RNA-seq of cells with centrosome amplification
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Cell scraper, NEB Next Ultra RNA Library Prep Kit for Illumina, NextSeq 500, RNeasy kit
ORGANISM(S): Homo sapiens
SUBMITTER: Selwin Wu
PROVIDER: E-MTAB-11126 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The presence of extra centrosomes is a feature of human tumours. However, it is unclear what are the changes elicited by the presence of these abnormalities. To determine the changes in gene expression induced by centrosome amplification, human mammary epithelial cells, MCF10A, expressing a doxycycline inducible PLK4 cDNA were used. Centrosome amplification was induced for 48 hrs upon the addition of doxycyclin to the culture medium. RNA was purified from MCF10A cells without extra centrosomes (no dox) and with extra centrosomes (dox) and processed for microarray analysis.
2018-02-10 | E-MTAB-6415 | biostudies-arrayexpress
Project description:A non-functional myosin Vb motor in duodenal enterocytes results in disruption of epithelial cell polarity characterized by complete loss of microvilli and mislocalization of apical brush border proteins in the cytoplasm which finally cause a devastating disease in neonates with severe malabsorption defects accompanied by protracted diarrhea during infancy, classified as microvillus inclusion disease (MVID). The exact mechanisms how loss-of-function of MYO5B induces polarity loss are not completely understood in MVID pathogenesis. Obtaining better insights in cell polarity defects caused by loss of MYO5B, we performed microarray- in combination with protein expression-analysis in an inducible CaCo2 MYO5B RNAi cell system. Surprisingly, in MYO5B-depleted CaCo2 cells, CDH1 coding for the cell adhesion protein E-Cadherin and important for cell adhesion and therefore maintenance of cell polarity, was significantly downregulated. Interestingly, mesenchymal cell markers, specifically Vimentin and N-Cadherin, physiologically not expressed in differentiated epithelium, were upregulated and accompanied by increased phospho-c-jun levels in the nucleus. Importantly phospho-c-jun was also found in nuclei of duodenal enterocytes in MVID patients, indicating loss of MYO5B induces epithelial cell scattering in enterocytes. 3 Myosin 5B KD versus 3 control samples
2013-03-14 | E-GEOD-45134 | biostudies-arrayexpress
Project description:Centrosome amplification is a common feature of human tumors, but whether this is a cause or a consequence of human cancer remains unclear. Here, we report the creation of a mouse model in which centrosome number can be persistently increased in the absence of additional genetic defects. We show that extra centrosomes increase tumor initiation in a mouse model of intestinal neoplasia. Most importantly, we demonstrate that supernumerary centrosomes are sufficient to drive development of spontaneous tumors in multiple tissues. Tumors with centrosome amplification exhibit frequent mitotic errors and possess complex karyotypes, recapitulating a common feature of human cancer. Together, our data support a direct causal relationship between centrosome amplification, genomic instability and tumor development. The sequences in this dataset result from random whole-genome DNA sequencing of spontaneous T- cell lymphomas, B-cell lymphomas, squamous cell carcinomas and one sarcoma from doxycycline-treated Plk4 mice.
2017-02-04 | E-MTAB-5043 | biostudies-arrayexpress
Project description:Although splicing occurs in most multi-exon genes, the generation of distinct isoforms through the alternate use of mutually exclusive exons is less prevalent. As exon-switching events have the potential to give rise to isoforms with different cellular functions, we have explored the role of the muscle-specific (Mef2Da2) and ubiquitously expressed (Mef2Da1) isoforms of the transcription factor Mef2D in myogenesis. Here we show that both isoforms of Mef2D bind a largely overlapping subset of genomic loci, yet only the muscle-specific Mef2Da2 isoform can activate the late myogenic gene expression program. This differential ability to activate transcription is modulated by PKA signaling where Mef2Da1 is efficiently phosphorylated by the kinase to enhance its association with repressive HDAC-deacetylase complexes. In contrast, alternate exon usage in Mef2Da2 renders the protein resistant to PKA phosphorylation, allowing it to interact with transcriptionally permissive Ash2L-trithorax complex. Our findings support a model wherein alternative exon usage allows Mef2D to transition from a repressor to activator in a myogenic environment rich in PKA activity. Thus we have identified a novel paradigm in which a ubiquitously expressed transcription factor has evolved to undergo tissue-specific alternative exon usage to permit the proper temporal activation of a gene expression program during differentiation. RNA-Seq profiling of C2C12 cells with exogenous expression of Mef2Da1 and Mef2Da2
2013-06-03 | E-GEOD-46363 | biostudies-arrayexpress
Project description:They aim of the study is to identify targets of Carboxypeptidase E (CPE) as well as signaling cascades that are affected by CPE which are specific for transmitting its anti-migratory effects in glioma cells by overexpressing CPE and using transcriptomics profiling of mRNAs and microRNAs.
