Summary of Study ST003427
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.
| Study ID | ST003427 |
| Study Title | Intracellular and medium metabolomics of BT-474 cells treated with dimethylmalonate |
| Study Summary | BT-474 human breast cancer cells were treated with various concentrations of dimethylmalonate (DMM) for 24 h. |
| 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, PA 19104, USA |
| dmukha@wistar.org | |
| Phone | +12154956903 |
| Submit Date | 2024-08-21 |
| Num Groups | 16 |
| Total Subjects | 48 |
| Publications | Submission Pending |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-09-10 |
| Release Version | 1 |
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: | SU003554 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 60 |
| Gender: | Female |
| Cell Strain Details: | BT-474, breast cancer cell line |
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 |
|---|---|---|---|---|
| SA377713 | 13 BT-474 DMM 0.1 mM cells | BT-474 breast cancer cells | Intracellular | 0.1 mM dimethylmalonate |
| SA377714 | 27 BT-474 DMM 0.1 mM med | BT-474 breast cancer cells | Intracellular | 0.1 mM dimethylmalonate |
| SA377715 | 20 BT-474 DMM 0.1 mM cells | BT-474 breast cancer cells | Intracellular | 0.1 mM dimethylmalonate |
| SA377716 | 06 BT-474 DMM 0.1 mM cells | BT-474 breast cancer cells | Intracellular | 0.1 mM dimethylmalonate |
| SA377717 | 21 BT-474 DMM 0.5 mM cells | BT-474 breast cancer cells | Intracellular | 0.5 mM dimethylmalonate |
| SA377718 | 14 BT-474 DMM 0.5 mM cells | BT-474 breast cancer cells | Intracellular | 0.5 mM dimethylmalonate |
| SA377719 | 28 BT-474 DMM 0.5 mM med | BT-474 breast cancer cells | Intracellular | 0.5 mM dimethylmalonate |
| SA377720 | 07 BT-474 DMM 0.5 mM cells | BT-474 breast cancer cells | Intracellular | 0.5 mM dimethylmalonate |
| SA377725 | 10 BT-474 DMM 10 mM cells | BT-474 breast cancer cells | Intracellular | 10 mM dimethylmalonate |
| SA377726 | 17 BT-474 DMM 10 mM cells | BT-474 breast cancer cells | Intracellular | 10 mM dimethylmalonate |
| SA377727 | 24 BT-474 DMM 10 mM cells | BT-474 breast cancer cells | Intracellular | 10 mM dimethylmalonate |
| SA377721 | 22 BT-474 DMM 1 mM cells | BT-474 breast cancer cells | Intracellular | 1 mM dimethylmalonate |
| SA377722 | 08 BT-474 DMM 1 mM cells | BT-474 breast cancer cells | Intracellular | 1 mM dimethylmalonate |
| SA377723 | 15 BT-474 DMM 1 mM cells | BT-474 breast cancer cells | Intracellular | 1 mM dimethylmalonate |
| SA377724 | 29 BT-474 DMM 1 mM med | BT-474 breast cancer cells | Intracellular | 1 mM dimethylmalonate |
| SA377728 | 11 BT-474 DMM 20 mM cells | BT-474 breast cancer cells | Intracellular | 20 mM dimethylmalonate |
| SA377729 | 18 BT-474 DMM 20 mM cells | BT-474 breast cancer cells | Intracellular | 20 mM dimethylmalonate |
| SA377730 | 25 BT-474 DMM 20 mM cells | BT-474 breast cancer cells | Intracellular | 20 mM dimethylmalonate |
| SA377731 | 23 BT-474 DMM 5 mM cells | BT-474 breast cancer cells | Intracellular | 5 mM dimethylmalonate |
| SA377732 | 09 BT-474 DMM 5 mM cells | BT-474 breast cancer cells | Intracellular | 5 mM dimethylmalonate |
| SA377733 | 16 BT-474 DMM 5 mM cells | BT-474 breast cancer cells | Intracellular | 5 mM dimethylmalonate |
| SA377734 | 05 BT-474 DMM 0 mM cells | BT-474 breast cancer cells | Intracellular | Control |
| SA377735 | 19 BT-474 DMM 0 mM cells | BT-474 breast cancer cells | Intracellular | Control |
