Summary of Study ST003397
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 PR001988. The data can be accessed directly via it's Project DOI: 10.21228/M8RJ07 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 | ST003397 |
| Study Title | Glutamine Tracing in Mice injected with HKJS001 and Malonic Acid |
| Study Summary | Mice were injected by IP with 13C515N2-glutamine solution. Each mice was injected with 15µL of 50mg/mL glutamine solution per gram of mouse. Mice were injected with DMSO as a control, HKJS001 compound, 1M malonic acid, or a combination of HKJS001 and Malonic Acid. The mice were sacrificed and the liver was harvested. Polar metabolites extraction performed on the liver tissue. |
| Institute | UMass Chan Medical School |
| Last Name | UMass Chan |
| First Name | Spinelli Lab |
| Address | 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA |
| spinellilab@gmail.com | |
| Phone | (508) 856-8989 ext. 68148 |
| Submit Date | 2024-07-25 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-02-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001988 |
| Project DOI: | doi: 10.21228/M8RJ07 |
| Project Title: | Rhodoquinone is an Electron Carrier in the Mammalian Electron Transport Chain |
| Project Summary: | Ubiquinone (UQ), the only known electron carrier in the mammalian electron transport chain (ETC), delivers electrons to both oxygen (O2) and fumarate as terminal electron acceptors. As fumarate has a lower reduction potential than UQ, fumarate reduction is only thermodynamically favorable when ubiquinol, the reduced form of UQ, accumulates. Paradoxically, some tissues reduce fumarate without ubiquinol buildup, suggesting another mechanism enables fumarate reduction in mammals. Here, we identify rhodoquinone (RQ), a novel mammalian electron carrier that directs electrons to fumarate, instead of O2, as the favored terminal electron acceptor. RQ, which is undetectable in cultured mammalian cells, is enriched in tissues that catalyze fumarate reduction. RQ and UQ-directed ETC circuits support distinct programs of mitochondrial function. Through expression of a bacterial enzyme that converts UQ into RQ and development a novel RQ analog, we demonstrate that reprogramming the mammalian ETC from the UQ to RQ circuit renders cells highly resistant to hypoxia exposure. Thus, we establish RQ as a fundamental component of the mammalian ETC and unveil reprogramming the ETC to the RQ-circuit as a tractable strategy to treat hypoxia-related diseases. |
| Institute: | UMass Chan Medical School |
| Department: | Program in Molecular Medicine |
| Laboratory: | Spinelli Lab |
| Last Name: | UMass Chan |
| First Name: | Spinelli Lab |
| Address: | 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA |
| Email: | spinellilab@gmail.com |
| Phone: | (508) 856-8989 ext. 68148 |
Subject:
| Subject ID: | SU003522 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Standards for Standard Curve and Treatment |
|---|---|---|---|
| SA371488 | Liver 14 | Liver | Combo HKJS001 and Malonic Acid |
| SA371489 | Liver 16 | Liver | Combo HKJS001 and Malonic Acid |
| SA371490 | Liver 15 | Liver | Combo HKJS001 and Malonic Acid |
| SA371491 | Liver 13 | Liver | Combo HKJS001 and Malonic Acid |
| SA371492 | Liver 6 | Liver | HKJS001 Injected |
| SA371493 | Liver 7 | Liver | HKJS001 Injected |
| SA371494 | Liver 8 | Liver | HKJS001 Injected |
| SA371495 | Liver 5 | Liver | HKJS001 Injected |
| SA371496 | Liver 9 | Liver | Malonic Acid Injected |
| SA371497 | Liver 10 | Liver | Malonic Acid Injected |
| SA371498 | Liver 11 | Liver | Malonic Acid Injected |
| SA371499 | Liver 12 | Liver | Malonic Acid Injected |
| SA371500 | Liver 3 | Liver | Vehicle |
| SA371501 | Liver 4 | Liver | Vehicle |
| SA371502 | Liver 1 | Liver | Vehicle |
| SA371503 | Liver 2 | Liver | Vehicle |
| SA371504 | Standard 2 | Succinate and Fumarate Reagent Mixture | Measurable Standard Curve |
| SA371505 | Standard 3 | Succinate and Fumarate Reagent Mixture | Measurable Standard Curve |
