Summary of Study ST000089
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 PR000079. The data can be accessed directly via it's Project DOI: 10.21228/M82S3K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000089 |
| Study Title | A study of changes in lipid metabolism of ovarian cancer cells co-cultured with adipocytes: UHPLC-QTOF MS analysis |
| Study Type | timecourse study |
| Study Summary | This West Coast Metabolomics Center pilot and feasibility project was granted to Ernst Lengyel (University of Chicago). The biology of ovarian cancer (OvCa) is clearly distinct from that of most epithelial tumors, in that hematogenous metastases are rare, and ovarian tumors remain confined to the peritoneal cavity. The omentum, a large pad of fat tissue (20x13x3cm) covering the bowel, is the most common site of OvCa metastasis. It consists primarily of adipocytes, which become the principal microenvironment for the OvCa cells. The underlying hypothesis for this application is that, in the presence of adipocytes, the metabolism of OvCa cells is reprogramed and shifts towards lipid utilization, which provides energy that facilitates tumor growth and metastasis. Preliminary results suggest that primary human omental adipocytes secrete cytokines which promote the metastasis of OvCa cells to the omentum and their subsequent invasion. Once metastasis has occurred, OvCa cells induce lipolysis in omental adipocytes, and use the energy derived from these lipids to proliferate. To study the metabolic changes in the tumor microenvironment we have established a 3D organotypic culture of the human omentum using primary human cells established from patient tissue. Metabolic studies will be performed on adipocytes and OvCa cells individually, on conditioned media and on adipocytes and OvCa cells co-cultured in our 3D model, with the goal of arriving at a comprehensive analysis of primary metabolites and lipids in the tumor microenvironment. In the current investigation, untargeted analysis of primary metabolites and complex lipids were conducted on adipocytes and OvCa cells individually, on conditioned media and on adipocytes and OvCa cells co-cultured in our 3D model. Analysis of oxylipins was conducted on conditioned media. To gain better understanding of the dynamic regulation of metabolic pathways we will also perform metabolic flux analysis using labeled cells (13C-glucose, 13C-glutamine) in the 3D culture model. The primary objective of this study is to gain insight into the dynamic interactions between OvCa cells and human adipocytes with the anticipation of elucidating targets of therapeutic intervention. |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility 451 Health Sciences Drive Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2014-06-11 |
| Num Groups | 2 |
| Total Subjects | 14 |
| Study Comments | Lipidomics profiles for study For the co-culture Human Adipocytes were grown in presence of SKOV3ip1 ovarian cancer cells For control samples the adipocytes were grown in the absence of SKOV3ip1 ovarian cancer cells --- Exp design 2 x 14 Final result is obtained by merging results from both files and applying dilution factor. Reason was high TG concentration in positive mode only Raw Data File (Positive Mode_TGs) (dilution1) Raw Data File (Positive Mode_Non-TGs) (dilution2) |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Uploaded File Size | 14 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2014-09-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000079 |
| Project DOI: | doi: 10.21228/M82S3K |
| Project Title: | A study of changes in lipid metabolism of ovarian cancer cells co-cultured with adipocytes |
| Project Type: | timecourse study |
| Project Summary: | A study of changes in lipid metabolism of ovarian cancer cells co-cultured with adipocytestimecourse studyThis West Coast Metabolomics Center pilot and feasibility project was granted to Ernst Lengyel (University of Chicago). The biology of ovarian cancer (OvCa) is clearly distinct from that of most epithelial tumors, in that hematogenous metastases are rare, and ovarian tumors remain confined to the peritoneal cavity. The omentum, a large pad of fat tissue (20x13x3cm) covering the bowel, is the most common site of OvCa metastasis. It consists primarily of adipocytes, which become the principal microenvironment for the OvCa cells. The underlying hypothesis for this application is that, in the presence of adipocytes, the metabolism of OvCa cells is reprogramed and shifts towards lipid utilization, which provides energy that facilitates tumor growth and metastasis. Preliminary results suggest that primary human omental adipocytes secrete cytokines which promote the metastasis of OvCa cells to the omentum and their subsequent invasion. Once metastasis has occurred, OvCa cells induce lipolysis in omental adipocytes, and use the energy derived from these lipids to proliferate. To study the metabolic changes in the tumor microenvironment we have established a 3D organotypic culture of the human omentum using primary human cells established from patient tissue. Metabolic studies will be performed on adipocytes and OvCa cells individually, on conditioned media and on adipocytes and OvCa cells co-cultured in our 3D model, with the goal of arriving at a comprehensive analysis of primary metabolites and lipids in the tumor microenvironment. In the current investigation, untargeted analysis of primary metabolites and complex lipids were conducted on adipocytes and OvCa cells individually, on conditioned media and on adipocytes and OvCa cells co-cultured in our 3D model. Analysis of oxylipins was conducted on conditioned media. To gain better understanding of the dynamic regulation of metabolic pathways we will also perform metabolic flux analysis using labeled cells (13C-glucose, 13C-glutamine) in the 3D culture model. The primary objective of this study is to gain insight into the dynamic interactions between OvCa cells and human adipocytes with the anticipation of elucidating targets of therapeutic intervention. |
