Summary of Study ST003257

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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 IDST003257
Study TitleExploration of EMT-dependent changes in the lipidome of KPC cells
Study SummaryKPC cell lines that are mesenchymal (lines KPC550 and KPC701), mesenchymal/epithelial mixed (lines KPC524 and KPC438), epithelial (lines KPC661 and KPC792) and KPC cell lines with Zeb1 knockout (lines KPCZ519, KPCZ436, KPCZ426) 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. "200326_Brabletz_EMT_ZEB1_PE_dil_1_10.wiff", "200326_Brabletz_EMT_ZEB1_PC_dil_1_10.wiff" or "200326_Brabletz_EMT_ZEB1_PI_dil_1_10.wiff").
University of Innsbruck
DepartmentMichael Popp Institute
Last NameKoeberle
First NameAndreas
AddressMitterweg 24, Innsbruck, Tyrol, 6020, Austria
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 application/zip

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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
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 ID:SU003378
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090


Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Phenotype
SA354052200326_Brabletz_EMT_ZEB1_16_KPC792_1Pancreatic Cancer cells epithelial
SA354053200326_Brabletz_EMT_ZEB1_18_KPC792_3Pancreatic Cancer cells epithelial
SA354054200326_Brabletz_EMT_ZEB1_17_KPC792_2Pancreatic Cancer cells epithelial
SA354055200326_Brabletz_EMT_ZEB1_15_KPC661_3Pancreatic Cancer cells epithelial
SA354056200326_Brabletz_EMT_ZEB1_14_KPC661_2Pancreatic Cancer cells epithelial
SA354057200326_Brabletz_EMT_ZEB1_13_KPC661_1Pancreatic Cancer cells epithelial
SA354058200326_Brabletz_EMT_ZEB1_2_KPC550_2Pancreatic Cancer cells mesenchymal
SA354059200326_Brabletz_EMT_ZEB1_6_KPC701_3Pancreatic Cancer cells mesenchymal
SA354060200326_Brabletz_EMT_ZEB1_5_KPC701_2Pancreatic Cancer cells mesenchymal
SA354061200326_Brabletz_EMT_ZEB1_4_KPC701_1Pancreatic Cancer cells mesenchymal
SA354062200326_Brabletz_EMT_ZEB1_3_KPC550_3Pancreatic Cancer cells mesenchymal
SA354063200326_Brabletz_EMT_ZEB1_1_KPC550_1Pancreatic Cancer cells mesenchymal
SA354064200326_Brabletz_EMT_ZEB1_12_KPC438_3Pancreatic Cancer cells mesenchymal/epithelial mixed
SA354065200326_Brabletz_EMT_ZEB1_11_KPC438_2Pancreatic Cancer cells mesenchymal/epithelial mixed
SA354066200326_Brabletz_EMT_ZEB1_10_KPC438_1Pancreatic Cancer cells mesenchymal/epithelial mixed
SA354067200326_Brabletz_EMT_ZEB1_9_KPC524_3Pancreatic Cancer cells mesenchymal/epithelial mixed
SA354068200326_Brabletz_EMT_ZEB1_8_KPC524_2Pancreatic Cancer cells mesenchymal/epithelial mixed
SA354069200326_Brabletz_EMT_ZEB1_7_KPC524_1Pancreatic Cancer cells mesenchymal/epithelial mixed
SA354043200326_Brabletz_EMT_ZEB1_27_KPCZ426_3Pancreatic Cancer cells Zeb1 knockout
SA354044200326_Brabletz_EMT_ZEB1_26_KPCZ426_2Pancreatic Cancer cells Zeb1 knockout
SA354045200326_Brabletz_EMT_ZEB1_25_KPCZ426_1Pancreatic Cancer cells Zeb1 knockout
SA354046200326_Brabletz_EMT_ZEB1_24_KPCZ346_3Pancreatic Cancer cells Zeb1 knockout
SA354047200326_Brabletz_EMT_ZEB1_23_KPCZ346_2Pancreatic Cancer cells Zeb1 knockout
SA354048200326_Brabletz_EMT_ZEB1_22_KPCZ346_1Pancreatic Cancer cells Zeb1 knockout
SA354049200326_Brabletz_EMT_ZEB1_21_KPCZ519_3Pancreatic Cancer cells Zeb1 knockout
SA354050200326_Brabletz_EMT_ZEB1_20_KPCZ519_2Pancreatic Cancer cells Zeb1 knockout
SA354051200326_Brabletz_EMT_ZEB1_19_KPCZ519_1Pancreatic Cancer cells Zeb1 knockout
Showing results 1 to 27 of 27


Collection ID:CO003371
Collection Summary:Cultured cells were washed, trypsinized, counted and flash-frozen in liquid N2 and stored at -80°C.
Sample Type:Tumor cells
Storage Conditions:-80℃


Treatment ID:TR003387
Treatment Summary:Tumor-derived pancreatic cancer KPC cells that are mesenchymal (lines KPC550 and KPC701), mesenchymal/epithelial mixed (lines KPC524 and KPC438), epithelial (lines KPC661 and KPC792) and KPC cell lines with Zeb1 knockout (lines KPCZ519, KPCZ436, KPCZ426) were obtained from tumors of KPC mice as described (Krebs et al. 2017, DOI: 10.1038/ncb3513).

Sample Preparation:

Sampleprep ID:SP003385
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 AN005342
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 instrument type QTRAP
MS instrument name ABI Sciex 6500+
Units relative intensities


Chromatography ID:CH004044
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:5% Water, 95% Acetonitrile; 2 mM ammonium acetate
Chromatography Type:Reversed phase


MS ID:MS005072
Analysis ID:AN005342
Instrument Name:ABI Sciex 6500+
Instrument Type:QTRAP
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). Phospholipids were analyzed in the negative ion mode, and both fatty acid anion fragments were detected by multiple reaction monitoring (MRM). For quantitation, the mean of both transitions was calculated. For the calculation of relative intensities (i.e., the proportion of lipids), all analyzed signals within the subgroup were summarized (= 100%), and the signals of individual lipid species or lipid subfractions are expressed as percentage of this sum.