Summary of Study ST003431

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 PR001941. The data can be accessed directly via it's Project DOI: 10.21228/M8TM76 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 IDST003431
Study TitleMetabolomics analysis of breast cancer cell lines treated with dimethylmalonate (DMM), GSK2194069, and their combination.
Study SummarySeven breast cancer cell lines (MDA-MB-468, SUM159PT, MCF7, HCC1806, MDA-MB-231, HS578T, CAL120) were treated with 5 mM DMM, 1 uM GSK2194069, and their combination, for 24 h. Intracellular samples were collected for the metabolomics analysis.
Institute
Wistar Institute
DepartmentMolecular and Cellular Oncogenesis Program, Ellen and Ronald Caplan Cancer Center
LaboratorySchug's Lab
Last NameMukha
First NameDzmitry
Address3601 Spruce St, Philadelphia, PA 19104, USA
Emaildmukha@wistar.org
Phone+12154956903
Submit Date2024-08-21
Num Groups17
Total Subjects51
PublicationsSubmission Pending
Raw Data AvailableYes
Raw Data File Type(s)mzML, wiff
Analysis Type DetailLC-MS
Release Date2024-09-12
Release Version1
Dzmitry Mukha Dzmitry Mukha
https://dx.doi.org/10.21228/M8TM76
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001941
Project DOI:doi: 10.21228/M8TM76
Project Title:The shutdown of NADH oxidation via Respiratory Complex I mimics fatty acid biosynthesis inhibition
Project Type:LC-MS Quantitative Analysis
Project Summary:Proliferating cancer cells actively utilize anabolic processes for biomass production, including de novo biosynthesis of amino acids, nucleotides, and fatty acids. The key enzyme of the fatty acid biosynthesis pathway, fatty acid synthase (FASN), is widely recognized as a promising therapeutic target in cancer and other health conditions. Here, we establish a metabolic signature of FASN inhibition using a panel of pharmacological inhibitors (GSK2194069, TVB-2640, TVB-3166, C75, cerulenin, and Fasnall). We find that the activity of some commonly used FASN inhibitors is inconsistent with the metabolic signature of FASN inhibition (accumulation of malonate, succinate, malonyl coenzyme A, succinyl coenzyme A, and other metabolic perturbations). Moreover, we show that one of these putative FASN inhibitors, Fasnall, is a respiratory Complex I inhibitor that mimics FASN inhibition through NADH accumulation and consequent depletion of the tricarboxylic acid cycle metabolites. We demonstrate that Fasnall impairs tumor growth in several oxidative phosphorylation-dependent cancer models, including combination therapy-resistant melanoma patient-derived xenografts. Fasnall administration does not reproduce neurological side effects in mice reported for other Complex I inhibitors. Our results have significant implications for understanding the FASN role in human health and disease and provide evidence of therapeutic potential for Complex I inhibitors with fast systemic clearance. Our findings also highlight the continuing need for validation of small molecule inhibitors to distinguish high-quality chemical probes and to expand the understanding of their application.
Institute:Wistar Institute
Department:Molecular and Cellular Oncogenesis Program, Ellen and Ronald Caplan Cancer Center
Laboratory:Schug's Lab
Last Name:Mukha
First Name:Dzmitry
Address:3601 Spruce St., Philadelphia, Pennsylvania 19104, USA
Email:dmukha@wistar.org
Phone:+12154956903
Funding Source:This work was supported by grants from the National Institutes of Health (NIH) National Cancer Institute (NCI) DP2 CA249950-01 (Z.T.S.), NIH NCI P01 CA114046 (Z.T.S.), Melanoma Research Foundation 717173 (Z.T.S.), and Susan G. Komen CCR19608782 (Z.T.S.).
Publications:Submission Pending
Contributors:Dzmitry Mukha, Jena Dessain, Seamus O’Connor, Katherine Pniewski, Fabrizio Bertolazzi, Jeet Patel, Mary Mullins, Zachary T. Schug

Subject:

Subject ID:SU003558
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Female
Cell Strain Details:MDA-MB-468, SUM159PT, MCF7, HCC1806, MDA-MB-231, HS578T, CAL120

Factors:

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

mb_sample_id local_sample_id Sample source Sample Type Drug Treatment
SA37792043 CAL120 GSK 1 uMCAL120 breast cancer cells Intracellular 1 uM GSK214069
SA37792140 CAL120 GSK 1 uMCAL120 breast cancer cells Intracellular 1 uM GSK214069
SA37792242 CAL120 DMM 5 mMCAL120 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37792339 CAL120 DMM 5 mMCAL120 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37792444 CAL120 CombinationCAL120 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37792541 CAL120 CombinationCAL120 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37792625 HCC1806 GSK 1 uMHCC1806 breast cancer cells Intracellular 1 uM GSK214069
SA37792722 HCC1806 GSK 1 uMHCC1806 breast cancer cells Intracellular 1 uM GSK214069
SA37792821 HCC1806 DMM 5 mMHCC1806 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37792924 HCC1806 DMM 5 mMHCC1806 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37793026 HCC1806 CombinationHCC1806 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37793123 HCC1806 CombinationHCC1806 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37793237 HS578T GSK 1 uMHS578T breast cancer cells Intracellular 1 uM GSK214069
SA37793334 HS578T GSK 1 uMHS578T breast cancer cells Intracellular 1 uM GSK214069
SA37793436 HS578T DMM 5 mMHS578T breast cancer cells Intracellular 5 mM dimethylmalonate
SA37793533 HS578T DMM 5 mMHS578T breast cancer cells Intracellular 5 mM dimethylmalonate
SA37793638 HS578T CombinationHS578T breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37793735 HS578T CombinationHS578T breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37793816 MCF7 GSK 1 uMMCF7 breast cancer cells Intracellular 1 uM GSK214069
SA37793919 MCF7 GSK 1 uMMCF7 breast cancer cells Intracellular 1 uM GSK214069
SA37794015 MCF7 DMM 5 mMMCF7 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37794118 MCF7 DMM 5 mMMCF7 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37794217 MCF7 CombinationMCF7 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37794320 MCF7 CombinationMCF7 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37794428 MDA-MB-231 GSK 1 uMMDA-MB-231 breast cancer cells Intracellular 1 uM GSK214069
SA37794531 MDA-MB-231 GSK 1 uMMDA-MB-231 breast cancer cells Intracellular 1 uM GSK214069
SA37794630 MDA-MB-231 DMM 5 mMMDA-MB-231 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37794727 MDA-MB-231 DMM 5 mMMDA-MB-231 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37794829 MDA-MB-231 CombinationMDA-MB-231 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37794932 MDA-MB-231 CombinationMDA-MB-231 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37795007 MDA-MB-468 GSK 1 uMMDA-MB-468 breast cancer cells Intracellular 1 uM GSK214069
SA37795104 MDA-MB-468 GSK 1 uMMDA-MB-468 breast cancer cells Intracellular 1 uM GSK214069
SA37795203 MDA-MB-468 DMM 5 mMMDA-MB-468 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37795306 MDA-MB-468 DMM 5 mMMDA-MB-468 breast cancer cells Intracellular 5 mM dimethylmalonate
SA37795408 MDA-MB-468 CombinationMDA-MB-468 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37795505 MDA-MB-468 CombinationMDA-MB-468 breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37795646 BlankNA Blank NA
SA37795701 BlankNA Blank NA
SA37795802 DMEM/F12 no addsNA QC NA
SA37795945 DMEM/F12 no addsNA QC NA
SA37796013 SUM159PT GSK 1 uMSUM159PT breast cancer cells Intracellular 1 uM GSK214069
SA37796110 SUM159PT GSK 1 uMSUM159PT breast cancer cells Intracellular 1 uM GSK214069
SA37796209 SUM159PT DMM 5 mMSUM159PT breast cancer cells Intracellular 5 mM dimethylmalonate
SA37796312 SUM159PT DMM 5 mMSUM159PT breast cancer cells Intracellular 5 mM dimethylmalonate
SA37796411 SUM159PT CombinationSUM159PT breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
SA37796514 SUM159PT CombinationSUM159PT breast cancer cells Intracellular 5 mM dimethylmalonate + 1 uM GSK214069
Showing results 1 to 46 of 46

