Summary of Study ST001983

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 PR001259. The data can be accessed directly via it's Project DOI: 10.21228/M8ZX2N This work is supported by NIH grant, U2C- DK119886.

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Study IDST001983
Study TitleMetabolomic Fingerprinting of Human High Grade Serous Ovarian Carcinoma Cell Lines
Study SummaryFocusing on defining the metabolomic basis of intratumoral heterogeneity in ovarian cancer, the metabolic diversity of a panel of high grade serous ovarian carcinoma (HGSOC) cell-lines we investigated using a metabolomics platform that interrogate 731 compounds. Metabolic fingerprinting followed by 2-dimensional and 3-dimensional principal component analysis defined the heterogeneity of the HGSOC cells and clustered them into five distinct metabolic groups. An overall increase in the metabolites associated with aerobic glycolysis and phospholipid metabolism were observed in the majority of the cancer cells. A preponderant increase in the levels of metabolites involved in trans-sulfuration and glutathione synthesis was also observed. Subsets of HGSOC cells showed an increase in the levels of 5-Hydroxytryptamine, gamma-aminobutyric acid, or glutamate, pointing to their potential role as oncometabolites. In summary, our results identify increased glycolysis, phospholipid metabolism and amino acid metabolism with the resultant increase in the levels of 5-Hydoxytryptamine, GABA, and Glutamate as metabolomic correlates underlying the heterogeneity of ovarian cancer cell lines.
Institute
University of Oklahoma Health Sciences Center
DepartmentCell Biology
LaboratoryDanny N Dhanasekaran
Last NameJayaraman
First NameMuralidharan
Address975 NE 10th street, BRC1470, Oklahoma City, Oklahoma, 73104, USA
EmailMuralidharan-Jayaraman@ouhsc.edu
Phone4052718001 x 30492
Submit Date2021-09-20
Num Groups2
Total Subjects30
Num Females15
Study CommentsOvarian cancer cell lines
Analysis Type DetailLC-MS
Release Date2021-12-01
Release Version1
Muralidharan Jayaraman Muralidharan Jayaraman
https://dx.doi.org/10.21228/M8ZX2N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001259
Project DOI:doi: 10.21228/M8ZX2N
Project Title:Metabolomic Fingerprinting of Human High Grade Serous Ovarian Carcinoma Cell Lines
Project Type:Cell line analysis
Project Summary:Focusing on defining the metabolomic basis of intratumoral heterogeneity in ovarian cancer, the metabolic diversity of a panel of high grade serous ovarian carcinoma (HGSOC) cell-lines we investigated using a metabolomics platform that interrogate 731 compounds. Metabolic fingerprinting followed by 2-dimensional and 3-dimensional principal component analysis defined the heterogeneity of the HGSOC cells and clustered them into five distinct metabolic groups. An overall increase in the metabolites associated with aerobic glycolysis and phospholipid metabolism were observed in the majority of the cancer cells. A preponderant increase in the levels of metabolites involved in trans-sulfuration and glutathione synthesis was also observed. Subsets of HGSOC cells showed an increase in the levels of 5-Hydroxytryptamine, gamma-aminobutyric acid, or glutamate, pointing to their potential role as oncometabolites. In summary, our results identify increased glycolysis, phospholipid metabolism and amino acid metabolism with the resultant increase in the levels of 5-Hydoxytryptamine, GABA, and Glutamate as metabolomic correlates underlying the heterogeneity of ovarian cancer cell lines.
Institute:University of Oklahoma Health Sciences Center
Department:Cell Biology
Laboratory:Danny N Dhanasekaran
Last Name:Jayaraman
First Name:Muralidharan
Address:975 NE 10th street, BRC1470, Oklahoma City, Oklahoma, 73104, USA
Email:Muralidharan-Jayaraman@ouhsc.edu
Phone:4052718001 x 30492
Contributors:Danny N. Dhanasekaran, Jihee Ha, Padmaja Dhanasekaran, Mingda Yan

Subject:

