Summary of Study ST002555
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 PR001647. The data can be accessed directly via it's Project DOI: 10.21228/M8T413 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002555 |
| Study Title | Ethnicity-Specific Differences in Ovarian Cancer Metabolic Signatures |
| Study Type | Cultured cells |
| Study Summary | Ovarian cancer is a leading cause of cancer-related deaths among women worldwide. Cancer cell metabolism plays a critical role in tumor growth and progression, and metabolic alterations in cancer cells have been implicated in treatment resistance. In this study, we performed metabolomic analysis using ovarian cancer cells derived from patients in the United States and Korea. Our results reveal significant ethnic-specific differences in the metabolic signatures of ovarian cancer cells, with differential regulation of metabolites derived from glycolytic pathways, lipid metabolism, and microbiome modified metabolites. These findings have important therapeutic implications, as differences in ovarian cancer metabolism between ethnic groups may influence treatment response and resistance. Targeting the unique metabolic signatures of ovarian cancer cells based on ethnic specificity may improve the effectiveness of precision medicine approaches in the treatment of ovarian cancer. This study highlights the potential for personalized and targeted therapeutic options based on the tumor metabolome and ethnic background of the patient. Overall, our results suggest that investigating ethnic-specific differences in cancer metabolism is critical for developing effective and personalized cancer therapies. The identification of unique metabolic signatures in ovarian cancer cells based on ethnic specificity provides a promising avenue for improving treatment outcomes and advancing the field of precision medicine in ovarian cancer. |
| 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 BRC1468 Oklahoma City OK 73104 |
| Muralidharan-Jayaraman@ouhsc.edu | |
| Phone | 405-271-8001 x30492 |
| Submit Date | 2023-03-03 |
| Num Groups | 3 |
| Total Subjects | 48 |
| Num Females | 12 |
| Study Comments | Ovarian cancer cell lines |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004207 | AN004208 | AN004209 | AN004210 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Fold change over standard | Fold change over standard | Fold change over standard | Fold change over standard |
Chromatography:
| Chromatography ID: | CH003118 |
| Chromatography Summary: | Low pH polar (Metabolon). 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 as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in methanol, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003119 |
| Chromatography Summary: | Low pH Lipophilic (Metabolon). 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 as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in 50% methanol/50% acetonitrile, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003120 |
| Chromatography Summary: | High pH (Metabolon). 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 as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99%B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 6.5 mM ammonium bicarbonate in water, pH 8 |
| Solvent B: | 6.5 mM ammonium bicarbonate in 95% methanol/5% water |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003121 |
| Chromatography Summary: | HILIC (Metabolon). 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 as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 10 mM ammonium formate in 15% water/5% methanol/ 80% acetonitrile (effective pH 10.16 with NH4OH) |
| Solvent B: | 10 mM ammonium formate in 50% water/50% acetonitrile (effective pH 10.60 with NH4OH) |
| Chromatography Type: | HILIC |