| Institute: | University of California, Davis |
| Department: | Genome and Biomedical Sciences Facility |
| Laboratory: | WCMC Metabolomics Core |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 1315 Genome and Biomedical Sciences Facility,451 Health Sciences Drive, Davis, CA 95616 |
| Email: | ofiehn@ucdavis.edu |
| Phone: | (530) 754-8258 |
| Funding Source: | NIH U24DK097154 |
Subject:
| Subject ID: | SU000108 |
| Subject Type: | Human cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | Human Adipocytes |
| Species Group: | Human |
Factors:
Subject type: Human cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Time Point |
|---|---|---|---|
| SA004874 | S23F | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004875 | S19F | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004876 | S24F | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004877 | S20F | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004878 | S26F | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004879 | S17F_QC | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004880 | S25F | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004881 | S17F | Human Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) | 4 hours |
| SA004882 | S26G | Human Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) | 4 hours |
| SA004883 | S25G | Human Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) | 4 hours |
| SA004884 | S23G | Human Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) | 4 hours |
| SA004885 | S17G | Human Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) | 4 hours |
| SA004886 | S24G | Human Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) | 4 hours |
| SA004887 | S19G | Human Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) | 4 hours |
| SA004888 | S20G | Human Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) | 4 hours |
| SA004897 | S26C | Media from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured | 4 hours |
| SA004898 | S20C | Media from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured | 4 hours |
| SA004899 | S23C | Media from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured | 4 hours |
| SA004900 | S19C | Media from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured | 4 hours |
| SA004901 | S25C | Media from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured | 4 hours |
| SA004902 | S24C | Media from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured | 4 hours |
| SA004903 | S17C | Media from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured | 4 hours |
| SA004890 | S17A | Media from Human Adipocytes Culturing Only | 4 hours |
| SA004891 | S26A | Media from Human Adipocytes Culturing Only | 4 hours |
| SA004892 | S20A | Media from Human Adipocytes Culturing Only | 4 hours |
| SA004893 | S24A | Media from Human Adipocytes Culturing Only | 4 hours |
| SA004894 | S23A | Media from Human Adipocytes Culturing Only | 4 hours |
| SA004895 | S25A | Media from Human Adipocytes Culturing Only | 4 hours |
| SA004896 | S19A | Media from Human Adipocytes Culturing Only | 4 hours |
| SA004904 | S19B | Media from SKOV3ip1 OvCa Cells Culturing Only | 4 hours |
| SA004905 | S17B | Media from SKOV3ip1 OvCa Cells Culturing Only | 4 hours |
| SA004906 | S23B | Media from SKOV3ip1 OvCa Cells Culturing Only | 4 hours |
| SA004907 | S26B | Media from SKOV3ip1 OvCa Cells Culturing Only | 4 hours |
| SA004908 | S20B | Media from SKOV3ip1 OvCa Cells Culturing Only | 4 hours |
| SA004909 | S24B | Media from SKOV3ip1 OvCa Cells Culturing Only | 4 hours |
| SA004910 | S25B | Media from SKOV3ip1 OvCa Cells Culturing Only | 4 hours |
| SA004912 | S17D | SKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) | 4 hours |
| SA004913 | S19D | SKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) | 4 hours |
| SA004914 | S25D | SKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) | 4 hours |
| SA004915 | S20D | SKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) | 4 hours |
| SA004916 | S24D | SKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) | 4 hours |
| SA004917 | S19E | SKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) | 4 hours |
| SA004918 | S17E | SKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) | 4 hours |
| SA004919 | S20E | SKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) | 4 hours |
| SA004920 | S24E | SKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) | 4 hours |
| SA004921 | S26E | SKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) | 4 hours |
| SA004922 | S25E | SKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) | 4 hours |
| Showing results 1 to 47 of 47 |
Collection:
Treatment:
Sample Preparation:
Combined analysis:
| Analysis ID | AN000141 | AN000142 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH000101 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99% B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 1.67 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Weak Wash Volume: | 5 seconds |
| Strong Wash Solvent Name: | Same |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel generated |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000117 |
| Analysis ID: | AN000141 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
| MS ID: | MS000118 |
| Analysis ID: | AN000142 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 13 l/min |
| Dry Gas Temp: | 200 |
| Fragment Voltage: | 175 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Neg |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
