Regulation of Embryonic and Induced Pluripotency by Aurora Kinase-p53 Signaling
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE23541 | GEO | 2012/05/30
SECONDARY ACCESSION(S): PRJNA131833
REPOSITORIES: GEO
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Project description:Illumina Beadchip array analyses of mouse embryonic stem cell gene expression profiles in the presence of or upon knockdown of Aurka. An ES complementation 'rescue' system was employed to measure the effects of knockdown (minus Dox). Aurka was rescued to wildtype levels in the presence of Dox (plus Dox). A control rescue ES cell line, with a Luciferase-targeting shRNA, was also assessed. Total of 12 samples; Aurka_R (+/-Dox) and Control_R (+/-Dox); all performed in triplicates
2012-05-29 | E-GEOD-23541 | biostudies-arrayexpress
Project description:Illumina BeadChip array analyses of mouse embryonic stem cell gene expression profiles in the presence of or upon knockdown of 4 candidate factors regulating genomic integrity -- Chek1, Ppm1g, Ppp2r1b and Bub1b. An ES complementation 'rescue' system was employed to measure the effects of knockdown (minus Dox). The 4 candidate factors are rescued to wildtype levels in the presence of Dox (plus Dox). A control rescue ES cell line, with a Luciferase-targeting shRNA, was also assessed.
2018-11-01 | GSE111982 | GEO
Project description:Purpose: The goal of this study was to determine a specific gene expression profile of Nuclear Aurora-A Kinase expressing cells. It has been previously shown that AURKA localizes to the nucleus in patient biopsies in multiple aggressive malignancies including breast cancer but functional significance of this localization in cancer progression is still undetermined. To define the role nuclear AURKA plays in metastatic dissemination and colonization of distant organs, we created TNBC (triple negative breast cancer) cell lines with CRISPR/Cas9 based deletion of endogenous AURKA and rescue with exogenous AURKA specifically targeted to the nucleus, cytoplasm or both. The TNBC cells expressing nuclear AURKA show significant increase in dissemination and colonization of multiple organs when compared to controls. The RNA sequencing analysis of nuclear AURKA expressing cell lines shows significant changes in gene expression profile associated with hypoxia, migration/invasion and survival/death pathways supporting the metastatic phenotype observed in vivo. Methods: The total RNA was isolated using Quagen RNeasy kit, the library was build using KAPA mRNA Hyper Prep Kit with TruSeq adapters for the build, RNA profiles of WT-AURKA, NES-AURKA, NLS-AURKA and Empty (including no-localization tag-Empty, NLS-empty, NES-empty) vector controls expressing MDA-MB-231 cells were generated by deep sequencing of 2 biological clones of each cell line in triplicate, using Illumina HiSeq2500, 2 x 50 paired-end reads in the High Output Mode. The sequence reads that passed quality filters were analyzed with Hisat2 followed by Samtools. Genes whose expression is changed between the control samples and WT, NES, NLS-AURKA samples were identified using Partek Genomic Suite and functions associated with that set of genes mapped using Ingenuity Pathway Analysis. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow, we identified 33,563 transcripts after mapping reads to the human genome. Approximately 3,000 of the transcripts showed differential expression between the Empty control and NLS-AURKA and NES-AURKA, with a fold change ≥1.5 and p value <0.05. Altered expression of 96 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several well characterized genes that contribute to hypoxia, migration/invasion and survival/death pathways. Data analysis revealed a significant changes in transcriptome profiling upon introduction of AURKA in the nucleus supporting its active role on regulation of transcription. Conclusions: Our study represents the first detailed analysis of transcriptome changes upon manipulation of AURKA localization in triple negative breast cancer cells, with multiple biologic and technical replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles in patient samples in future studies. Our results show that AURKA expression in nucleus might be a key event triggering metastatic dissemination and offers a comprehensive and qualitative evaluation of mRNA content. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions of nuclear AURKA.
