Summary of Study ST003336
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 PR002065. The data can be accessed directly via it's Project DOI: 10.21228/M8PR7B 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.
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| Study ID | ST003336 |
| Study Title | Differentiation between cytotoxic stress-induced PUFA biosynthesis and PUFA incorporation into phospholipids by metabolic flux studies in fibroblasts |
| Study Summary | Metabolic flux studies addressing the incorporation of i) deuterium labeled polyunsaturated fatty acids (20:4, 22:4, 22:5, 22:6) having one or two acetate-d3 incorporated or ii) one arachidonic acid-d8 or its elongation product adrenic acid-d8 into cellular phosphatidylcholines of NIH-3T3 fibroblasts that were treated with TOFA, VAL or a combination of both |
| 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 | 2024-07-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-01-06 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002065 |
| Project DOI: | doi: 10.21228/M8PR7B |
| Project Title: | Changes in phospholipid fatty acid composition under cytotoxic stress facilitate peroxidation |
| Project Summary: | Programs leading to cell death, such as apoptosis, necroptosis, and ferroptosis, involve an oxidative component linked to lipid metabolism that influences membrane homeostasis. Emerging evidence suggests inter-program cross-talk, emphasizing the need for overarching regulatory mechanisms. We show that under specific cytotoxic stress conditions, exogenous or released polyunsaturated fatty acids (PUFAs) are channeled into overall depleting phospholipids that become vulnerable to peroxidation in the presence of associated redox stress. In fibroblasts, this reprogramming results from reduced growth factor receptor tyrosine kinase (RTK) and phosphatidylinositol-3-kinase (PI3K)/Akt signaling, which reduces de novo fatty acid biosynthesis by mechanisms that differ depending on the specific cytotoxic stressors. We conclude that alterations in PUFA metabolism during cytotoxic stress render cells prone to oxidative modifications in phospholipids. |
| 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: | Austrian Science Fund (FWF) (P 36299). German Research Council (GRK 1715 and KO 4589/4-1), the Phospholipid Research Center Heidelberg (AKO-2015-037/1-1, AKO-2019-070/2-1, AKO-2O22-100/2-2), the University of Jena (DRM/2013-05 and 2.7-05). |
| Contributors: | André Gollowitzer, Helmut Pein, Konstantin Loeser, Maria Thuermer, and Andreas Koeberle |
Subject:
| Subject ID: | SU003457 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | treatment A | treatment B | treatment C |
|---|---|---|---|---|---|
| SA362682 | 200709_PUFA_PC_dPUFA_dAa_n2_TOFA_dAa | cultured cells | TOFA | - | dAA |
| SA362683 | 200705_PUFA_PC_dPUFA_dAA_n_1_TOFA_dAA_4 | cultured cells | TOFA | - | dAA |
| SA362684 | 200709_PUFA_PC_dPUFA_dAa_n3_TOFA_dAa | cultured cells | TOFA | - | dAA |
| SA362685 | 200705_PUFA_PC_dPUFA_dAC_n_1_TOFA_dAc_4 | cultured cells | TOFA | - | dAc |
| SA362686 | 200709_PUFA_PC_dPUFA_dAc_n2_TOFA_dAc | cultured cells | TOFA | - | dAc |
| SA362687 | 200709_PUFA_PC_dPUFA_dAc_n3_TOFA_dAc | cultured cells | TOFA | - | dAc |
| SA362688 | 200709_PUFA_PC_dPUFA_dAa_n2_TOFA_VAL_dAa | cultured cells | TOFA | VAL | dAA |
| SA362689 | 200705_PUFA_PC_dPUFA_dAA_n_1_TOFA_VAL_dAA_8 | cultured cells | TOFA | VAL | dAA |
| SA362690 | 200709_PUFA_PC_dPUFA_dAa_n3_TOFA_VAL_dAa | cultured cells | TOFA | VAL | dAA |
| SA362691 | 200709_PUFA_PC_dPUFA_dAc_n3_TOFA_VAL_dAc | cultured cells | TOFA | VAL | dAc |
