Summary of Study ST003259
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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST003259 |
| Study Title | Exploration of EMT-dependent changes of phosphatidylethanolamine profiles in KPC allografts |
| Study Summary | Cryo-conserved tumors from subcutaneous allografts as described (Krebs et al. 2017, DOI: 10.1038/ncb3513) were retrieved. Three tumors derived from mesenchymal KPC cell lines (lines KPC550 and KPC701) and epithelial KPC cell lines (lines KPC438 and KPC661) were analyzed for their phosphatidylethanolamine profile by UPLC-MS/MS. |
| Institute | University of Innsbruck |
| Department | Michael Popp Institute |
| Last Name | Koeberle |
| First Name | Andreas |
| Address | Mitterweg 24, Innsbruck, Tyrol, 6020, Austria |
| Andreas.Koeberle@uibk.ac.at | |
| Phone | +43 512 507 57903 |
| Submit Date | 2024-05-27 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-05 |
| Release Version | 1 |
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: | SU003379 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Phenotype |
|---|---|---|---|
| SA354070 | 230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01 | Pancreatic Cancer cell allografts | epithelial/mixed |
| SA354071 | 230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02 | Pancreatic Cancer cell allografts | epithelial/mixed |
| SA354072 | 230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03 | Pancreatic Cancer cell allografts | epithelial/mixed |
| SA354073 | 230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04 | Pancreatic Cancer cell allografts | mesenchymal |
| SA354074 | 230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05 | Pancreatic Cancer cell allografts | mesenchymal |
| SA354075 | 230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06 | Pancreatic Cancer cell allografts | mesenchymal |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO003372 |
| Collection Summary: | Cryo-conserved tumors from subcutaneous allografts described in (Krebs et al. 2017, DOI: 10.1038/ncb3513) were retrieved. |
| Sample Type: | Tumor allograft |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003388 |
| Treatment Summary: | KPC cells were subcutaneously injected into the flanks of C57BL/6 mice for engraftment as described (Krebs et al. 2017, DOI: 10.1038/ncb3513). Three tumor allografts derived from mesenchymal KPC cell lines (lines KPC550 and KPC701) and epithelial KPC cell lines (lines KPC438 and KPC661) were collected, cryo-conserved and stored at -80°C. |
Sample Preparation:
| Sampleprep ID: | SP003386 |
| Sampleprep Summary: | Phospholipids were extracted from allograft tumor tissue 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 | AN005343 |
|---|---|
| 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: | CH004045 |
| 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: | 5% Water, 95% Acetonitrile; 2 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005073 |
| Analysis ID: | AN005343 |
| 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). 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. |
| Ion Mode: | NEGATIVE |
