Summary of Study ST000096
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 | ST000096 |
| Study Title | A study of changes in lipid metabolism of ovarian cancer cells co-cultured with adipocytes: UPLC-QTRAP MS analysis |
| Study Type | Timecourse |
| Study Summary | The study investigated the interaction between omental adipocytes and OvCa cells, as a follow up to preliminary data indicating this leads to reprograming of metabolic (especially lipid) profiles in both adipocytes and OvCa cells as ovarian cancer cells (OvCa) readily metastasize to the omental fat pad in the abdomen and stimulate the release of fatty acids. In order to mimic the interaction between OvCa and omental adipocytes during metastasis, a coculture system was used that employed OvCa cells and primary human adipocytes isolated from omentum. Human primary adipocytes were isolated from omental explants from patients undergoing surgery for benign conditions. After surgical removal, omental tissue was digested with collagenase I, and primary cultures of adipocytes were established, characterized, and incorporated into the co-culture. The primary adipocytes were isolated and co-cultured with the OvCa cell line Skov3ip1. In this current submission, the the samples will be collected at 4, 18 and 24 hour time points post co-culture to determine the time dependent effect on lipid mediators, including oxylipins and ceramides. The study results included in this DRCC submission were the 18 hour time point data for oxylipins and ceramides from targeted metabolomic analysis of lipid mediators performed by the Newman lab. |
| Institute | University of California, Davis |
| Department | U.S.D.A. Western Human Nutrition Research Center |
| Laboratory | Newman |
| Last Name | Newman |
| First Name | John |
| Address | 430 W. Health Sciences Dr., Davis, CA 95616 |
| john.newman@ars.usda.gov | |
| Phone | +1-530-752-1009 |
| Submit Date | 2014-07-24 |
| Num Groups | 3 |
| Total Subjects | 21 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Uploaded File Size | 30 M |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-02-03 |
| 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: | SU000115 |
| Subject Type: | Human cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Cell Strain Details: | SKOV3ip1 |
| Subject Comments: | p80, p85, p86, p89 |
| Cell Passage Number: | p80, p85, p86, p89 |
| Cell Counts: | p80, p85, p86, p89 |
| Species Group: | Mammals |
Factors:
Subject type: Human cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample Type | Timepoint |
|---|---|---|---|
| SA005411 | S33A | Adipocyte | 18 hours |
| SA005412 | S35A | Adipocyte | 18 hours |
| SA005413 | S32A | Adipocyte | 18 hours |
| SA005414 | S34A | Adipocyte | 18 hours |
| SA005415 | S29A | Adipocyte | 18 hours |
| SA005416 | S30A | Adipocyte | 18 hours |
| SA005417 | S31A | Adipocyte | 18 hours |
| SA005418 | S17A | Adipocyte | 4 hours |
| SA005419 | S25A | Adipocyte | 4 hours |
| SA005420 | S19A | Adipocyte | 4 hours |
| SA005421 | S24A | Adipocyte | 4 hours |
| SA005422 | S26A | Adipocyte | 4 hours |
| SA005423 | S23A | Adipocyte | 4 hours |
| SA005424 | S20A | Adipocyte | 4 hours |
| SA005425 | S34C | Co-culture | 18 hours |
| SA005426 | S32C | Co-culture | 18 hours |
| SA005427 | S33C | Co-culture | 18 hours |
| SA005428 | S31C | Co-culture | 18 hours |
| SA005429 | S30C | Co-culture | 18 hours |
| SA005430 | S29C | Co-culture | 18 hours |
| SA005431 | S35C | Co-culture | 18 hours |
| SA005432 | S17C | Co-culture | 4 hours |
| SA005433 | S24C | Co-culture | 4 hours |
| SA005434 | S25C | Co-culture | 4 hours |
| SA005435 | S23C | Co-culture | 4 hours |
| SA005436 | S20C | Co-culture | 4 hours |
| SA005437 | S19C | Co-culture | 4 hours |
| SA005438 | S26C | Co-culture | 4 hours |
| SA005439 | S35B | Control | 18 hours |
| SA005440 | S31B | Control | 18 hours |
| SA005441 | S30B | Control | 18 hours |
| SA005442 | S32B | Control | 18 hours |
| SA005443 | S29B | Control | 18 hours |
| SA005444 | S33B | Control | 18 hours |
| SA005445 | S34B | Control | 18 hours |
| SA005446 | S24B | Control | 4 hours |
| SA005447 | S26B | Control | 4 hours |
| SA005448 | S23B | Control | 4 hours |
| SA005449 | S25B | Control | 4 hours |
| SA005450 | S19B | Control | 4 hours |
| SA005451 | S20B | Control | 4 hours |
| SA005452 | S17B | Control | 4 hours |
| SA005453 | Media blank | Media blank | 4 hours |
| SA005454 | Blank media | Media blank | NA |
| Showing results 1 to 44 of 44 |
Collection:
| Collection ID: | CO000098 |
| Collection Summary: | Samples were collected at 18 hours post co-culture |