Subject ID:SU002064
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Female
Cell Biosource Or Supplier:OVCAR4 cell line was obtained from Dr. Thomas Hamilton (Fox Chase Cancer Center, PA) and OVCAR8 cells were from National Cancer Institute (NCI). Kuramochi, TYKNU, OVKATE and OVSAHO cell lines were from the JCRB Cell Bank, Tokyo, Japan. SNU119, SNU251, ES-2, OVCAR3, CAOV3 and OV90 cells were from Seoul National University, Seoul, Korea, and COV362, OAW28 and COV318 cells were purchased from Sigma-Aldrich (St. Louis, MO).
Cell Passage Number:3 and 4
Cell Counts:20 million cells

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA185669OUHSC-22No treatment
SA185670OUHSC-23No treatment
SA185671OUHSC-21No treatment
SA185672OUHSC-19No treatment
SA185673OUHSC-18No treatment
SA185674OUHSC-24No treatment
SA185675OUHSC-20No treatment
SA185676OUHSC-25No treatment
SA185677OUHSC-29No treatment
SA185678OUHSC-30No treatment
SA185679OUHSC-28No treatment
SA185680OUHSC-27No treatment
SA185681OUHSC-26No treatment
SA185682OUHSC-17No treatment
SA185683OUHSC-16No treatment
SA185684OUHSC-6No treatment
SA185685OUHSC-7No treatment
SA185686OUHSC-5No treatment
SA185687OUHSC-4No treatment
SA185688OUHSC-2No treatment
SA185689OUHSC-3No treatment
SA185690OUHSC-8No treatment
SA185691OUHSC-9No treatment
SA185692OUHSC-14No treatment
SA185693OUHSC-15No treatment
SA185694OUHSC-13No treatment
SA185695OUHSC-12No treatment
SA185696OUHSC-10No treatment
SA185697OUHSC-11No treatment
SA185698OUHSC-1No treatment
Showing results 1 to 30 of 30

Collection:

Collection ID:CO002057
Collection Summary:Immortalized normal fallopian-tube-derived epithelial cells (FTE188) have been previously described and used here (1). High grade serous carcinoma cell line OVCAR3, OVCAR8, OVKATE, SNU119, SNU251, OVCAR4, OVSAHO, and Kuramochi cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Cellgro, Manassas, VA), COV362, COV318, OAW28 and CAOV3 cells were maintained in Dulbecco’s modified Eagle’s (DMEM) Medium (Cellgro, Manassas, VA). OV90 cells were maintained in MCDB105: M199 (1:1) Medium (Thermo Fisher Scientific, Waltham, MA) and TYKNU cells were maintained in Minimum Essential Medium (MEM) (Cellgro, Manassas, VA). ES-2 cells were maintained in McCoy’s 5A medium (Sigma-Aldrich, St. Louis, MO). All cells were maintained at 37°C in a 5% CO2 incubator. All media were supplemented with 10% FBS (Gemini Bio-Products, West Sacramento, CA), 50 U/mL penicillin, 50 μg/ml streptomycin (Cellgro, Manassas, VA). Cells were grown to 20 million cells and washed with cold PBS. Cells were collected by scraping them off the plates.
Sample Type:Ovarian cancer cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002076
Treatment Summary:No treatment was done.

Sample Preparation:

Sampleprep ID:SP002070
Sampleprep Summary:Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. In order to dissociate small molecules bound to or trapped in proteins, lysate was precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN003234
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters ACQUITY ultra-performance liquid chromatography (UPLC)
Column Waters UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode UNSPECIFIED
Units ratio

Chromatography:

Chromatography ID:CH002385
Instrument Name:Waters ACQUITY ultra-performance liquid chromatography (UPLC)
Column Name:Waters UPLC BEH C18 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003008
Analysis ID:AN003234
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Raw data files are archived and extracted using proprietary, Metabolon LIMS data structures and analysis software (Metabolon Inc, Durham). Briefly, raw data was extracted, peak-identified and QC processed using Metabolon’s hardware and software. Biochemical identifications are based on three criteria: retention index within a narrow RI window of the proposed identification, accurate mass match to the library +/- 10 ppm, and the MS/MS forward and reverse scores between the experimental data and authentic standards.
Ion Mode:UNSPECIFIED
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