2021-01-31 | GSE154494 | GEO
Project description:The exon junction complex is involved in gene expression regulation on multiple co- and post-transcriptional levels. We aimed to investigate in HeLa Tet-Off cells which gene expression alterations can be observed upon knockdown of core EJC factors (EIF4A3, RBM8A and MAGOH) or upon EIF4A3 knockdown and rescue with EIF4A3 wild type construct by using RNA-Seq analyses. The rescue construct was stably integrated into the genome using the PiggyBac transposon system. As control Luciferase (Luc) siRNA was used.
2022-05-06 | E-MTAB-10771 | biostudies-arrayexpress
Project description:CXCR7, an atypical chemokine receptor (ACKR3), is up-regulated in NEPC, and its expression is associated with molecular markers of NEPC and cell proliferation. Transcriptomic analyses revealed a major role of CXCR7 in regulating downstream genes involved in the cell cycle and mitotic spindle. Membrane-bound CXCR7 is known to recruit β-arrestin (ARRB2), and the complex internalizes into clathrin-coated vesicles where they act as a scaffold for cytoplasmic kinase assembly and substrate activation. We identify Aurora Kinase A (AURKA) as a top candidate that is binding to and activated by CXCR7-ARRB2. Immunofluorescence confocal microscopy detected high-density CXCR7, ARRB2, and AURKA in the pericentrosomal area with focal staining of ARRB2 and ARUKA at centrosomes. Mass spectrometry showed that CXCR7 interacts with many proteins associated with intracellular vesicles, microtubules, and Golgi apparatus. CXCR7-ARRB2-containing vesicles traffic along the microtubules to the perinuclear Golgi apparatus, where CXCR7-ARRB2 interacts with AURKA to promote its activation and cell growth. Finally, we showed that pharmacological inhibitors of AURKA abolish CXCR7-driven tumor growth. Our study reveals CXCR7-mediated activation of AURKA and establishes CXCR7 and its downstream kinases as critical targets for therapeutic intervention in CRPC or NEPC patients.
2023-05-14 | GSE199274 | GEO
Project description:To unravel the molecular mechanism by which HOXB4 promotes the expansion of early hematopoietic progenitors within differentiating ES cells, we analzed the gene expression profiles of embryoid bodies (EBs) in which transcription of HOXB4 had been induced or not induced. A substantial number of the identified HOXB4 target genes are involved in signaling pathways important for controlling self-renewal, maintenance and differentiation of stem cells. Furthermore, we demonstrate that HOXB4 activity and FGF-signaling are intertwined. HOXB4-mediated expansion of ES cell-derived early progenitors was enhanced by specific and complete inhibition of FGF-receptors. In contrast, the expanding activity of HOXB4 on hematopoietic progenitors in day4-6 embryoid bodies was blunted in the presence of basic FGF (FGF2) indicating a dominant negative effect of FGF-signaling on the earliest hematopoietic cells. Taken together, we show that modulation of FGF signaling is an essential feature of HOXB4 activity in the context of embryonic hematopoiesis. Keywords: plus/minus induction of HOXB4 gene expression by treatment with doxycycline (Dox)
2007-09-19 | GSE9044 | GEO
Project description:A number of key regulators of mouse embryonic stem (ES) cell identity, including the transcription factor Nanog, show strong expression fluctuations at the single cell level. The molecular basis for these fluctuations is unknown. Here we used a genetic complementation strategy to investigate expression changes during transient periods of Nanog downregulation. Employing an integrated approach, that includes high-throughput single cell transcriptional profiling and mathematical modelling, we found that early molecular changes subsequent to Nanog loss are stochastic and reversible. However, analysis also revealed that Nanog loss severely compromises the self-sustaining feedback structure of the ES cell regulatory network. Consequently, these nascent changes soon become consolidated to committed fate decisions in the prolonged absence of Nanog. Consistent with this, we