Summary of Study ST003435
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 | ST003435 |
Study Title | Metabolomics analysis of zebrafish embryos treated with rotenone, Fasnall, TVB-2640, and GSK2194069 |
Study Summary | To compare the metabolic effects and toxicity of Fasnall with rotenone in vivo, zebrafish embryos 48 h post-fertilization were exposed to a drug-containing medium for 6 h. Rotenone at 25 nM is lethal to fish embryos, while 5 nM concentration leads to a ~15-fold lactate accumulation. Similarly, Fasnall treatment increases lactate content, although the magnitude of the effect is significantly lower. Unlike 5 nM rotenone, Fasnall treatment does not cause visible phenotypic changes in the yolk. The zebrafish model suggests that Fasnall acts as a Complex I inhibitor in vivo. |
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, wiff |
Analysis Type Detail | LC-MS |
Release Date | 2024-09-12 |
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: | SU003562 |
Subject Type: | Fish |
Subject Species: | Danio rerio |
Taxonomy ID: | 7955 |
Gender: | Pooled |
Species Group: | Fish |
Factors:
Subject type: Fish; Subject species: Danio rerio (Factor headings shown in green)
mb_sample_id | local_sample_id | Sample source | Sample Type | Drug Treatment |
---|---|---|---|---|
SA378125 | 24 Blank | NA | Blank | NA |
SA378126 | 49 Blank | NA | Blank | NA |
SA378127 | 01 Blank | NA | Blank | NA |
SA378128 | 02 DMEM/F12 no adds | NA | QC | NA |
SA378129 | 48 DMEM/F12 no adds | NA | QC | NA |
SA378130 | 36 13-1 Rotenone 1 nM Medium 1 | Zebrafish medium | Zebrafish medium | 1 nM rotenone |
SA378131 | 38 13-3 Rotenone 1 nM Medium 3 | Zebrafish medium | Zebrafish medium | 1 nM rotenone |
SA378132 | 37 13-2 Rotenone 1 nM Medium 2 | Zebrafish medium | Zebrafish medium | 1 nM rotenone |
SA378133 | 43 21-2 Fasnall 20 uM Medium 2 | Zebrafish medium | Zebrafish medium | 20 uM Fasnall |
SA378134 | 44 21-3 Fasnall 20 uM Medium 3 | Zebrafish medium | Zebrafish medium | 20 uM Fasnall |
SA378135 | 42 21-1 Fasnall 20 uM Medium 1 | Zebrafish medium | Zebrafish medium | 20 uM Fasnall |
SA378136 | 45 25-1 Fasnall 40 uM Medium 1 | Zebrafish medium | Zebrafish medium | 40 uM Fasnall |
SA378137 | 46 25-2 Fasnall 40 uM Medium 2 | Zebrafish medium | Zebrafish medium | 40 uM Fasnall |
SA378138 | 47 25-3 Fasnall 40 uM Medium 3 | Zebrafish medium | Zebrafish medium | 40 uM Fasnall |
SA378139 | 31 05-2 GSK 40 uM Medium 2 | Zebrafish medium | Zebrafish medium | 40 uM GSK2194069 |
SA378140 | 30 05-1 GSK 40 uM Medium 1 | Zebrafish medium | Zebrafish medium | 40 uM GSK2194069 |
SA378141 | 32 05-3 GSK 40 uM Medium 3 | Zebrafish medium | Zebrafish medium | 40 uM GSK2194069 |
SA378142 | 34 09-2 TVB-2640 40 uM Medium 2 | Zebrafish medium | Zebrafish medium | 40 uM TVB-2640 |
SA378143 | 33 09-1 TVB-2640 40 uM Medium 1 | Zebrafish medium | Zebrafish medium | 40 uM TVB-2640 |
SA378144 | 35 09-3 TVB-2640 40 uM Medium 3 | Zebrafish medium | Zebrafish medium | 40 uM TVB-2640 |
SA378145 | 40 17-2 Rotenone 5 nM Medium 2 | Zebrafish medium | Zebrafish medium | 5 nM rotenone |
SA378146 | 41 17-3 Rotenone 5 nM Medium 3 | Zebrafish medium | Zebrafish medium | 5 nM rotenone |
SA378147 | 39 17-1 Rotenone 5 nM Medium 1 | Zebrafish medium | Zebrafish medium | 5 nM rotenone |
SA378148 | 29 01-3 DMSO Medium 3 | Zebrafish medium | Zebrafish medium | Vehicle |
SA378149 | 28 01-2 DMSO Medium 2 | Zebrafish medium | Zebrafish medium | Vehicle |
SA378150 | 27 01-1 DMSO Medium 1 | Zebrafish medium | Zebrafish medium | Vehicle |
SA378151 | 06 14 Rotenone 1 nM 1 | Zebrafish | Zebrafish embryo metabolite extract | 1 nM rotenone |
SA378152 | 20 16 Rotenone 1 nM 3 * | Zebrafish | Zebrafish embryo metabolite extract | 1 nM rotenone |
SA378153 | 13 15 Rotenone 1 nM 2 | Zebrafish | Zebrafish embryo metabolite extract | 1 nM rotenone |