2017-11-29 | E-MTAB-5297 | biostudies-arrayexpress
Project description:They aim of the study is to identify targets of Carboxypeptidase E (CPE) as well as signaling cascades that are affected by CPE which are specific for transmitting its anti-migratory effects in glioma cells by overexpressing CPE and using transcriptomics profiling of mRNAs and microRNAs.
2017-11-29 | E-MTAB-5299 | biostudies-arrayexpress
Project description:Polo-like kinase 4 (PLK4) is the master regulator of centriole duplication in metazoan organisms. Catalytic activity and protein turnover of PLK4 are tightly coupled in human cells, since changes in PLK4 concentration and catalysis have profound effects on centriole duplication and supernumerary centrosomes, which are associated with aneuploidy and cancer. Recently, PLK4 has been targeted with a variety of small molecule kinase inhibitors exemplified by centrinone, which induces inhibitory effects on PLK4 and can lead to on-target centrosome depletion. Despite this, relatively few PLK4 substrates have been identified unequivocally in human cells, and the extent of PLK4 signalling remains poorly characterised. We report an unbiased mass spectrometry-based quantitative analysis of cellular protein phosphorylation in stable PLK4-expressing human cells exposed to the small molecule inhibitor centrinone. PLK4 phosphorylation was itself sensitive to brief exposure to centrinone, resulting in PLK4 stabilization. A drug-resistant PLK4 mutant (G95R) confirmed several on-target effects of the compound towards PLK4. Using this experimental system, we report hundreds of centrinone-regulated phosphoproteins in U2OS cells, including centrosomal and cell cycle proteins and a variety of likely non cell-cycle substrates. Surprisingly, sequence interrogation of ~300 significantly downregulated phosphoproteins reveals an extensive network of centrinone-sensitive [Ser/Thr]Pro phosphorylation target sequence motifs, which based on our analysis might be either direct or indirect targets of PLK4. In addition, we confirm NMYC and PTPN12 as new PLK4 substrates, both in vitro and in human cells. Our findings suggest that PLK4 catalytic output directly controls the phosphorylation of a diverse set of cellular proteins, including Pro-directed targets that are likely to be important in PLK4-mediated cell signalling.
2021-06-14 | PXD018704 | Pride
Project description:This study aimed to further our understanding of the role that CXCR6 plays in breast cancer progression. Microarrays were searched for some genes that had correlated expression with CXCR6 mRNA. According to fold-change screening between restoring expression of CXCR6 and its respective control cells in MDA-MB-231 and MCF-7 cells, both up-regulated and down-regulated genes were shown. The restoring of CXCR6 expression in MDA-MB-231 and MCF-7 cells were respectively noted as MDA-MB-231-CXCR6 and MCF-7-CXCR6 cells and the respective controls were noted as MDA-MB-231-GFP and MCF-7-GFP cells.
2015-06-30 | E-GEOD-60484 | biostudies-arrayexpress
Project description:Immunotherapy efficacy is limited in melanoma, and combinations of immunotherapies with other modalities have yielded limited improvements but also adverse events requiring cessation of treatment. In addition to ineffective patient stratification, efficacy is impaired by paucity of intratumoral immune cells (itICs)—thus, effective strategies to safely increase itICs are needed. We report that dietary administration of L-fucose induces fucosylation and cell surface enrichment of the MHC-II protein HLA-DRB1 in melanoma cells, triggering CD4+T cell-mediated increases in ItICs and anti-tumor immunity, enhancing immune checkpoint blockade responses. Melanoma fucosylation and fucosylated HLA-DRB1 associate with intratumoral T cell abundance and anti-PD1 responder status in patient melanoma specimens, suggesting the potential use of melanoma fucosylation as a strategy for stratifying patients for immunotherapies. Our findings demonstrate that fucosylation is a key mediator of anti-tumor immunity, and importantly, suggest that L-fucose is a powerful agent for safely increasing ItICs and immunotherapy efficacy in melanoma.
2022-12-16 | PXD038303 | Pride
Project description:MicroRNAs can play important roles in gene regulation affecting both normal development and diseases, including cancer. This microarray experiment was performed to identify genes and pathways differentially expressed in MOLT4 T-leukemia cells engineered to overexpress hsa-pre-miR-22-3p. MOLT4 cells transduced with an empty or hsa-pre-miR-22-3p lentiviral vectors were collected, processed for RNA extraction and hybridized on Affymetrix Clariom™ S Human arrays (n=3 replicates/group). Raw microarray data are available together with the applied protocols.
2020-07-30 | E-MTAB-9280 | biostudies-arrayexpress