Collection:

Collection ID:CO003551
Collection Summary:For intracellular metabolite samples, the medium was aspirated, and cells were washed with PBS volume matching the volume of the medium. Metabolites were extracted with ice-cold 80% methanol. The volume of the solvent was 500 µl per 6-cm Petri dish (scaled according to the ratio of surface areas for other cell containers). After adding the methanol solution, cells were scraped from the plates, and all the content was transferred to Eppendorf tubes.
Collection Protocol Filename:DM_metabolomics_samples.txt
Sample Type:Breast cancer cells
Collection Method:80% methanol extraction
Storage Conditions:-80℃
Collection Vials:1.5 ml plastic centrifuge tubes
Storage Vials:1.5 ml plastic centrifuge tubes

Treatment:

Treatment ID:TR003567
Treatment Summary:Cells were grown in RPMI-1640 supplemented with 10% dialyzed FBS and treated with various concentrations of rotenone for 24 h.
Treatment Compound:Dimethylmalonate (DMM) and GSK2194069
Treatment Vehicle:DMSO
Cell Growth Container:6-cm Petri dishes
Cell Media:RPMI-1640
Cell Envir Cond:37C, 5% CO2
Cell Pct Confluence:~70%
Cell Media Lastchanged:24 h before collection

Sample Preparation:

Sampleprep ID:SP003565
Sampleprep Summary:Intracellular metabolites were extracted with ice-cold 80% methanol, and medium samples were extracted with 100% methanol. The samples were centrifuged at 18,000 g 4C for 20 min. After transferring the supernatant to new tubes, centrifugation was repeated with the same parameters.
Sampleprep Protocol Filename:DM_metabolomics_samples.txt
Processing Storage Conditions:4℃
Extraction Method:80% methanol
Extract Enrichment:None
Extract Cleanup:None
Extract Storage:-80℃
Sample Resuspension:None
Sample Derivatization:None
Sample Spiking:None
Subcellular Location:Intracellular metabolites and medium metabolites

Combined analysis:

Analysis ID AN005635 AN005636
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Shimadzu 20AD Shimadzu 20AD
Column Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap ABI Sciex 5500 QTrap
Ion Mode NEGATIVE POSITIVE
Units Counts per second (cps) Counts per second (cps)

Chromatography:

Chromatography ID:CH004280
Instrument Name:Shimadzu 20AD
Column Name:Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Column Pressure:900-3000 psi
Column Temperature:40
Flow Gradient:0-12.5 min, 80-30% B; 12.5-15 min, 30% B; 15-15.2 min, 30-80% B; 15.2-22.5 min, 80% B
Flow Rate:0-20 min, 0.2 ml/min; 20-21 min 0.2-0.3 ml/min; 21-22 min, 0.3 ml/min; 22-22.1 min, 0.2 ml/min; 22.1-22.5 min, 0.2 ml/min
Injection Temperature:4
Sample Injection:1-5 ul
Solvent A:100% Water; 0.01% ammonium hydroxide; 20 mM ammonium bicarbonate
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS005359
Analysis ID:AN005635
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Data were analyzed with SCIEX Multiquant 3.0.3.
Ion Mode:NEGATIVE
Capillary Temperature:500 °C
Capillary Voltage:-4500
Dry Gas Flow:70
Dry Gas Temp:500 °C
Ion Source Temperature:500 °C
Ion Spray Voltage:-4500
Mass Accuracy:UNIT
Source Temperature:500 °C
Spray Voltage:-4500
Desolvation Gas Flow:70
Desolvation Temperature:500 °C
  
MS ID:MS005360
Analysis ID:AN005636
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Data were analyzed with SCIEX Multiquant 3.0.3.
Ion Mode:POSITIVE
Capillary Temperature:500 °C
Capillary Voltage:4500
Dry Gas Flow:70
Dry Gas Temp:500 °C
Ion Source Temperature:500 °C
Ion Spray Voltage:4500
Mass Accuracy:UNIT
Source Temperature:500 °C
Spray Voltage:4500
Desolvation Gas Flow:70
Desolvation Temperature:500 °C
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