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

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Download all metabolite data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data
Study IDST000465
Study TitleUniquely Tumor-Selective Englerin A Profoundly Alters Lipid Metabolism in Renal Cell Carcinoma inducing ER-Stress and an Acute Inflammatory Response
Study TypeMetabolomic effect of Englerin A on renal cell carcinoma
Study SummaryThis 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
DepartmentDepartment of Pediatrics
Last NameBatova
First NameAyse
AddressLa Jolla, CA 92093
Emailabatova@ucsd.edu
Phone619-543-1962
Submit Date2016-09-09
Num GroupsTwo groups for 24 h treatment (control and Eglerin treatment) and two groups for 48 h treatment. Each has 4 replicates
Total Subjects16
Analysis Type DetailLC-MS
Release Date2016-12-22
Release Version1
Ayse Batova Ayse Batova
https://dx.doi.org/10.21228/M8WW32
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA023582624hr Control
SA023583824hr Control
SA023584524hr Control
SA023585724hr Control
SA023586224hr Englerin (100 nM)
SA023587424hr Englerin (100 nM)
SA023588124hr Englerin (100 nM)
SA023589324hr Englerin (100 nM)
SA0235901348hr Control
SA0235911548hr Control
SA0235921648hr Control
SA0235931448hr Control
SA023594948hr Englerin (100 nM)
SA0235951048hr Englerin (100 nM)
SA0235961148hr Englerin (100 nM)
SA0235971248hr 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 column Luna NH2 aminopropyl HPLC column
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
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 with 23.18mM NH4OH+20 mM formic acid (Ph 9.4)
Solvent B:100% acetonitirle
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
  logo