| SA371506 | Standard 4 | Succinate and Fumarate Reagent Mixture | Measurable Standard Curve |
| SA371507 | Standard 5 | Succinate and Fumarate Reagent Mixture | Measurable Standard Curve |
| SA371508 | Standard 6 | Succinate and Fumarate Reagent Mixture | Measurable Standard Curve |
| SA371509 | Standard 7 | Succinate and Fumarate Reagent Mixture | Measurable Standard Curve |
| SA371510 | Standard 8 | Succinate and Fumarate Reagent Mixture | Measurable Standard Curve |
| Showing results 1 to 23 of 23 |
Collection:
| Collection ID: | CO003515 |
| Collection Summary: | Mice were sacrificed and liver tissue was collected. Tissues were flash frozen in liquid nitrogen and powdered using a mortar and pestle. Approximately 10 mg of tissue powder was transferred into an Eppendorf tube. |
| Sample Type: | Liver |
Treatment:
| Treatment ID: | TR003531 |
| Treatment Summary: | 13C515N2-glutamine was resuspended to 50 mg/mL in 1X PBS. C57BL/6 mice between the ages of 10-16 weeks were weighed to allow injection of 0.75 g/kg. Mice that were injected with HKJS001 was resuspended in DMSO to have a final concentration of 3.33 mg/mL and 2µL of HKJS001 was injected per gram of mouse. Mice that were injected with malonic acid was resuspended in water to a molarity of 1M and 1.6µL of malonic acid was injected per gram of mouse. |
Sample Preparation:
| Sampleprep ID: | SP003529 |
| Sampleprep Summary: | he tissue powder was re-suspended in 800 µL pre-cooled HPLC-grade 60:40 Methanol:Water and then vortexed for 15 minutes at 4°C. 500 µL of pre-cooled LC-MS grade chloroform was added to the lysate and again vortexed for 15 minutes at 4°C. Samples were then centrifuged at 16,000 x g for 10 minutes at 4°C, creating three layers: the top layer containing polar metabolites, the middle layer containing protein, and the bottom layer containing non-polar metabolites. The top layer was transferred into a new Eppendorf tube, dried down in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap-105 Cold Trap, and stored at -80°C until they were re-suspended for LC-MS analysis. The non-polar layer was discarded, and the remaining protein layer was saved for protein quantification. |
Combined analysis:
| Analysis ID | AN005575 | AN005576 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5µm) | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5µm) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH004237 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5µm) |
| Column Temperature: | 25 |
| Flow Gradient: | 20 min, 80% - 20% B; 0.5 min, 20% - 80% B; 7.5min, 80% B |
| Flow Rate: | 0.15ml/min |
| Solvent A: | 100% water; 0.1% ammonium hydroxide; 20mM ammonium carbonate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005300 |
| Analysis ID: | AN005575 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer was set to full scan (70-1000 m/z), with the spray voltage set to 4.0 kV, heated capillary to 350°C, and the HESI probe at 30 °C. The sheath gas flow was set at 10 units, auxiliary gas at 1 units, and sweep gas flow at 1 unit. The resolution of scan was set to 70,000, AGC target to 1x106, and maximum injection time at 20 msec. Data acquired by Thermo Fisher's Xcalibur software and analyzed by their Tracefinder software. The raw files provided contain data from both positive and negative ion mode. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005301 |
| Analysis ID: | AN005576 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer had the spray voltage set to 4.0 kV, heated capillary to 350°C, and the HESI probe at 30 °C. The sheath gas flow was set at 10 units, auxiliary gas at 1 units, and sweep gas flow at 1 unit. An additional scan between 220-700 m/z was used to enhance nucleotide detection in the negative mode as well with the maximum injection time set to 80 msec. Data acquired by Thermo Fisher's Xcalibur software and analyzed by their Tracefinder software. The raw files provided contain data from both positive and negative ion mode. |
| Ion Mode: | NEGATIVE |
