Summary of Study ST001751

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 PR001114. The data can be accessed directly via it's Project DOI: 10.21228/M8Q39V This work is supported by NIH grant, U2C- DK119886.

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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 IDST001751
Study TitleFree fatty acid analysis of NIH-3T3 cells treated with apoptotic inducers
Study TypeTargeted lipidomics
Study SummaryChanges of free fatty acid profiles in mouse NIH-3T3 fibroblasts treated with mechanistically diverse apoptotic inducers for 48h.
Institute
University of Innsbruck
DepartmentMichael Popp Institute
Last NameKoeberle
First NameAndreas
AddressMitterweg 24, Innsbruck, Tyrol, 6020, Austria
Emailandreas.koeberle@uibk.ac.at
Phone+43 512 507 57903
Submit Date2021-04-02
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2021-05-01
Release Version1
Andreas Koeberle Andreas Koeberle
https://dx.doi.org/10.21228/M8Q39V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001114
Project DOI:doi: 10.21228/M8Q39V
Project Title:Regulation of stress signalling by SCD1-derived phosphatidylinositols
Project Type:Targeted lipidomics
Project Summary:Cytotoxic stress activates stress-activated kinases, initiates adaptive mechanisms, including the unfolded protein response (UPR) and autophagy, and induces programmed cell death. Fatty acid unsaturation, controlled by stearoyl-CoA desaturase (SCD)1, prevents cytotoxic stress but the mechanisms are diffuse. We found that 1,2-dioleoyl-sn-glycero-3-phospho-(1’-myo-inositol) [PI(18:1/18:1)] is a SCD1-derived signaling lipid, which inhibits p38 mitogen-activated protein kinase (MAPK) activation, counteracts UPR, autophagy and apoptosis induction, and maintains cell morphology and proliferation. SCD1 expression and the cellular PI(18:1/18:1) proportion decrease during the onset of cell death, thereby activating stress signaling. This counter-regulation applies to mechanistically diverse death-inducing conditions and occurs in tissues of Scd1-defective mice.
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:German Research Council (GRK 1715 and KO 4589/4-1), Phospholipid Research Center Heidelberg (AKO-2019-070/2-1 and AKO-2015-037/1-1), University of Jena (DRM/2013-05 and 2.7-05), Free State of Thuringia (41-5507-2016) and Leibniz ScienceCampus InfectoOptics (SAS-2015-HKI-LWC).
Publications:PI(18:1/18:1) is a SCD1-derived lipokine that limits stress signaling. Thürmer M, Gollowitzer A, Pein H, Neukirch K, Gelmez E, Waltl L, Wielsch N, Winkler R, Löser K, Grander J, Hotze M, Harder S, Döding A, Meßner M, Troisi F, Ardelt M, Schlüter H, Pachmayr J, Gutiérrez-Gutiérrez Ó, Rudolph KL, Thedieck K, Schulze-Späte U, González-Estévez C, Kosan C, Svatoš A, Kwiatkowski M, Koeberle A. Nat Commun. 2022 May 27;13(1):2982. doi: 10.1038/s41467-022-30374-9.

Subject:

Subject ID:SU001828
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id hours treatment concentration
SA163885VJ_17.05.17-n3_#21 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00548 CHX 20 µg/ml
SA163886VJ_17.05.13_2_#21 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00548 CHX 20 µg/ml
SA163887VJ_17.05.17_#21 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00548 CHX 20 µg/ml
SA163888VJ_17.05.17_#22 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00648 ETO 10 µM
SA163889VJ_17.05.13_2_#22 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00648 ETO 10 µM
SA163890VJ_17.05.17-n3_#22 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00648 ETO 10 µM
SA163891VJ_17.05.13_2_#27 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_01148 I3M 10 µM
SA163892VJ_17.05.17_#27 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_01148 I3M 10 µM
SA163893VJ_17.05.17-n3_#27 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_01148 I3M 10 µM
SA163894VJ_17.05.17_#26 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_01048 MC 10 µM
SA163895VJ_17.05.13_2_#26 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_01048 MC 10 µM
SA163896VJ_17.05.17-n3_#26 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_01048 MC 10 µM
SA163900VJ_17.05.17_#25 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00948 Serum -
SA163901VJ_17.05.17-n3_#25 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00948 Serum -
SA163902VJ_17.05.13_2_#25 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00948 Serum -
SA163897VJ_17.05.17-n3_#20 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00448 STS 0.3 µM
SA163898VJ_17.05.13_2_#20 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00448 STS 0.3 µM
SA163899VJ_17.05.17_#20 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00448 STS 0.3 µM
SA163903VJ_17.05.13_2_#19 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00348 TNFα 10 ng/ml
SA163904VJ_17.05.17-n3_#19 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00348 TNFα 10 ng/ml
SA163905VJ_17.05.17_#19 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00348 TNFα 10 ng/ml
SA163906VJ_17.05.17-n3_#23 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00748 TPG 2 µM
SA163907VJ_17.05.17_#23 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00748 TPG 2 µM
SA163908VJ_17.05.13_2_#23 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00748 TPG 2 µM
SA163909VJ_17.05.13_2_#24 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00848 VAL 10 µM
SA163910VJ_17.05.17-n3_#24 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00848 VAL 10 µM
SA163911VJ_17.05.17_#24 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00848 VAL 10 µM
SA163912VJ_17.05.17-n3_#28 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_01248 vehicle (DMSO) -
SA163913VJ_17.05.17_#28 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_01248 vehicle (DMSO) -
SA163914VJ_17.05.13_2_#28 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_01248 vehicle (DMSO) -
SA163915VJ_17.05.17-n3_#18 - VJ_17.05.17_Kinase_screeneing_48h_n3_FFA_00248 vehicle (DMSO) -
SA163916VJ_17.05.17_#18 - VJ_17.05.17_Kinase_screeneing_48h_n2_FFA_00248 vehicle (DMSO) -
SA163917VJ_17.05.13_2_#18 - VJ_17.05.13_Kinase_screeneing_48h_n1_FFA_00248 vehicle (DMSO) -
Showing results 1 to 33 of 33

Collection:

Collection ID:CO001821
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:TR001841
Treatment Summary:Mouse NIH-3T3 fibroblasts were cultivated in DMEM high glucose medium containing heat-inactivated fetal calf serum (FCS, 10%). After cultivation for 24 h, cells were treated with vehicle, TNFα (10 ng/ml), STS (0.3 µM), CHX (20 µg/ml), ETO (10 µM), TPG (2 µM), VAL (10 µM), MC (10 µM) at 37°C and 5% CO2. Serum depletion of NIH-3T3 fibroblasts was achieved by cultivation of cells in serum-free DMEM.
Treatment Vehicle:DMSO
Cell Media:DMEM + 10% FCS
Cell Envir Cond:37°C, 5% CO2

Sample Preparation:

Sampleprep ID:SP001834
Sampleprep Summary:Fatty acids 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:-20℃

Combined analysis:

Analysis ID AN002854
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity H-Class
Column Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode NEGATIVE
Units relative intensities

Chromatography:

Chromatography ID:CH002113
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 BEH C8 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002647
Analysis ID:AN002854
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Multiple ion monitoring with pre-optimized settings and subsequent automated integration of selected signals using Analyst 1.6 (Sciex).
Ion Mode:NEGATIVE
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