| Collection Protocol Filename: | Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Ceramide_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Enpdfannabinoid_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_4hr.pdf Newman_Lab_Ceramide_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_4hr.pdf |
| Sample Type: | Media |
| Storage Conditions: | -80 C |
Treatment:
| Treatment ID: | TR000116 |
| Treatment Summary: | The study investigated the interaction between omental adipocytes and OvCa cells, as a follow up to preliminary data indicating this leads to reprograming of metabolic (especially lipid) profiles in both adipocytes and OvCa cells as ovarian cancer cells (OvCa) readily metastasize to the omental fat pad in the abdomen and stimulate the release of fatty acids. In order to mimic the interaction between OvCa and omental adipocytes during metastasis, a coculture system was used that employed OvCa cells and primary human adipocytes isolated from omentum. Human primary adipocytes were isolated from omental explants from patients undergoing surgery for benign conditions. After surgical removal, omental tissue was digested with collagenase I, and primary cultures of adipocytes were established, characterized, and incorporated into the co-culture. The primary adipocytes were isolated and co-cultured with the OvCa cell line Skov3ip1. In this current submission, the the samples will be collected at 4, 18 and 24 hour time points post co-culture to determine the time dependent effect on lipid mediators, including oxylipins and ceramides. The study results included in this DRCC submission were the 18 hour time point data for oxylipins and ceramides. |
| Treatment Protocol Filename: | Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Ceramide_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Enpdfannabinoid_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_4hr.pdf Newman_Lab_Ceramide_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_4hr.pdf |
| Cell Storage: | -80 C |
Sample Preparation:
| Sampleprep ID: | SP000111 |
| Sampleprep Summary: | See sample prep protocol file |
| Sampleprep Protocol Filename: | Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Ceramide_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Enpdfannabinoid_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_4hr.pdf Newman_Lab_Ceramide_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_4hr.pdf |
| Processing Storage Conditions: | - 20 °C |
| Extraction Method: | SPE |
| Extract Concentration Dilution: | 250 µL |
| Extract Cleanup: | SPE |
| Extract Storage: | - 20 °C |
| Sample Resuspension: | 100 µL |
| Sample Spiking: | See sample prep protocol file |
Combined analysis:
| Analysis ID | AN000152 | AN000153 | AN000154 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | |||
| Chromatography system | |||
| Column | |||
| MS Type | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap |
| Ion Mode | NEGATIVE | POSITIVE | POSITIVE |
| Units | Area % | nM | nM |
Chromatography:
| Chromatography ID: | CH000108 |
| Chromatography Summary: | Oxylipin analysis |
| Methods Filename: | Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_18hr.pdf Newman_Lab_Oxylipin_Extraction_&_Analysis_Protocol_Lengyel_WCMC_P&F_4hr.pdf |
| Column Temperature: | 60 C |
| Flow Gradient: | See protocol/methods file |
| Flow Rate: | 0.25 |
| Internal Standard: | See protocol/methods file |
| Retention Time: | See protocol/methods file |
| Sample Injection: | 5 L |
| Solvent A: | 100% water; 0.1% acetic acid |
| Solvent B: | 90% acetonitrile/ 10% isopropanol |
| Analytical Time: | 16 min |
| Weak Wash Solvent Name: | 20% methanol, 10% isopropanol |
| Weak Wash Volume: | 600 L |
| Strong Wash Solvent Name: | 50:50 Acetonitrile:Methanol |
| Strong Wash Volume: | 600 L |
| Sample Loop Size: | 17 L |
MS:
| MS ID: | MS000128 |
| Analysis ID: | AN000152 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Oxylipins analysis |
| Ion Mode: | NEGATIVE |
| Ion Source Temperature: | See protocol/methods file |
| Ion Spray Voltage: | See protocol/methods file |
| MS ID: | MS000129 |
| Analysis ID: | AN000153 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Ceramide analysis |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | See protocol/methods file |
| Ion Spray Voltage: | See protocol/methods file |
| MS ID: | MS000130 |
| Analysis ID: | AN000154 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Endocannabinoid analysis |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | See protocol/methods file |
| Ion Spray Voltage: | See protocol/methods file |
