Anticancer metabolites discovered by Computational Metabolomics
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE9648 | GEO | 2008/08/04
SECONDARY ACCESSION(S): PRJNA103513
REPOSITORIES: GEO
Similar Datasets
Project description:CoMet, a fully automated Computational Metabolomics method to predict changes in metabolite levels in cancer cells compared to normal references has been developed and applied to Jurkat T leukemia cells with the goal of testing the following hypothesis: up or down regulation in cancer cells of the expression of genes encoding for metabolic enzymes leads to changes in intracellular metabolite concentrations that contribute to disease progression. Nine metabolites predicted to be lowered in Jurkat cells with respect to normal lymphoblasts were examined: riboflavin, tryptamine, 3-sulfino-L-alanine, menaquinone, dehydroepiandrosterone, α-hydroxystearic acid, hydroxyacetone, seleno-L-methionine and 5,6-dimethylbenzimidazole. All, alone or in combination, exhibited antiproliferative activity. Of eleven metabolites predicted to be increased or unchanged in Jurkat cells, only two (bilirubin and androsterone) exhibited significant antiproliferative activity. These results suggest that cancer cell metabolism may be regulated to reduce the intracellular concentration of certain antiproliferative metabolites, resulting in uninhibited cellular growth and have the implication that many other endogenous metabolites with important roles in carcinogenesis are awaiting discovery. Experiment Overall Design: The first step of the CoMet approach consists of the classification of each enzyme-coding human gene into four possible groups: G1) upregulated in cancer cells, G2) downregulated in cancer cells, G3) expressed in both, normal and cancer cells, at levels that are statistically indistinguishable, and G4) not expressed in both, normal and cancer cells. We used two types of data for the classification: the log base 2 signal intensities and the presence calls of the corresponding probe sets, as reported by the Affymetrix Microarray Suite Software 5.0 (MAS 5.0). First, an â??offâ?? status is provisionally assigned to each gene in each of the two studied conditions (normal and cancer) if the mean fraction of presence calls labeled as â??marginalâ?? or â??absentâ?? in the corresponding probe sets is at least 80%; otherwise, an â??onâ?? status is assigned. Then, each gene is temporarily classified into the G1, G2, G3 or G4 group, according to its on/off status in normal and cancer conditions. Finally, genes in the temporary G3 or G4 groups are transferred to the G1 or G2 groups if they fulfill the following criterion for differential expression: the signal intensities in normal and cancer samples exhibit a statistically significant difference in at least 40% of the corresponding probe sets, as evaluated by an ANOVA two-tailed test with P < 0.005. Experiment Overall Design: RNA extraction, amplification and microarray data processing. Total RNA was extracted from cell lines using Trizol (Invitrogen) and processed using the RiboAmp OA or HS kit (Arcturus) in conjunction with the IVT Labeling Kit from Affymetrix, to produce an amplified, biotin-labeled mRNA suitable for hybridizing to GeneChip Probe Arrays (Affymetrix). Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner. Affymetrix .CEL files were processed using the Affymetrix Expression Console (EC) Software Version 1.1. Files were processed using the default MAS5 3â?? expression workflow which includes scaling all probes to a target intensity (TGT) of 500. Spiked in report controls used were AFFX-BioB, AFFX-BioC, AFFX-BioDn, and AFFX-CreX. Affymetrix .CEL files for three normal lymphoblast samples used as a normal reference to compare Jurkat cells expression data were directly retrieved from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/, samples GSM113678, GSM113802 and GSM113803 of untreated GM15851 cells from the Series GSE5040).
2008-10-20 | E-GEOD-9648 | biostudies-arrayexpress
Project description:Altered metabolism is increasingly acknowledged as an important aspect of cancer, and thus serves as a potentially fertile area for the identification of therapeutic targets or leads. Our recent work using transcriptional data to predict metabolite levels in cancer cells led to preliminary evidence of the antiproliferative role of menaquinone (vitamin K2) in the Jurkat cell line model of acute lymphoblastic leukemia. However, nothing is known about the direct metabolic impacts of menaquinone in cancer, which could provide insights into its mechanism of action. Here, we used metabolomics to investigate the process by which menaquinone exerts antiproliferative activity on Jurkat cells. We first validated the dose-dependent, semi-selective, pro-apoptotic activity of menaquinone treatment on Jurkat cells relative to non-cancerous lymphoblasts. We then used mass spectrometry-based metabolomics to identify systems-scale changes in metabolic dynamics that are distinct from changes induced in noncancerous cells or by other chemotherapeutics. One of the most significantly affected metabolites was phosphoethanolamine, which exhibited a two-fold increase in menaquinone-treated Jurkat cells compared to vehicle-treated cells at 24 h, growing to a five-fold increase at 72 h. Phosphoethanolamine elevation was observed prior to the induction of apoptosis, and was not observed in menaquinonetreated lymphoblasts or chemotherapeutic-treated Jurkat cells. We also validated the link between menaquinone and phosphoethanolamine in an ovarian cancer cell line, suggesting potentially broad applicability of their relationship. This metabolomics-based work is the first detailed characterization of the metabolic impacts of menaquinone treatment and the first identified link between phosphoethanolamine and menaquinone-induced apoptosis.