| SA362692 | 200709_PUFA_PC_dPUFA_dAc_n2_TOFA_VAL_dAc | cultured cells | TOFA | VAL | dAc |
| SA362693 | 200705_PUFA_PC_dPUFA_dAC_n_1_TOFA_VAL_dAc_8 | cultured cells | TOFA | VAL | dAc |
| SA362694 | 200709_PUFA_PC_dPUFA_dAa_n2_VAL_dAa | cultured cells | VAL | - | dAA |
| SA362695 | 200709_PUFA_PC_dPUFA_dAa_n3_VAL_dAa | cultured cells | VAL | - | dAA |
| SA362696 | 200705_PUFA_PC_dPUFA_dAA_n_1_VAL_dAA_6 | cultured cells | VAL | - | dAA |
| SA362697 | 200709_PUFA_PC_dPUFA_dAc_n3_VAL_dAc | cultured cells | VAL | - | dAc |
| SA362698 | 200709_PUFA_PC_dPUFA_dAc_n2_VAL_dAc | cultured cells | VAL | - | dAc |
| SA362699 | 200705_PUFA_PC_dPUFA_dAC_n_1_VAL_dAc_6 | cultured cells | VAL | - | dAc |
| SA362700 | 200709_PUFA_PC_dPUFA_dAc_n3_DMSO | cultured cells | vehicle (DMSO) | - | - |
| SA362701 | 200705_PUFA_PC_dPUFA_dAA_n_1_DMSO_1 | cultured cells | vehicle (DMSO) | - | - |
| SA362702 | 200709_PUFA_PC_dPUFA_dAa_n3_DMSO | cultured cells | vehicle (DMSO) | - | - |
| SA362703 | 200709_PUFA_PC_dPUFA_dAc_n2_DMSO | cultured cells | vehicle (DMSO) | - | - |
| SA362704 | 200709_PUFA_PC_dPUFA_dAa_n2_DMSO | cultured cells | vehicle (DMSO) | - | - |
| SA362705 | 200705_PUFA_PC_dPUFA_dAC_n_1_DMSO_1 | cultured cells | vehicle (DMSO) | - | - |
| SA362706 | 200705_PUFA_PC_dPUFA_dAA_n_1_DMSO_dAA_2 | cultured cells | vehicle (DMSO) | - | dAA |
| SA362707 | 200709_PUFA_PC_dPUFA_dAa_n3_DMSO_dAa | cultured cells | vehicle (DMSO) | - | dAA |
| SA362708 | 200709_PUFA_PC_dPUFA_dAa_n2_DMSO_dAa | cultured cells | vehicle (DMSO) | - | dAA |
| SA362709 | 200709_PUFA_PC_dPUFA_dAc_n2_DMSO_dAc | cultured cells | vehicle (DMSO) | - | dAc |
| SA362710 | 200705_PUFA_PC_dPUFA_dAC_n_1_DMSO_dAc_2 | cultured cells | vehicle (DMSO) | - | dAc |
| SA362711 | 200709_PUFA_PC_dPUFA_dAc_n3_DMSO_dAc | cultured cells | vehicle (DMSO) | - | dAc |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO003450 |
| Collection Summary: | Cultured cells were washed, trypsinized, counted and flash-frozen in liquid N2 and stored at -80°C. |
| Sample Type: | Fibroblasts |
| Collection Method: | Trypsinization of cultured cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003466 |
| Treatment Summary: | For metabolic flux studies, NIH-3T3 cells were incubated with acetate-d3 (30 µM) or arachidonic acid-d8 (1 µM) and treated with vehicle (DMSO), TOFA (5 µM), VAL (10 µM), or both VAL and TOFA. |
Sample Preparation:
| Sampleprep ID: | SP003464 |
| 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, diluted, and subjected to UPLC-MS/MS. |
| Extract Storage: | -20℃ |
Combined analysis:
| Analysis ID | AN005468 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Sciex ExionLC AD |
| 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 | nmol / 10^6 cells |
Chromatography:
| Chromatography ID: | CH004153 |
| Chromatography Summary: | Chromatographic separation of (deuterated) phospholipids was carried out on an Acquity BEH C8 column (1.7 μm, 2.1×100 mm, Waters, Milford, MA) using an ExionLC AD UHPLC system (Sciex). |
| Instrument Name: | Sciex ExionLC AD |
| 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% A over 5 min and further increased to 100% A within 2 min, followed by isocratic elution for another 2 min. |
| Flow Rate: | 0.75 ml/min |
| Solvent A: | 5% Water/95% Acetonitrile; 2 mM ammonium acetate |
| Solvent B: | 90% Water/10% Acetonitrile; 2 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005194 |
| Analysis ID: | AN005468 |
| 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 and 1.7 (Sciex). |
| Ion Mode: | NEGATIVE |
