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.

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Study IDST000089
Study TitleA study of changes in lipid metabolism of ovarian cancer cells co-cultured with adipocytes: UHPLC-QTOF MS analysis
Study Typetimecourse study
Study SummaryThis 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
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility 451 Health Sciences Drive Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2014-06-11
Num Groups2
Total Subjects14
Study CommentsLipidomics 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
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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 AvailableYes
Raw Data File Type(s).cd,.cG,.bin,.xml,.stg,.
Uploaded File Size14 G
Analysis Type DetailLC-MS
Release Date2014-09-18
Release Version1
Oliver Fiehn Oliver Fiehn
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: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
SA004874S23FHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004875S19FHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004876S24FHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004877S20FHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004878S26FHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004879S17F_QCHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004880S25FHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004881S17FHuman Adipocytes grown in the ABSENCE of SKOV3ip1 OvCa Cells (Control) 4 hours
SA004882S26GHuman Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) 4 hours
SA004883S25GHuman Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) 4 hours
SA004884S23GHuman Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) 4 hours
SA004885S17GHuman Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) 4 hours
SA004886S24GHuman Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) 4 hours
SA004887S19GHuman Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) 4 hours
SA004888S20GHuman Adipocytes grown in the PRESENCE of SKOV3ip1 OvCa cells (Co-Culture) 4 hours
SA004897S26CMedia from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured 4 hours
SA004898S20CMedia from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured 4 hours
SA004899S23CMedia from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured 4 hours
SA004900S19CMedia from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured 4 hours
SA004901S25CMedia from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured 4 hours
SA004902S24CMedia from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured 4 hours
SA004903S17CMedia from Human Adipocytes and SKOV3ip1 OvCa Cells Co-Cultured 4 hours
SA004890S17AMedia from Human Adipocytes Culturing Only 4 hours
SA004891S26AMedia from Human Adipocytes Culturing Only 4 hours
SA004892S20AMedia from Human Adipocytes Culturing Only 4 hours
SA004893S24AMedia from Human Adipocytes Culturing Only 4 hours
SA004894S23AMedia from Human Adipocytes Culturing Only 4 hours
SA004895S25AMedia from Human Adipocytes Culturing Only 4 hours
SA004896S19AMedia from Human Adipocytes Culturing Only 4 hours
SA004904S19BMedia from SKOV3ip1 OvCa Cells Culturing Only 4 hours
SA004905S17BMedia from SKOV3ip1 OvCa Cells Culturing Only 4 hours
SA004906S23BMedia from SKOV3ip1 OvCa Cells Culturing Only 4 hours
SA004907S26BMedia from SKOV3ip1 OvCa Cells Culturing Only 4 hours
SA004908S20BMedia from SKOV3ip1 OvCa Cells Culturing Only 4 hours
SA004909S24BMedia from SKOV3ip1 OvCa Cells Culturing Only 4 hours
SA004910S25BMedia from SKOV3ip1 OvCa Cells Culturing Only 4 hours
SA004912S17DSKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) 4 hours
SA004913S19DSKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) 4 hours
SA004914S25DSKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) 4 hours
SA004915S20DSKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) 4 hours
SA004916S24DSKOV3ip1 OvCa cells grown in the ABSENCE of human adipocytes (Control) 4 hours
SA004917S19ESKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) 4 hours
SA004918S17ESKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) 4 hours
SA004919S20ESKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) 4 hours
SA004920S24ESKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) 4 hours
SA004921S26ESKOV3ip1 OvCa cells grown in the PRESENCE of Human Adipocytes (Co-Culture) 4 hours
SA004922S25ESKOV3ip1 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:60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid
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
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