{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003259","ANALYSIS_ID":"AN005343","PROJECT_ID":"PR002015","VERSION":"1","CREATED_ON":"May 27, 2024, 11:18 am"},

"PROJECT":{"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"},

"STUDY":{"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","EMAIL":"Andreas.Koeberle@uibk.ac.at","PHONE":"+43 512 507 57903"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"KPC661",
"Sample ID":"230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01",
"Factors":{"Sample source":"KPC allografts","Phenotype":"epithelial/mixed"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name (Analyst file name))":"230221_PE_KPC-Brabletz_1-30-dil_.wiff"}
},
{
"Subject ID":"KPC661",
"Sample ID":"230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02",
"Factors":{"Sample source":"KPC allografts","Phenotype":"epithelial/mixed"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name (Analyst file name))":"230221_PE_KPC-Brabletz_1-30-dil_.wiff"}
},
{
"Subject ID":"KPC438",
"Sample ID":"230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03",
"Factors":{"Sample source":"KPC allografts","Phenotype":"epithelial/mixed"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name (Analyst file name))":"230221_PE_KPC-Brabletz_1-30-dil_.wiff"}
},
{
"Subject ID":"KPC701",
"Sample ID":"230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04",
"Factors":{"Sample source":"KPC allografts","Phenotype":"mesenchymal"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name (Analyst file name))":"230221_PE_KPC-Brabletz_1-30-dil_.wiff"}
},
{
"Subject ID":"KPC550",
"Sample ID":"230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05",
"Factors":{"Sample source":"KPC allografts","Phenotype":"mesenchymal"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name (Analyst file name))":"230221_PE_KPC-Brabletz_1-30-dil_.wiff"}
},
{
"Subject ID":"KPC550",
"Sample ID":"230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06",
"Factors":{"Sample source":"KPC allografts","Phenotype":"mesenchymal"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name (Analyst file name))":"230221_PE_KPC-Brabletz_1-30-dil_.wiff"}
}
],
"COLLECTION":{"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_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."},

"SAMPLEPREP":{"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℃"},

"CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity H-Class","COLUMN_NAME":"Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)","SOLVENT_A":"water/acetonitrile 90/10, 2 mM ammonium acetate","SOLVENT_B":"water/acetonitrile 5/95, 2 mM ammonium acetate","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","COLUMN_TEMPERATURE":"45"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex 6500+","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","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)."},

"MS_METABOLITE_DATA":{
"Units":"relative intensities",

"Data":[{"Metabolite":"PE 14:0_16:0","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"0.0267275951","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"0.0407931480","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"0.0665213963","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"0.0547799102","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"0.0444761201","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"0.0857394433"},{"Metabolite":"PE 16:0/16:0","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"0.1600781989","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"0.1706996434","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"0.3178626739","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"0.2521749731","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"0.2306752654","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"0.4494248188"},{"Metabolite":"PE 16:0_16:1","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"0.2885058007","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"0.3856817697","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"0.4066306823","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"0.4896299015","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"0.3009908905","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"0.6038978939"},{"Metabolite":"PE 16:1_18:0","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"0.6020019029","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"0.5775701434","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"0.6517087497","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"0.8960915507","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"0.3218924817","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"0.7601011771"},{"Metabolite":"PE 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16:0_18:1","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"4.1592961053","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"4.5082153866","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"5.2584478786","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"3.1195542965","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"2.1008874344","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"2.7773604233"},{"Metabolite":"PE 16:1_18:1","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"0.4571373325","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"0.6887914090","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"0.5007447580","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"0.6406973038","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"0.2513491958","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"0.5592956600"},{"Metabolite":"PE 18:0_18:1","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"36.7208369708","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"37.2108073323","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"29.4787741108","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"20.0328546981","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"8.1413426155","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"10.1445426162"},{"Metabolite":"PE 18:1/18:1","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"8.9417571438","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"6.6191087146","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"5.4253298164","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"4.7532054608","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"2.3830771956","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"3.2708963287"},{"Metabolite":"PE 16:0_18:2","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"0.9579561967","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"1.8731596285","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"1.8409575708","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"1.5244505131","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"2.1114778177","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"1.7580295823"},{"Metabolite":"PE 18:0_18:2","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_01":"6.4453982512","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_02":"6.8924572476","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_03":"7.7247453916","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_04":"9.1021543352","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_05":"9.9016012475","230221_PE_KPC-Brabletz_1-30-dil_Sample-1-24_06":"8.1882159233"},{"Metabolite":"PE 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}

}