2015-10-19 | MTBLS226 | MetaboLights
Project description:Background: Autonomous cortisol secretion (ACS), results from cortisol-producing adenomas (CPA), causes endogenous steroid-induced osteoporosis (SIOP). However, how other adrenal steroid metabolites affect bone status is unclear. Methods: ACS was diagnosed at serum cortisol after 1-mg dexamethasone suppression test (DST-cortisol) ≥ 1.8 g/dL. Using liquid chromatography-tandem mass spectrometry, we measured 21 plasma steroid metabolites in 73 patients with ACS and 85 with non-functioning adrenal tumors (NFAT). We also examined expression of steroidogenic enzymes and relevant steroid metabolites in some of CPA tissues. Results: In discriminant and principal component analysis, steroid profiles distinguished between the ACS and NFAT groups in premenopausal women. Premenopausal women with ACS exhibited higher levels of a mineralocorticoid metabolite; 11-deoxycorticosterone (11-DOC), with lower androgen metabolites; dehydroepiandrosterone-sulfate and androsterone-glucuronide. In premenopausal women with ACS, DST-cortisol was negatively correlated with trabecular bone score (TBS). Additionally, 11-DOC was negatively correlated with lumbar spine-bone mineral density (r = -0.603), while androsterone-glucuronide was positively correlated with TBS (r = 0.681), which was supported by Bayesian kernel machine regression analysis. There were no such correlations in postmenopausal women and men. The CPA tissues showed increased levels of 11-DOC, with increased expression of CYP21A2, which is essential for 11-DOC synthesis. The adrenal non-tumor tissues were atrophied with reduced expression of CYB5A, which is required for androgen synthesis. Conclusion: This study provides the first evidence that unbalanced production of adrenal steroid metabolites, which are derived from both adrenal tumors and non-tumor tissues, play a role in the pathogenesis of endogenous SIOP in premenopausal women with ACS.
2023-06-01 | E-MTAB-12895 | biostudies-arrayexpress
Project description:We assessed the apoptotic and antiproliferative effects of resveratrol, pycnogenol and its metabolites on HT1080 human fibrosarcoma cells in vitro. Viability, apoptosis and necrosis were quantified by FACS analysis (Propidiumiodide/AnnexinV staining). Gene expression was analysed by RNA-Microarray. Cell proliferation was analysed by BrdU ELISA assay.
2015-03-06 | GSE59704 | GEO
Project description:We report the altered metabolite changes by processing CT mRNA in the TNBC cell line, MDA-MB-468. It was confirmed that the treatment of CT mRNA disrupted the synthesis of dTTP during nucleic acid metabolism, increasing the signal related to DNA damage in the cell, and that the energy metabolism and NADPH metabolism in the cell were changed for its recovery. The main energy sources, glucose metabolism and glutamine metabolism, are closely linked to the mitochondrial TCA cycle products. In the CT mRNA treatment group, intracellular nucleic acid depletion was observed to increase glutamine metabolism as a source of N source, and the pathway of aspartate utilization was observed. It was confirmed that it was expanded. As a result, a significant increase in the cysteine influx was observed according to the occurrence of ROS, and an effort to regulate the intracellular NADPH balance was observed through the change of metabolites over time. Finally, it was observed that the oncogenic pathway was significantly reduced in the CT mRNA-treated group compared with all untreated groups or controls with other substrate specificities. This study characterizes changes in intracellular metabolites caused by specific dTTP biosynthesis disturbances.
