Summary of Study ST000465
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000357. The data can be accessed directly via it's Project DOI: 10.21228/M8WW32 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000465 |
| Study Title | Uniquely Tumor-Selective Englerin A Profoundly Alters Lipid Metabolism in Renal Cell Carcinoma inducing ER-Stress and an Acute Inflammatory Response |
| Study Type | Metabolomic effect of Englerin A on renal cell carcinoma |
| Study Summary | This targeted metabolomic analysis was performed on renal cell carcinoma A498 cells with or without anti-cancer drug Englerin treatment for 24 and 48 h. |
| Institute | University of California, San Diego |
| Department | Department of Pediatrics |
| Last Name | Batova |
| First Name | Ayse |
| Address | La Jolla, CA 92093 |
| abatova@ucsd.edu | |
| Phone | 619-543-1962 |
| Submit Date | 2016-09-09 |
| Num Groups | Two groups for 24 h treatment (control and Eglerin treatment) and two groups for 48 h treatment. Each has 4 replicates |
| Total Subjects | 16 |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-12-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000357 |
| Project DOI: | doi: 10.21228/M8WW32 |
| Project Title: | Uniquely Tumor-Selective Englerin A Profoundly Alters Lipid Metabolism in Renal Cell Carcinoma inducing ER-Stress and an Acute Inflammatory Response |
| Project Type: | Cancer cell |
| Project Summary: | Renal cell carcinoma (RCC) is among the top ten most common forms of cancer and is the most common malignancy of the kidney. Screening of plant extracts in search of new anti-cancer agents resulted in the discovery of englerin A, a guaiane sesquiterpene with potent cytotoxicity against renal cancer cells and a small subset of other cancer cells. the current study used a systems biology approach to explore the mechanism(s) of action of engerin A at a more global level.Our metabolomics analyses indicated that englerin A profoundly altered lipid metabolism in cc-RCC cell lines and generated significant levels of ceramides that were highly toxic to these cells. Microarray analyses determined that englerin A induced ER stress signaling and an acute inflammatory response, which was confirmed by quantitative PCR and Western Blot analyses.Our findings suggest that cc-RCC is highly sensitive to disruptions in lipid metabolism and ER stress and that these vulnerabilities can be targeted for the treatment of cc-RCC and possibly other lipid storing cancers. |
| Institute: | University of California, San Diego |
| Department: | Department of Pediatrics |
| Last Name: | Batova |
| First Name: | Ayse |
| Address: | La Jolla, CA 92093 |
| Email: | abatova@ucsd.edu |
| Phone: | 619-543-1962 |
Subject:
| Subject ID: | SU000486 |
| Subject Type: | Human renal cancer cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
Subject type: Human renal cancer cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Time | Treatment |
|---|---|---|---|
| SA023582 | 6 | 24hr | Control |
| SA023583 | 8 | 24hr | Control |
| SA023584 | 5 | 24hr | Control |
| SA023585 | 7 | 24hr | Control |
| SA023586 | 2 | 24hr | Englerin (100 nM) |
| SA023587 | 4 | 24hr | Englerin (100 nM) |
| SA023588 | 1 | 24hr | Englerin (100 nM) |
| SA023589 | 3 | 24hr | Englerin (100 nM) |
| SA023590 | 13 | 48hr | Control |
| SA023591 | 15 | 48hr | Control |
| SA023592 | 16 | 48hr | Control |
| SA023593 | 14 | 48hr | Control |
| SA023594 | 9 | 48hr | Englerin (100 nM) |
| SA023595 | 10 | 48hr | Englerin (100 nM) |
| SA023596 | 11 | 48hr | Englerin (100 nM) |
| SA023597 | 12 | 48hr | Englerin (100 nM) |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO000480 |
