Summary of Study ST003846
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 PR002404. The data can be accessed directly via it's Project DOI: 10.21228/M8WJ9W 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 | ST003846 |
| Study Title | Hepatic Coenzyme Q (CoQ) Deficiency Drives Reverse Electron Transport and Disrupts Hepatic Metabolic Homeostasis in Obesity |
| Study Summary | Mitochondrial reactive oxygen species (mROS) play a crucial role in physiology. While excessive mROS production has been associated with several disease states, its precise sources, regulation, and mechanisms of generation in vivo remain unclear, limiting translational efforts. mROS production is not a single process; at least 11 distinct sites associated with the electron transport chain and matrix substrate oxidation can partially reduce oxygen to superoxide and hydrogen peroxide. These sites exhibit substrate specificity and differ in their capacities to generate mROS. Here, we show that in obesity, hepatic coenzyme Q (CoQ) synthesis in vivo is impaired, leading to decreased CoQ9 levels and an increased CoQH₂/CoQ ratio. These alterations in CoQ metabolism drive excessive mROS production via reverse electron transport (RET) at site IQ of complex I. Using multiple complementary genetic and pharmacological in vivo models, we demonstrate that RET is critical for maintaining metabolic health. Furthermore, we show that in patients with steatosis, hepatic CoQ biosynthesis is also suppressed, and the CoQH₂/CoQ ratio positively correlates with steatosis grade. Our data identify a highly selective mechanism of pathological mROS production in obesity, which can be targeted to preserve metabolic homeostasis. |
| Institute | Harvard School of Public Health |
| Department | Molecular Metabolism |
| Laboratory | Hotamisligil Lab |
| Last Name | de Lima Sales Goncalves |
| First Name | Renata |
| Address | 665 Huntington Ave bld 1, room 609 |
| rgoncal@hsph.harvard.edu | |
| Phone | 4159402482 |
| Submit Date | 2025-03-24 |
| Num Groups | 4 |
| Total Subjects | 27 |
| Num Males | 27 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-04-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002404 |
| Project DOI: | doi: 10.21228/M8WJ9W |
| Project Title: | Hepatic Coenzyme Q (CoQ) Deficiency Drives Reverse Electron Transport and Disrupts Hepatic Metabolic Homeostasis in Obesity |
| Project Summary: | Mitochondrial reactive oxygen species (mROS) play a crucial role in physiology. While excessive mROS production has been associated with several disease states, its precise sources, regulation, and mechanisms of generation in vivo remain unclear, limiting translational efforts. mROS production is not a single process; at least 11 distinct sites associated with the electron transport chain and matrix substrate oxidation can partially reduce oxygen to superoxide and hydrogen peroxide. These sites exhibit substrate specificity and differ in their capacities to generate mROS. Here, we show that in obesity, hepatic coenzyme Q (CoQ) synthesis in vivo is impaired, leading to decreased CoQ9 levels and an increased CoQH₂/CoQ ratio. These alterations in CoQ metabolism drive excessive mROS production via reverse electron transport (RET) at site IQ of complex I. Using multiple complementary genetic and pharmacological in vivo models, we demonstrate that RET is critical for maintaining metabolic health. Furthermore, we show that in patients with steatosis, hepatic CoQ biosynthesis is also suppressed, and the CoQH₂/CoQ ratio positively correlates with steatosis grade. Our data identify a highly selective mechanism of pathological mROS production in obesity, which can be targeted to preserve metabolic homeostasis. |
| Institute: | Harvard School of Public Health |
| Department: | Molecular Metabolism |
| Laboratory: | Hotamisligil Lab |
| Last Name: | de Lima Sales Goncalves |
| First Name: | Renata |
