Summary of Study ST003256

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	ST003256
Study Title	Exploration of Zeb1-dependent changes in the redox-lipidome of MDA-MB-231 cells
Study 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 treated with DMSO or RSL3 (1 or 10 µM) for 2 h, 4 h, 6 h or 24 h. The cell pellets were collected and analyzed for their oxidized 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 (Ox-PE, Ox-PC, Ox-PI), therefore each sub-class has their own raw-data file marked by their corresponding abbreviation (Ox-PE, Ox-PC, Ox-PI; e.g. "210514_MDA_ZEB1_oxPE_dil_UD_std_1ul_JZ_oxPE_MRM_003.wiff", "210514_MDA_ZEB1_oxPC_dil_UD_std_1ul_JZ_oxPC_MRM_002.wiff" or "210514_MDA_ZEB1_oxPI_dil_UD_std_1ul_JZ_oxPI_MRM_001.wiff").
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
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

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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:	SU003375
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Genotype	Treatment	Treatment Time
SA353986	210514_MDA_ZEB1_n3_2h_sh-Ctrl_DMSO_22	shCtrl	DMSO	2 h
SA353987	210514_MDA_ZEB1_n2_2h_sh-Ctrl_DMSO_13	shCtrl	DMSO	2 h
SA353988	210514_MDA_ZEB1_n1_2h_sh-Ctrl_DMSO_4	shCtrl	DMSO	2 h
SA353992	210514_MDA_ZEB1_n2_2h_sh-Ctrl_RSL3_10_uM_15	shCtrl	RSL3 (10 µM)	2 h
SA353993	210514_MDA_ZEB1_n3_2h_sh-Ctrl_RSL3_10_uM_24	shCtrl	RSL3 (10 µM)	2 h
SA353994	210514_MDA_ZEB1_n1_2h_sh-Ctrl_RSL3_10_uM_6	shCtrl	RSL3 (10 µM)	2 h
SA353989	210514_MDA_ZEB1_n2_2h_sh-Ctrl_RSL3_1_uM_14	shCtrl	RSL3 (1 µM)	2 h
SA353990	210514_MDA_ZEB1_n3_2h_sh-Ctrl_RSL3_1_uM_23	shCtrl	RSL3 (1 µM)	2 h
SA353991	210514_MDA_ZEB1_n1_2h_sh-Ctrl_RSL3_1_uM_5	shCtrl	RSL3 (1 µM)	2 h
SA353995	210514_MDA_ZEB1_n2_2h_sh-ZEB1_DMSO_16	shZeb1	DMSO	2 h
SA353996	210514_MDA_ZEB1_n1_2h_sh-ZEB1_DMSO_7	shZeb1	DMSO	2 h
SA353997	210514_MDA_ZEB1_n3_2h_sh-ZEB1_DMSO_25	shZeb1	DMSO	2 h
SA354001	210514_MDA_ZEB1_n3_2h_sh-ZEB1_RSL3_10_uM_27	shZeb1	RSL3 (10 µM)	2 h
SA354002	210514_MDA_ZEB1_n1_2h_sh-ZEB1_RSL3_10_uM_9	shZeb1	RSL3 (10 µM)	2 h
SA354003	210514_MDA_ZEB1_n2_2h_sh-ZEB1_RSL3_10_uM_18	shZeb1	RSL3 (10 µM)	2 h
SA353998	210514_MDA_ZEB1_n2_2h_sh-ZEB1_RSL3_1_uM_17	shZeb1	RSL3 (1 µM)	2 h
SA353999	210514_MDA_ZEB1_n3_2h_sh-ZEB1_RSL3_1_uM_26	shZeb1	RSL3 (1 µM)	2 h
SA354000	210514_MDA_ZEB1_n1_2h_sh-ZEB1_RSL3_1_uM_8	shZeb1	RSL3 (1 µM)	2 h
SA353944	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_24h_DMSO_7	WT	DMSO	24 h
SA353945	210317_MDA_ZEB1_TC_pre_RSL3_WT_n5_24h_DMSO_77	WT	DMSO	24 h
SA353946	210317_MDA_ZEB1_TC_pre_RSL3_WT_n4_24h_DMSO_65	WT	DMSO	24 h
SA353947	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_24h_DMSO_46	WT	DMSO	24 h
SA353948	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_24h_DMSO_23	WT	DMSO	24 h
SA353935	210514_MDA_ZEB1_n3_2h_WT_DMSO_19	WT	DMSO	2 h
SA353936	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_2h_DMSO_17_correct	WT	DMSO	2 h
SA353937	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_2h_RSL3_1uM_18	WT	DMSO	2 h
SA353938	210317_MDA_ZEB1_TC_pre_RSL3_WT_n5_2h_DMSO_73	WT	DMSO	2 h
SA353939	210317_MDA_ZEB1_TC_pre_RSL3_WT_n4_2h_DMSO_61	WT	DMSO	2 h
SA353940	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_2h_DMSO_37	WT	DMSO	2 h
SA353941	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_2h_DMSO_1	WT	DMSO	2 h
SA353942	210514_MDA_ZEB1_n1_2h_WT_DMSO_1	WT	DMSO	2 h
SA353943	210514_MDA_ZEB1_n2_2h_WT_DMSO_10	WT	DMSO	2 h
SA353949	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_4h_DMSO_19	WT	DMSO	4 h
SA353950	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_4h_DMSO_40	WT	DMSO	4 h
SA353951	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_4h_DMSO_3	WT	DMSO	4 h
SA353952	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_6h_DMSO_43	WT	DMSO	6 h