| SA377736 | 26 BT-474 DMM 0 mM med | BT-474 breast cancer cells | Intracellular | Control |
| SA377737 | 12 BT-474 DMM 0 mM cells | BT-474 breast cancer cells | Intracellular | Control |
| SA377738 | 36 BT-474 DMM 0.1 mM med | BT-474 breast cancer cells | Medium | 0.1 mM dimethylmalonate |
| SA377739 | 45 BT-474 DMM 0.1 mM med | BT-474 breast cancer cells | Medium | 0.1 mM dimethylmalonate |
| SA377740 | 46 BT-474 DMM 0.5 mM med | BT-474 breast cancer cells | Medium | 0.5 mM dimethylmalonate |
| SA377741 | 37 BT-474 DMM 0.5 mM med | BT-474 breast cancer cells | Medium | 0.5 mM dimethylmalonate |
| SA377744 | 50 BT-474 DMM 10 mM med | BT-474 breast cancer cells | Medium | 10 mM dimethylmalonate |
| SA377745 | 41 BT-474 DMM 10 mM med | BT-474 breast cancer cells | Medium | 10 mM dimethylmalonate |
| SA377746 | 32 BT-474 DMM 10 mM med | BT-474 breast cancer cells | Medium | 10 mM dimethylmalonate |
| SA377742 | 47 BT-474 DMM 1 mM med | BT-474 breast cancer cells | Medium | 1 mM dimethylmalonate |
| SA377743 | 38 BT-474 DMM 1 mM med | BT-474 breast cancer cells | Medium | 1 mM dimethylmalonate |
| SA377747 | 42 BT-474 DMM 20 mM med | BT-474 breast cancer cells | Medium | 20 mM dimethylmalonate |
| SA377748 | 33 BT-474 DMM 20 mM med | BT-474 breast cancer cells | Medium | 20 mM dimethylmalonate |
| SA377749 | 51 BT-474 DMM 20 mM med | BT-474 breast cancer cells | Medium | 20 mM dimethylmalonate |
| SA377750 | 52 BT-474 DMM 40 mM med | BT-474 breast cancer cells | Medium | 40 mM dimethylmalonate |
| SA377751 | 43 BT-474 DMM 40 mM med | BT-474 breast cancer cells | Medium | 40 mM dimethylmalonate |
| SA377752 | 34 BT-474 DMM 40 mM med | BT-474 breast cancer cells | Medium | 40 mM dimethylmalonate |
| SA377753 | 40 BT-474 DMM 5 mM med | BT-474 breast cancer cells | Medium | 5 mM dimethylmalonate |
| SA377754 | 31 BT-474 DMM 5 mM med | BT-474 breast cancer cells | Medium | 5 mM dimethylmalonate |
| SA377755 | 49 BT-474 DMM 5 mM med | BT-474 breast cancer cells | Medium | 5 mM dimethylmalonate |
| SA377756 | 35 BT-474 DMM 0 mM med | BT-474 breast cancer cells | Medium | Control |
| SA377757 | 44 BT-474 DMM 0 mM med | BT-474 breast cancer cells | Medium | Control |
| SA377758 | 54 Blank | NA | Blank | NA |
| SA377759 | 04 Blank | NA | Blank | NA |
| SA377760 | 39 Bottle medium | NA | Medium | Control |
| SA377761 | 30 Bottle medium | NA | Medium | Control |
| SA377762 | 48 Bottle medium | NA | Medium | Control |
| SA377763 | 01 DMEM/F12 no adds | NA | QC | NA |
| SA377764 | 53 DMEM/F12 no adds | NA | QC | NA |
| SA377765 | 03 DMM 1000 | NA | Standard | NA |
| SA377766 | 02 DMM 50 | NA | Standard | NA |
| Showing results 1 to 54 of 54 |
Collection:
| Collection ID: | CO003547 |
| 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: | TR003563 |
| Treatment Summary: | Cells were grown in RPMI-1640 supplemented with 10% dialyzed FBS and treated with various concentrations of dimethylmalonate (DMM) for 24 h. |
| Treatment Compound: | Dimethylmalonate (DMM) |
| 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: | SP003561 |
| 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 | AN005627 | AN005628 |
|---|---|---|
| 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: | CH004276 |
| 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: | MS005351 |
| Analysis ID: | AN005627 |
| 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: | MS005352 |
| Analysis ID: | AN005628 |
| 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 |