| Collection Summary: | Cell extracts were obtained by the addition of 1 ml of ice-cold methanol:water (80:20) to each dish followed by scraping cells into 1.7ml Eppendorf tubes and vortexing vigorously for 30 sec. A 50 ul aliquot of sample was removed for the picogreen DNA assay for purposes of biomass normalization, and the remaining sample was kept at -80˚C until ready for metabolomic analysis. |
| Sample Type: | Kidney |
Treatment:
| Treatment ID: | TR000500 |
| Treatment Summary: | A498 cells were plated in 100mm dishes at 0.5 x 106 and 1 x 106 cells/dish in complete RPMI for control and treated cells, respectively. The following day, cells were refed with complete RPMI containing 0.1% DMSO or 100 nM englerin A in DMSO with each condition being conducted in quadruplicate. Cells were incubated with vehicle or englerin A for 24 or 48 h and then they were snap frozen with liquid nitrogen. |
| Treatment: | Anticaner drug |
| Treatment Compound: | Englerin A |
| Treatment Route: | Direct incubation |
| Treatment Dose: | 100 nM |
| Treatment Doseduration: | 24hr and 48hr |
Sample Preparation:
| Sampleprep ID: | SP000493 |
| Sampleprep Summary: | Typically, 300 µl of cells in methanol:water (80:20) was thawed on ice and transferred to a 1.7 ml Eppendorf tube. Five µl of a cocktail containing 25-35 commercial stable isotope internal standards, and 5.0 µl of 57 stable isotope internal standards that were custom-synthesized in E. coli and S. cerevisiae by metabolic labeling with 13C-glucose, and 13C-bicarbonate, were added, and vortexed vigorously for 30 sec. Macromolecules (protein, DNA, RNA, glycans, etc.) then were removed by centrifugation at 16,000g x 10 min at 4˚C. The supernatants containing the extracted metabolites and internal standards were transferred to labeled cryotubes and stored at -80˚C for LC-MS/MS analysis. |
| Extract Storage: | -80C |
| Sample Derivatization: | No |
| Sample Spiking: | Five µl of a cocktail containing 25-35 commercial stable isotope internal standards, and 5.0 µl of 57 stable isotope internal standards that were custom-synthesized in E. coli and S. cerevisiae by metabolic labeling with 13C-glucose, and 13C-bicarbonate, were added |
| Cell Type: | Renal cancer cell |
Combined analysis:
| Analysis ID | AN000726 | AN000727 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Shimadzu 20AD | Shimadzu 20AD |
| Column | Luna NH2 aminopropyl HPLC | Luna NH2 aminopropyl HPLC |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 5500 QTrap | ABI Sciex 5500 QTrap |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | AUC | AUC |
Chromatography:
| Chromatography ID: | CH000520 |
| Chromatography Summary: | HILIC |
| Instrument Name: | Shimadzu 20AD |
| Column Name: | Luna NH2 aminopropyl HPLC |
| Column Temperature: | 25C |
| Flow Gradient: | 0 min-95% B, 4 min-B, 19 min-2% B, 22 min-2% B, 23 min-95% B, 28 min-end. |
| Flow Rate: | 0.3 ml/min |
| Solvent A: | 95% water; 23.18mM NH4OH+20 mM formic acid (Ph 9.4) |
| Solvent B: | 100% acetonitrile |
| Analytical Time: | 28 min |
| Oven Temperature: | 25C |
| Target Sample Temperature: | 4C |
| Sample Loop Size: | 10 ul |
| Sample Syringe Size: | 100 ul |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000643 |
| Analysis ID: | AN000726 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Collision Energy: | Compound-specific |
| Collision Gas: | High |
| Fragmentation Method: | MRM |
| Ion Source Temperature: | 500C |
| Ionization: | ESI |
| Mass Accuracy: | 0.1Da |
| MS ID: | MS000644 |
| Analysis ID: | AN000727 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Collision Energy: | Compound-specific |
| Collision Gas: | High |
| Fragmentation Method: | MRM |
| Ion Source Temperature: | 500C |
| Ionization: | ESI |
| Mass Accuracy: | 0.1Da |