SA353953	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_6h_DMSO_21	WT	DMSO	6 h
SA353954	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_6h_DMSO_5	WT	DMSO	6 h
SA353977	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_24h_RSL3_10uM_48	WT	RSL3 (10 µM)	24 h
SA353978	210317_MDA_ZEB1_TC_pre_RSL3_WT_n4_24h_RSL3_10uM_66	WT	RSL3 (10 µM)	24 h
SA353979	210317_MDA_ZEB1_TC_pre_RSL3_WT_n5_24h_RSL3_10uM_78	WT	RSL3 (10 µM)	24 h
SA353971	210317_MDA_ZEB1_TC_pre_RSL3_WT_n4_2h_RSL3_10uM_62	WT	RSL3 (10 µM)	2 h
SA353972	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_2h_RSL3_10uM_39	WT	RSL3 (10 µM)	2 h
SA353973	210514_MDA_ZEB1_n2_2h_WT_RSL3_10_uM_12	WT	RSL3 (10 µM)	2 h
SA353974	210514_MDA_ZEB1_n3_2h_WT_RSL3_10_uM_21	WT	RSL3 (10 µM)	2 h
SA353975	210317_MDA_ZEB1_TC_pre_RSL3_WT_n5_2h_RSL3_10uM_74	WT	RSL3 (10 µM)	2 h
SA353976	210514_MDA_ZEB1_n1_2h_WT_RSL3_10_uM_3	WT	RSL3 (10 µM)	2 h
SA353980	210317_MDA_ZEB1_TC_pre_RSL3_WT_n5_4h_RSL3_10uM_75	WT	RSL3 (10 µM)	4 h
SA353981	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_4h_RSL3_10uM_42	WT	RSL3 (10 µM)	4 h
SA353982	210317_MDA_ZEB1_TC_pre_RSL3_WT_n4_4h_RSL3_10uM_63	WT	RSL3 (10 µM)	4 h
SA353983	210317_MDA_ZEB1_TC_pre_RSL3_WT_n5_6h_RSL3_10uM_76	WT	RSL3 (10 µM)	6 h
SA353984	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_6h_RSL3_10uM_45	WT	RSL3 (10 µM)	6 h
SA353985	210317_MDA_ZEB1_TC_pre_RSL3_WT_n4_6h_RSL3_10uM_64	WT	RSL3 (10 µM)	6 h
SA353962	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_24h_RSL3_1uM_24	WT	RSL3 (1 µM)	24 h
SA353963	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_24h_RSL3_1uM_47	WT	RSL3 (1 µM)	24 h
SA353964	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_24h_RSL3_1uM_8	WT	RSL3 (1 µM)	24 h
SA353955	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_2h_RSL3_1uM_2	WT	RSL3 (1 µM)	2 h
SA353956	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_2h_RSL3_1uM_18_correct	WT	RSL3 (1 µM)	2 h
SA353957	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_2h_DMSO_17	WT	RSL3 (1 µM)	2 h
SA353958	210514_MDA_ZEB1_n2_2h_WT_RSL3_1_uM_11	WT	RSL3 (1 µM)	2 h
SA353959	210514_MDA_ZEB1_n1_2h_WT_RSL3_1_uM_2	WT	RSL3 (1 µM)	2 h
SA353960	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_2h_RSL3_1uM_38	WT	RSL3 (1 µM)	2 h
SA353961	210514_MDA_ZEB1_n3_2h_WT_RSL3_1_uM_20	WT	RSL3 (1 µM)	2 h
SA353965	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_4h_RSL3_1uM_4	WT	RSL3 (1 µM)	4 h
SA353966	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_4h_RSL3_1uM_41	WT	RSL3 (1 µM)	4 h
SA353967	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_4h_RSL3_1uM_20	WT	RSL3 (1 µM)	4 h
SA353968	210317_MDA_ZEB1_TC_pre_RSL3_WT_n3_6h_RSL3_1uM_44	WT	RSL3 (1 µM)	6 h
SA353969	210317_MDA_ZEB1_TC_pre_RSL3_WT_n1_6h_RSL3_1uM_6	WT	RSL3 (1 µM)	6 h
SA353970	210317_MDA_ZEB1_TC_pre_RSL3_WT_n2_6h_RSL3_1uM_22	WT	RSL3 (1 µM)	6 h

Showing results 1 to 69 of 69

Showing results 1 to 69 of 69

Collection:

Collection ID:	CO003368
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:	TR003384
Treatment Summary:	Brest cancer cells (MDA-MB-231 cells) for oxPE, oxPC, oxPI: 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 treated with vehicle (DMSO) or RSL3 (1 and 10 µM) for 2 h, 4 h, 6 h, 24 h or 48 h at 37°C and 5% CO2.

Treatment ID:

TR003384

Treatment Summary:

Brest cancer cells (MDA-MB-231 cells) for oxPE, oxPC, oxPI: 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 treated with vehicle (DMSO) or RSL3 (1 and 10 µM) for 2 h, 4 h, 6 h, 24 h or 48 h at 37°C and 5% CO2.

Sample Preparation:

Sampleprep ID:	SP003382
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℃

Chromatography:

Chromatography ID:	CH004040
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

Analysis:

Analysis ID:	AN005338
Analysis Type:	MS
Chromatography ID:	CH004040
Num Factors:	18
Num Metabolites:	38
Units:	absolute intensities