequestering the Rho GTPases. The model was constructed with the intent of analyzing the role of RhoGDIs in Rho GTPase signaling.
2019-12-17 | BIOMD0000000899 | BioModels
Project description:We performed CBX3 knockdown in lung adenocarcinoma cells along with RNA sequencing. The expression profiling showed Rho GTPases signaling as a potential CBX3 target and the conclusions were also verified in clinical samples.
2021-05-05 | GSE173858 | GEO
Project description:Although Rho GTPases are essential molecular switches involved in many cellular processes, an unbiased experimental comparison of their interaction partners was not yet performed. Here, we develop quantitative GTPase affinity purification (qGAP) to systematically identify interaction partners of six Rho GTPases (Cdc42, Rac1, RhoA, RhoB, RhoC, RhoD) depending on their nucleotide loading state. We use Stable isotope labeling by Amino acids in cell culture (SILAC) and label free quantification (LFQ). Our interaction network contains many new proteins, reveals highly promiscuous binding of several effectors and mirrors evolutionary relationships of Rho GTPases.
2016-12-23 | PXD004190 | Pride
Project description:Rho-GTPases are small GTP-binding proteins that contribute to the epithelial-to-mesenchymal transition by regulating several cellular processes including organization of the actin cytoskeleton, cell motility, transcription, and cell proliferation. Overexpression of RhoC-GTPases (RhoC) in breast cancer has been implicated in poor disease prognosis due to increased cancer cells invasion, migration, and motility, which warranted its consideration as a therapeutic target for inhibiting breast cancer metastasis. Using silencing RNA (siRNA) molecules to knockdown RhoC expression is a promising approach to inhibit breast cancer metastases.
2015-02-11 | ST000282 | MetabolomicsWorkbench