Summary of Study ST003245

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 PR002015. The data can be accessed directly via it's Project DOI: 10.21228/M85238 This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003245
Study TitleExploration of Zeb1-dependent changes in the lipidome of MDA-MB-231 cells
Study SummaryHuman breast cancer MDA-MB-231 wildtype (WT) cells and the stably transduced MDA-MB-231 shZeb1 (stable Zeb1 knockdown) and shCtrl cell lines (control cell line for the stable Zeb1 knockdown) (Spaderna et al. 2008, DOI: 10.1158/0008-5472.CAN-07-5682) were analyzed for their phospholipid profile by UPLC-MS/MS. Please note that one sample set was measured three times with the same sample-ID, but with different methods (PE, PC, PI), therefore each sub-class has their own raw-data file marked by their corresponding abbreviation (PE, PC, PI; e.g. "210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002.wiff", "210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002.wiff" or "210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002.wiff").
Institute
University of Innsbruck
DepartmentMichael Popp Institute
Last NameKoeberle
First NameAndreas
AddressMitterweg 24, Innsbruck, Tyrol, 6020, Austria
EmailAndreas.Koeberle@uibk.ac.at
Phone+43 512 507 57903
Submit Date2024-05-27
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2024-07-05
Release Version1
Andreas Koeberle Andreas Koeberle
https://dx.doi.org/10.21228/M85238
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002015
Project DOI:doi: 10.21228/M85238
Project Title:Zeb1-mediated control of the phospholipid PUFA/MUFA ratio in EMT/plasticity-associated 1 cancer cell ferroptosis
Project Summary:Therapy resistance and metastasis, the most fatal steps in cancer, are often triggered by a (partial) activation of the epithelial-mesenchymal-transition (EMT)-program. A mesenchymal phenotype predisposes to ferroptosis, a cell death pathway exerted by an iron and oxygen-radical mediated peroxidation of phospholipids containing polyunsaturated fatty acids (PUFAs). We here describe that various forms of EMT-activation increase ferroptosis-susceptibility in cancer cells, which depends on the EMT-transcription factor Zeb1. To further investigate the underlying mechanisms of an EMT/Zeb1-coupled ferroptosis sensitivity, we analyzed key determinants of ferroptotic cell death, focusing on the proportion and (per)oxidation of fatty acid species in phospholipid subclasses. Using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), we demonstrate that GPX4 inhibition in human breast cancer MDA-MB-231 cells (Zeb1high) led to a rapid (per)oxidation of PUFA-containing phospholipids (oxPL), which is absent in cells depleted of Zeb1 (shZeb1). Mechanistically, Zeb1 increases the ratio of phospholipids containing pro-ferroptotic PUFAs over cyto-protective monounsaturated fatty acids (MUFAs) in MDA-MB-231 cells, tumor-derived pancreatic cancer KPC cells as well as mice tumor allografts via the modulation of crucial lipogenic enzymes.
Institute:University of Innsbruck
Department:Michael Popp Institute
Last Name:Koeberle
First Name:Andreas
Address:Mitterweg 24, Innsbruck, Tyrol, 6020, Austria
Email:Andreas.Koeberle@uibk.ac.at
Phone:+43 512 507 57903
Funding Source:the Austrian Science Fund (FWF) (P 36299), the German Research Council (GRK 1715), and the Phospholipid Research Center (Grant Number AKO‐2019‐070/2‐1, AKO-2O22-100/2-2), the Tyrolean Science Fund (TWF) (F.33467/7-2021).
Publications:in revision
Contributors:Zhigang Rao, Jie Zhang, André Gollowitzer, Leonhard Bereuter, Andreas Koeberle

Subject:

Subject ID:SU003364
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sample source Genotype
SA353432220408_MDA shCtrl_1_10_PC_8Breast cancer cell line control for Zeb1 stable knockdown
SA353433230309_shCTRL shZEB1_Rao_shCTRL_5Breast cancer cell line control for Zeb1 stable knockdown
SA353434230309_shCTRL shZEB1_Rao_shCTRL_6Breast cancer cell line control for Zeb1 stable knockdown
SA353435230309_shCTRL shZEB1_Rao_shCTRL_7Breast cancer cell line control for Zeb1 stable knockdown
SA353436230309_shCTRL shZEB1_Rao_shCTRL_8Breast cancer cell line control for Zeb1 stable knockdown
SA353437220408_MDA shZEB1_1_10_PE_7Breast cancer cell line control for Zeb1 stable knockdown
SA353438220408_MDA shCtrl_1_10_PC_7Breast cancer cell line control for Zeb1 stable knockdown
SA353439220408_MDA shCtrl_1_10_PC_6Breast cancer cell line control for Zeb1 stable knockdown
SA353440220408_MDA shCtrl_1_10_PC_5Breast cancer cell line control for Zeb1 stable knockdown
SA353441220408_MDA shZEB1_1_10_PE_8Breast cancer cell line control for Zeb1 stable knockdown
SA353442220408_MDA shZEB1_1_10_PE_6Breast cancer cell line control for Zeb1 stable knockdown
SA353443210514_MDA_ZEB1_n3_2h_sh-Ctrl_DMSO_22Breast cancer cell line control for Zeb1 stable knockdown
SA353444210514_MDA_ZEB1_n2_2h_sh-Ctrl_DMSO_13Breast cancer cell line control for Zeb1 stable knockdown
SA353445210514_MDA_ZEB1_n1_2h_sh-Ctrl_DMSO_4Breast cancer cell line control for Zeb1 stable knockdown
SA353446190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#4_3Breast cancer cell line control for Zeb1 stable knockdown
SA353447190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#4_2Breast cancer cell line control for Zeb1 stable knockdown
SA353448190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#4_1Breast cancer cell line control for Zeb1 stable knockdown
SA353449190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#1_3Breast cancer cell line control for Zeb1 stable knockdown
SA353450190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#1_2Breast cancer cell line control for Zeb1 stable knockdown
SA353451190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#1_1Breast cancer cell line control for Zeb1 stable knockdown
SA353452220408_MDA shZEB1_1_10_PE_5Breast cancer cell line control for Zeb1 stable knockdown
SA353405210514_MDA_ZEB1_n3_2h_WT_DMSO_19Breast cancer cell line Wild-type
SA353406190905_AG_Brabletz_ZEB1_EMT_Lipidomics__MDA_MB_231_WT_2Breast cancer cell line Wild-type
SA353407190905_AG_Brabletz_ZEB1_EMT_Lipidomics__MDA_MB_231_WT_1Breast cancer cell line Wild-type
SA353408210514_MDA_ZEB1_n2_2h_WT_DMSO_10Breast cancer cell line Wild-type
SA353409210514_MDA_ZEB1_n1_2h_WT_DMSO_1Breast cancer cell line Wild-type
SA353410190905_AG_Brabletz_ZEB1_EMT_Lipidomics__MDA_MB_231_WT_3Breast cancer cell line Wild-type
SA353411190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#F10_2Breast cancer cell line Zeb1 stable knockdown
SA353412220408_MDA shCtrl_1_10_PE_4Breast cancer cell line Zeb1 stable knockdown
SA353413220408_MDA shCtrl_1_10_PE_3Breast cancer cell line Zeb1 stable knockdown
SA353414220408_MDA shCtrl_1_10_PE_2Breast cancer cell line Zeb1 stable knockdown
SA353415220408_MDA shCtrl_1_10_PE_1Breast cancer cell line Zeb1 stable knockdown
SA353416220408_MDA shZEB1_1_10_PC_2Breast cancer cell line Zeb1 stable knockdown
SA353417220408_MDA shZEB1_1_10_PC_3Breast cancer cell line Zeb1 stable knockdown
SA353418210514_MDA_ZEB1_n3_2h_sh-ZEB1_DMSO_25Breast cancer cell line Zeb1 stable knockdown
SA353419210514_MDA_ZEB1_n2_2h_sh-ZEB1_DMSO_16Breast cancer cell line Zeb1 stable knockdown
SA353420210514_MDA_ZEB1_n1_2h_sh-ZEB1_DMSO_7Breast cancer cell line Zeb1 stable knockdown
SA353421190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#F10_3Breast cancer cell line Zeb1 stable knockdown
SA353422190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#F10_1Breast cancer cell line Zeb1 stable knockdown
SA353423190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#13_3Breast cancer cell line Zeb1 stable knockdown
SA353424190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#13_2Breast cancer cell line Zeb1 stable knockdown
SA353425190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#13_1Breast cancer cell line Zeb1 stable knockdown
SA353426220408_MDA shZEB1_1_10_PC_4Breast cancer cell line Zeb1 stable knockdown
SA353427230309_shCTRL shZEB1_Rao_shZEB1_1Breast cancer cell line Zeb1 stable knockdown
SA353428230309_shCTRL shZEB1_Rao_shZEB1_2Breast cancer cell line Zeb1 stable knockdown
SA353429230309_shCTRL shZEB1_Rao_shZEB1_3Breast cancer cell line Zeb1 stable knockdown
SA353430230309_shCTRL shZEB1_Rao_shZEB1_4Breast cancer cell line Zeb1 stable knockdown
SA353431220408_MDA shZEB1_1_10_PC_1Breast cancer cell line Zeb1 stable knockdown
Showing results 1 to 48 of 48

Collection:

Collection ID:CO003357
Collection Summary:Cultured cells were washed, trypsinized, counted and flash-frozen in liquid N2 and stored at -80°C.
Sample Type:Breast cancer cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003373
Treatment Summary:Human breast cancer MDA-MB-231 wildtype (WT) cells and the stably transduced MDA-MB-231 shZeb1 (stable Zeb1 knockdown) and shCtrl cell lines (control cell line for the stable Zeb1 knockdown) (Spaderna et al. 2008, DOI: 10.1158/0008-5472.CAN-07-5682) were collected, snap-frozen and stored at -80°C.

Sample Preparation:

Sampleprep ID:SP003371
Sampleprep Summary:Phospholipids were extracted from cell pellets by successive addition of PBS pH 7.4, methanol, chloroform, and saline to a final ratio of 14:34:35:17. Evaporation of the organic layer yielded a lipid film that was dissolved in methanol and subjected to UPLC-MS/MS.
Extract Storage:-80℃

Combined analysis:

Analysis ID AN005315
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity H-Class
Column Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 6500+ QTrap
Ion Mode NEGATIVE
Units relative intensities

Chromatography:

Chromatography ID:CH004019
Chromatography Summary:Chromatographic separation of phospholipids was carried out on an Acquity BEH C8 column (1.7 μm, 2.1×100 mm, Waters, Milford, MA) using an Acquity UHPLC.
Instrument Name:Waters Acquity H-Class
Column Name:Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:The gradient was ramped from 75 to 85% B over 5 min and further increased to 100% B within 2 min, followed by isocratic elution for another 2 min
Flow Rate:0.75 mL/min
Solvent A:90% Water, 10% acetonitrile; 2 mM ammonium acetate
Solvent B:95% Acetonitrile, 5% Water; 2 mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS005045
Analysis ID:AN005315
Instrument Name:ABI Sciex 6500+ QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Targeted MRM with pre-optimized settings and subsequent automated integration of selected signals using Analyst 1.6.3 or Analyst 1.7.1 (Sciex).
Ion Mode:NEGATIVE
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