found that exogenous regulation of Nanog-dependent feedback control mechanisms produced more a homogeneous ES cell population. Taken together our results indicate that Nanog-dependent feedback loops play a role in controlling both ES cell fate decisions and population variability. Total of 30 samples, 10 conditions in triplicates; Cell samples were harvested at day0 (Dox present, Nanog expressing, NgR day0 +Dox), and at days 1,3 and 5 days after dox withdrawal (NgR day1 -Dox, NgR day3 -Dox and NgR day5 -Dox respectively). Additionally, at each time-point a set of samples was further treated with a twelve-hour pulse of dox before being harvested (NgR day1+ 12h Dox, NgR day3+12h Dox and NgR day5+12h Dox) and compared with untreated control samples harvested at the same time (NgR day1- 12h Dox, NgR day3-12h Dox and NgR day5-12h Dox) . All time points were performed in triplicates. We performed Affymetrix GeneChip® Mouse Gene 1.0 ST arrays analyses of mouse embryonic stem cell gene expression profiles at each time point. BD MacArthur and A Sevilla contributed equally to this study
2012-08-30 | E-GEOD-40335 | biostudies-arrayexpress
Project description:Gene expression in VCaP prostate cancer cells treated with or without androgen was analyzed. VCaP cells containing a dox-inducible shRNA against Dtx3L were compared with and without dox induction (Dtx3L knockdown), in the presence or absence of androgen.
2019-07-06 | GSE133876 | GEO
Project description:By integration of transcriptome, CHIP-seq, ATAC-seq, proteomic and metabolite screening followed by carbon tracing (U-13C-Glucose, U-13C-Glutamine and U-13C-Palmitic acid) and extracellular flux analysis we provided evidence that genetic (shRNA and CRISPR/Cas9) and pharmacological (Alisertib) AURKA inhibition elicited substantial metabolic reprogramming supported in part by inhibition of MYC targets and concomitant activation of PPARA signaling. While glycolysis was suppressed by AURKA inhibition, we noted a compensatory increase in oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO). Whereas interference with AURKA elicited a suppression of c-Myc, we detected an upregulation of PGC1α, a master regulator of oxidative metabolism, upon AURKA inhibition. Chromatin immunoprecipitation experiments confirmed binding of c-Myc to the promoter region of PGC1α, which is abrogated by AURKA inhibition and in turn unleashed PGC1α expression. To interfere with this oxidative metabolic reprogramming, we combined AURKA inhibitors with inhibitors of FAO (etomoxir) and electron transport chain (gamitrinib) and found substantial synergistic growth inhibition in patient derived xenograft in vitro and extension of overall survival without induction of toxicity in normal tissue.
2021-06-01 | GSE161573 | GEO
Project description:By integration of transcriptome, CHIP-seq, ATAC-seq, proteomic and metabolite screening followed by carbon tracing (U-13C-Glucose, U-13C-Glutamine and U-13C-Palmitic acid) and extracellular flux analysis we provided evidence that genetic (shRNA and CRISPR/Cas9) and pharmacological (Alisertib) AURKA inhibition elicited substantial metabolic reprogramming supported in part by inhibition of MYC targets and concomitant activation of PPARA signaling. While glycolysis was suppressed by AURKA inhibition, we noted a compensatory increase in oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO). Whereas interference with AURKA elicited a suppression of c-Myc, we detected an upregulation of PGC1α, a master regulator of oxidative metabolism, upon AURKA inhibition. Chromatin immunoprecipitation experiments confirmed binding of c-Myc to the promoter region of PGC1α, which is abrogated by AURKA inhibition and in turn unleashed PGC1α expression. To interfere with this oxidative metabolic reprogramming, we combined AURKA inhibitors with inhibitors of FAO (etomoxir) and electron transport chain (gamitrinib) and found substantial synergistic growth inhibition in patient derived xenograft in vitro and extension of overall survival without induction of toxicity in normal tissue.
2021-06-01 | GSE161572 | GEO