SA378154 | 22 24 Fasnall 20 uM 3 | Zebrafish | Zebrafish embryo metabolite extract | 20 uM Fasnall |
SA378155 | 15 23 Fasnall 20 uM 2 | Zebrafish | Zebrafish embryo metabolite extract | 20 uM Fasnall |
SA378156 | 08 22 Fasnall 20 uM 1 | Zebrafish | Zebrafish embryo metabolite extract | 20 uM Fasnall |
SA378157 | 16 27 Fasnall 40 uM 2 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM Fasnall |
SA378158 | 09 26 Fasnall 40 uM 1 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM Fasnall |
SA378159 | 23 28 Fasnall 40 uM 3 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM Fasnall |
SA378160 | 25 08 GSK 40 uM 3 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM GSK2194069 |
SA378161 | 04 06 GSK 40 uM 1 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM GSK2194069 |
SA378162 | 18 07 GSK 40 uM 2 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM GSK2194069 |
SA378163 | 11 07 GSK 40 uM 2 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM GSK2194069 |
SA378164 | 05 10 TVB-2640 40 uM 1 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM TVB-2640 |
SA378165 | 19 12 TVB-2640 40 uM 3 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM TVB-2640 |
SA378166 | 12 11 TVB-2640 40 uM 2 | Zebrafish | Zebrafish embryo metabolite extract | 40 uM TVB-2640 |
SA378167 | 21 19 Rotenone 5 nM 2 | Zebrafish | Zebrafish embryo metabolite extract | 5 nM rotenone |
SA378168 | 14 19 Rotenone 5 nM 2 | Zebrafish | Zebrafish embryo metabolite extract | 5 nM rotenone |
SA378169 | 07 18 Rotenone 5 nM 1 | Zebrafish | Zebrafish embryo metabolite extract | 5 nM rotenone |
SA378170 | 26 20 Rotenone 5 nM 3 | Zebrafish | Zebrafish embryo metabolite extract | 5 nM rotenone |
SA378171 | 17 04 DMSO 3 | Zebrafish | Zebrafish embryo metabolite extract | Vehicle |
SA378172 | 10 03 DMSO 2 | Zebrafish | Zebrafish embryo metabolite extract | Vehicle |
SA378173 | 03 02 DMSO 1 | Zebrafish | Zebrafish embryo metabolite extract | Vehicle |
Showing results 1 to 49 of 49 |
Collection:
Collection ID: | CO003555 |
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: | Media, Metabolite extract |
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: | TR003571 |
Treatment Summary: | The zebrafish research was approved by the University of Pennsylvania Institutional Animal Care and Use Committee. Husbandry was performed in accordance with institutional animal welfare guidelines. Embryos from wild type, Tübingen zebrafish were collected within 15 minutes of fertilization. Embryos between 2 and 3 crosses were equally pooled and allocated to treatment conditions for all experiments. Embryos were reared at 28 °C in E3 medium (4 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4, no methylene blue) until treatment. Pharmacological agents were diluted from stocks at room temperature in E3 for 15 minutes before treatment. For treatment at 48 h post-fertilization, embryos in their chorions were transferred to clean plates with the inhibitor-supplemented E3 and incubated for 6 hours. |
Treatment Compound: | Rotenone, Fasnall, TVB-2640, and GSK2194069 |
Treatment Route: | Drugs were dissolved in the medium |
Treatment Vehicle: | DMSO |
Sample Preparation:
Sampleprep ID: | SP003569 |
Sampleprep Summary: | Zebrafish embryos were combined by eight per Eppendorf tube, washed with PBS twice, and snap-frozen on dry ice. Frozen samples were ground at the temperature of liquid nitrogen by Retsch Cryomill. To each tube, 300 µl of 80% methanol were added. |
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 | AN005643 | AN005644 |
---|---|---|
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: | CH004284 |
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: | MS005367 |
Analysis ID: | AN005643 |
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: | MS005368 |
Analysis ID: | AN005644 |
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 |