MRNA profiling of Asns-silenced murine 4T1-T breast cancer cells grown in the presence and absence of Asparagine
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE104964 | GEO | 2018/02/07
REPOSITORIES: GEO
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Project description:Murine 4T1-T Breast cancer cells were infected with retroviral vectors harboring shRNAs for murine or a Renilla, as negative control. After selection cells were harvested and processed with the NuGen Ovation RNAseq system V2. Libraries were sequenced on an Illumina platform and mapped using Bowtie2 to the mm10 genome prior to transcript quantification using HT-Count.
2018-02-07 | GSE104967 | GEO
Project description:Germinal centre (GC) B cells proliferate at some of the highest rates of any mammalian cell. Yet the metabolic processes which enable this are poorly understood. We performed integrated metabolomic and transcriptomic profiling of GC B cells, and found that asparagine metabolism is highly upregulated. Asparagine is conditionally essential to B cells, and its synthetic enzyme, asparagine synthetase (ASNS) is markedly upregulated following their activation, through the integrated stress response sensor general control non-derepressible 2 (GCN2). When Asns is deleted, B cell survival in low asparagine conditions is severely impaired. Using stable isotope tracing, we found that metabolic adaptation to the absence of asparagine requires ASNS, and that the synthesis of nucleotides is particularly sensitive to asparagine deprivation. Conditional deletion of Asns in B cells selectively impairs GC formation, associated with a reduction in RNA synthesis rates. Finally, removal of environmental asparagine by asparaginase was found to also severely compromise the GC reaction.
2024-04-03 | GSE228845 | GEO
Project description:Murine 4T1-T breast cancer cells were infected with retroviral vectors harboring shRNAs for murine or a Renilla, as negative control. Cells were orthotopically injected into NSG mice. After 19 days mice were euthanized and tumors and lungs were removed and digested into single cells. Cells were then placed in culture dishes with 6TG. Surviving cells were then harvested and processed with the NuGen Ovation RNAseq system V2. Libraries were sequenced on an Illumina platform and mapped using Bowtie2 to the mm10 genome prior to transcript quantification using HT-Count.
2018-02-07 | GSE104966 | GEO
Project description:mRNA profiling of Asns-silenced murine 4T1-T breast cancer cells grown in the presence and absence of Asparagine
| PRJNA414244 | ENA
Project description:Single - cell profiling of patient tumours and of mouse models is revealing that many cancers are constituted of communities of genetically and phenotypically distinct clonal lineages 1 - 12. A functional model of breast cancer heterogeneity revealed that clonal sub - populations proficient at generating circulating tumour cells were not equally capable of forming metastases at secondary sites 13. A combination of differential expression and focused in vitro and in vivo RNAi screens revealed candidate drivers of metastasis discriminating these clones, which were then evaluated in gene expression datasets from breast cancer patients. Among these, Asparagine Synthetase (Asns) expression in a patient's primary tumour was most strongly correlated with later metastatic relapse. Silencing of Asns reduced both metastatic potential in vivo and invasive potential in vitro. Conversely, increasing the availability of extracellular asparagine increased the invasive potential of mouse and human breast cancer cells, and enforced Asns expression promoted metastasis. Decreasing asparagine availability in mice by treatment with L-asparaginase or even by dietary restriction strongly reduced metastasis from orthotopic tumours. Asparagine availability varies betwe en tissues, potentially explaining selective effects on particular steps of tumor progression. Asparagine limitation reduced the production of proteins that promote the epithelial to mesenchymal transition, providing one potential mechanism for how the availability of a single amino acid could regulate metastatic progression.
