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.

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Study IDST000096
Study TitleA study of changes in lipid metabolism of ovarian cancer cells co-cultured with adipocytes: UPLC-QTRAP MS analysis
Study TypeTimecourse
Study SummaryThe 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
DepartmentU.S.D.A. Western Human Nutrition Research Center
LaboratoryNewman
Last NameNewman
First NameJohn
Address430 W. Health Sciences Dr., Davis, CA 95616
Emailjohn.newman@ars.usda.gov
Phone+1-530-752-1009
Submit Date2014-07-24
Num Groups3
Total Subjects21
Raw Data AvailableYes
Raw Data File Type(s)mzML
Uploaded File Size30 M
Analysis Type DetailLC-MS
Release Date2015-02-03
Release Version1
John Newman John Newman
https://dx.doi.org/10.21228/M82S3K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:Human

Factors:

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

mb_sample_id local_sample_id Sample Type Timepoint
SA005411S33AAdipocyte 18 hours
SA005412S35AAdipocyte 18 hours
SA005413S32AAdipocyte 18 hours
SA005414S34AAdipocyte 18 hours
SA005415S29AAdipocyte 18 hours
SA005416S30AAdipocyte 18 hours
SA005417S31AAdipocyte 18 hours
SA005418S17AAdipocyte 4 hours
SA005419S25AAdipocyte 4 hours
SA005420S19AAdipocyte 4 hours
SA005421S24AAdipocyte 4 hours
SA005422S26AAdipocyte 4 hours
SA005423S23AAdipocyte 4 hours
SA005424S20AAdipocyte 4 hours
SA005425S34CCo-culture 18 hours
SA005426S32CCo-culture 18 hours
SA005427S33CCo-culture 18 hours
SA005428S31CCo-culture 18 hours
SA005429S30CCo-culture 18 hours
SA005430S29CCo-culture 18 hours
SA005431S35CCo-culture 18 hours
SA005432S17CCo-culture 4 hours
SA005433S24CCo-culture 4 hours
SA005434S25CCo-culture 4 hours
SA005435S23CCo-culture 4 hours
SA005436S20CCo-culture 4 hours
SA005437S19CCo-culture 4 hours
SA005438S26CCo-culture 4 hours
SA005439S35BControl 18 hours
SA005440S31BControl 18 hours
SA005441S30BControl 18 hours
SA005442S32BControl 18 hours
SA005443S29BControl 18 hours
SA005444S33BControl 18 hours
SA005445S34BControl 18 hours
SA005446S24BControl 4 hours
SA005447S26BControl 4 hours
SA005448S23BControl 4 hours
SA005449S25BControl 4 hours
SA005450S19BControl 4 hours
SA005451S20BControl 4 hours
SA005452S17BControl 4 hours
SA005453Media blankMedia blank 4 hours
SA005454Blank mediaMedia 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:0.1% acetic acid
Solvent B:90% ACN / 10% IPA
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
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