2022-05-06 | GSE202180 | GEO
Project description:We report the altered metabolite changes by processing CT mRNA in the TNBC cell line, BT-549. It was confirmed that the treatment of CT mRNA disrupted the synthesis of dTTP during nucleic acid metabolism, increasing the signal related to DNA damage in the cell, and that the energy metabolism and NADPH metabolism in the cell were changed for its recovery. The main energy sources, glucose metabolism and glutamine metabolism, are closely linked to the mitochondrial TCA cycle products. In the CT mRNA treatment group, intracellular nucleic acid depletion was observed to increase glutamine metabolism as a source of N source, and the pathway of aspartate utilization was observed. It was confirmed that it was expanded. As a result, a significant increase in the cysteine influx was observed according to the occurrence of ROS, and an effort to regulate the intracellular NADPH balance was observed through the change of metabolites over time. Finally, it was observed that the oncogenic pathway was significantly reduced in the CT mRNA-treated group compared with all untreated groups or controls with other substrate specificities. This study characterizes changes in intracellular metabolites caused by specific dTTP biosynthesis disturbances.
2022-05-07 | GSE202194 | GEO
Project description:We report the altered metabolite changes by processing CT mRNA in the TNBC cell line, MDA-MB-231. It was confirmed that the treatment of CT mRNA disrupted the synthesis of dTTP during nucleic acid metabolism, increasing the signal related to DNA damage in the cell, and that the energy metabolism and NADPH metabolism in the cell were changed for its recovery. The main energy sources, glucose metabolism and glutamine metabolism, are closely linked to the mitochondrial TCA cycle products. In the CT mRNA treatment group, intracellular nucleic acid depletion was observed to increase glutamine metabolism as a source of N source, and the pathway of aspartate utilization was observed. It was confirmed that it was expanded. As a result, a significant increase in the cysteine influx was observed according to the occurrence of ROS, and an effort to regulate the intracellular NADPH balance was observed through the change of metabolites over time. Finally, it was observed that the oncogenic pathway was significantly reduced in the CT mRNA-treated group compared with all untreated groups or controls with other substrate specificities. This study characterizes changes in intracellular metabolites caused by specific dTTP biosynthesis disturbances.
2022-04-28 | GSE201421 | GEO
Project description:Background: The role of HIV-1 Tat protein in gene expression deregulation and functional biology of CD4+ T lymphocytes was analyzed, as well as the function of Tat second exon for the complete activity of this protein. Gene expression deregulation profiles of triplicate samples from Jurkat cells expressing intracellular full-length Tat (1-101aa) in comparison with a truncated form lacking the second exon (1-72aa) was evaluated by bioinformatics using whole human genome microarrays. Results: More than 1000 genes were deregulated in Jurkat Tat101 cells, whereas less than 300 genes were deregulated in Jurkat Tat72 cells (q-value<5%; fold change >2 or <-2). Ontological analysis indicated that several functions were impaired mainly in Jurkat Tat101 as cellular movement, growth and proliferation, cell-to-cell signaling, molecular transport, cell death, cell morphology, and T-cell activation. In accordance, biological and functional analyses proved that Tat101 intracellular expression induced changes in cell size and complexity, cytoskeletal rearrangements and chemotaxis impairment, higher resistance to apoptosis, decrease in the surface expression of adhesion molecules and receptors, and higher basal transcriptional activation. These alterations were attenuated or absent in Jurkat Tat72 cells. Furthermore, computational modeling showed that the absence of second exon severely reduced the C-terminus of Tat72 with notable decrease of positive charging. Conclusion: Full-length Tat intracellular expression induced dramatic structural changes and impaired essential functions in CD4+ T cells, whereas Tat72 was less aggressive. Consequently, although Tat first exon is transcriptionally autonomous, second exon should be indispensable for triggering HIV-1 pathogenic events induced by Tat protein. Keywords: Microarray Genome-wide expression analysis. Comparison of genetically modified cells
2010-01-29 | GSE20088 | GEO
Project description:We investigated the metabolism of six secondary metabolite producing fungi of the Penicillium genus, during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. Coexpression analysis revealed that expression of secondary metabolite biosynthetic genes correlates with expression of genes associated with pathways responsible for generation of precursor metabolites for secondary metabolism. Our results highlight the main metabolic routes for precursor supply of the secondary metabolism during nutrient depletion, and suggests that regulation of fungal metabolism is tailored to meet the demands for secondary metabolite production. These findings can aid in identifying wild type species, which are optimized for production of specific secondary metabolites, and therefore can be utilized as high yielding cell factories.
2017-11-17 | GSE106983 | GEO