2018-02-08 | GSE107109 | GEO
Project description:Asparagine synthetase (ASNS) is a gene on the long arm of chromosome 7 that is copy number amplified in the majority of glioblastomas. ASNS copy number amplification is associated with a significantly decreased survival. Using patient-derived glioma stem cells (GSCs), we showed significant metabolic alterations occur in gliomas when perturbing the expression of asparagine synthetase, which is not merely restricted to amino acid homeostasis. ASNS-high GSCs maintained a slower basal metabolic profile yet readily shifted to a greatly increased capacity for glycolysis and oxidative phosphorylation when needed. This led ASNS-high cells to a greater ability to proliferate and spread into brain tissue. Finally, we demonstrate that these changes confer resistance to cellular stress, notably oxidative stress, through adaptive redox homeostasis which led to radiation resistance. Furthermore, ASNS overexpression led to modifications of the one-carbon metabolism to promote a more antioxidant tumor environment revealing a metabolic vulnerability that may be therapeutically exploited.
2021-08-18 | GSE171163 | GEO
Project description:Using a functional model of breast cancer heterogeneity, we previously showed that clonal sub-populations proficient at generating circulating tumour cells were not all equally capable of forming metastases at secondary sites1. A combination of differential expression and focused in vitro and in vivo RNAi screens revealed candidate drivers of metastasis that discriminated metastatic clones. Among these, Asparagine Synthetase (ASNS) expression in a patient’s primary tumour was most strongly correlated with later metastatic relapse. Here, we have shown that asparagine bioavailability strongly influences metastatic potential. Limiting asparagine by Asns knockdown, treatment with L-asparaginase, or dietary asparagine restriction reduced metastasis without impacting growth of the primary tumour, whereas increased dietary asparagine or enforced Asns expression promoted metastatic progression. Altering asparagine availability in vitro strongly influenced invasive potential, and this was correlated with an impact on proteins that promote the epithelial to mesenchymal transition. This provides at least one potential mechanism for how the bioavailability of a single amino acid could regulate metastatic progression.
2018-02-07 | PXD008805 | Pride
Project description:mRNA profiling of 4T1-T cells with altered asparagine bioavailability
| PRJNA414240 | ENA
Project description:Asparagine deprivation by L-Asparaginase is a successful therapeutic strategy in Acute Lymphoblastic Leukemia, with resistance occurring due to upregulation of ASNS. L-Asparaginase efficacy in solid tumors is hampered by dose-related toxicities. Large scale loss of function genetic screens identified ASNS, the only human enzyme synthetizing asparagine, as a cancer dependency in several solid malignancies, including melanoma. We here evaluate the therapeutic potential of targeting ASNS in melanoma cells in-vitro and in-vivo. Using ex-vivo quantitative proteome and transcriptome profiling, we observed that concomitant ASNS deletion and asparagine deprivation elicit a compensatory mechanism allowing tumor growth. Genome wide CRISPR screens upon manipulation of aminoacid levels identifies MAPK and GCN2 as critical nodes mediating the observed resistance mechanism. Importantly MEK and GCN2 inhibitor synergize with L-Asparaginase suggesting novel potential therapeutic strategy in melanoma.
2022-02-15 | PXD015152 | Pride
Project description:The integrated stress response (ISR) is a conserved pathway which is activated by cells that are exposed to stress. In lung adenocarcinoma (LUAD), activation of the ATF4 branch of the ISR by particular oncogenic mutations has been linked to the regulation of amino acid metabolism. In the present study, we provide evidence for ATF4 activation across multiple stages and molecular subtypes of human LUAD. In response to extracellular amino acid limitation, LUAD cells with diverse genotypes broadly induce ATF4 in an eIF2α dependent manner, which can be blocked pharmacologically using the integrated stress response inhibitor (ISRIB). Although suppressing eIF2α or ATF4 can trigger different biological consequences, adaptive cell cycle progression and cell migration are particularly sensitive to inhibition of the ISR. These phenotypes specifically require the ATF4 target gene asparagine synthetase (ASNS), which maintains protein translation independently of the mTOR/PI3K pathway. Moreover, NRF2 protein levels and oxidative stress can be modulated by the ISR downstream of ASNS. Finally, we demonstrate that the ISR via ASNS controls the biosynthesis of select proteins, including the cell cycle regulator cyclin B1, which are associated with poor LUAD patient prognosis. Our findings uncover new regulatory layers of the ISR pathway and its control of proteostasis in lung cancer cells as they adapt to metabolic barriers during tumor progression.
2019-10-23 | GSE126232 | GEO