| Address: | 665 Huntington Ave bld 1, room 609, Boston, MA, 02115, USA |
| Email: | rgoncal@hsph.harvard.edu |
| Phone: | 4159402482 |
Subject:
| Subject ID: | SU003980 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL-6J |
| Age Or Age Range: | 10 weeks |
| Gender: | Male |
| Animal Animal Supplier: | The Jackson Lab |
| Animal Housing: | 4 mice per cage HSPH Animal facility |
| Animal Light Cycle: | 12/12 dark/light |
| Animal Feed: | ad libtum |
| Animal Water: | ad libitum |
| Animal Inclusion Criteria: | wildtype lean and lepOB (ob/ob) obese or LepOB (ob/ob) obese mice expressing Ciona intestinalis Alternative oxidase (Aox) or green fluorescent protein (GFP) as control. |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA420557 | Blank | Blank | Blank |
| SA420558 | 20200304_1N_aox | liver | Aox |
| SA420559 | 20191110_aox | liver | Aox |
| SA420560 | 20191111_aox | liver | Aox |
| SA420561 | 20191108_aox | liver | Aox |
| SA420562 | 20191203_aox | liver | Aox |
| SA420563 | 20200304_5R_aox | liver | Aox |
| SA420564 | 20191204_aox | liver | Aox |
| SA420565 | 20200304_5LR_aox | liver | Aox |
| SA420566 | 20200304_1LR_aox | liver | Aox |
| SA420567 | 20200304_3N_aox | liver | Aox |
| SA420568 | 20191108_gfp | liver | GFP |
| SA420569 | 20200304_R_gfp | liver | GFP |
| SA420570 | 20200304_1R_gfp | liver | GFP |
| SA420571 | 20191110_gfp | liver | GFP |
| SA420572 | 20200304_1L_gfp | liver | GFP |
| SA420573 | 20200304_L_gfp | liver | GFP |
| SA420574 | 20191111_gfp | liver | GFP |
| SA420575 | 20191203_gfp | liver | GFP |
| SA420576 | 20191204_gfp | liver | GFP |
| SA420577 | lean_03 | liver | Lean wildtype |
| SA420578 | lean_04 | liver | Lean wildtype |
| SA420579 | lean_04_scanevent2 | liver | Lean wildtype |
| SA420580 | lean_02_scanevent2 | liver | Lean wildtype |
| SA420581 | lean_02 | liver | Lean wildtype |
| SA420582 | lean_01_scanevent2 | liver | Lean wildtype |
| SA420583 | lean_01 | liver | Lean wildtype |
| SA420584 | lean_03_scanevent2 | liver | Lean wildtype |
| SA420585 | obese_01 | liver | LepOB |
| SA420586 | obese_01_scanevent2 | liver | LepOB |
| SA420587 | obese_02 | liver | LepOB |
| SA420588 | obese_02_scanevent2 | liver | LepOB |
| SA420589 | obese_03 | liver | LepOB |
| SA420590 | obese_03_scanevent2 | liver | LepOB |
| SA420591 | obese_04 | liver | LepOB |
| SA420592 | obese_04_scanevent2 | liver | LepOB |
| Showing results 1 to 36 of 36 |
Collection:
| Collection ID: | CO003973 |
| Collection Summary: | Livers were extracted under freeze-clamp conditions using a Wollenberger clamp and immediately frozen. |
| Sample Type: | Liver |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003989 |
| Treatment Summary: | Livers from wild-type lean and LepOB (ob/ob) mice were homogenized in liquid nitrogen using a cold tissuelyzer. To the pulverized tissues, 40% methanol:40% acetonitrile (25 mg/mL) was added to each tube. The same protocol was used for liver samples from mice ectopically expressing Ciona intestinalis alternative oxidase (AOX) or green fluorescent protein (GFP) as a control. |
Sample Preparation:
| Sampleprep ID: | SP003986 |
| Sampleprep Summary: | 20-30mg of tissue were weighted in a previously chilled tube at -20oC and tissuelyser homogenizer beads. Tissues were homogenized in liquid nitrogen using a cold tissuelyzer. To the pulverized tissues, 40% methanol:40% acetonitrile (25 mg/mL) was added to each tube. Each tube was vortexed for the 10 sec., incubate for 10 min on ice and centrifuged 10 min at 3000rpm to pellet debris. 600uL of the supernatant was transferred to a new tube and centrifuged at max speed for 10’. 80uL of the clean extract was added to a fresh vial and analyzed via mass spec. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -20℃ |
Chromatography:
| Chromatography ID: | CH004795 |
| Chromatography Summary: | For small polar metabolite separation and data acquisition in extracted tissues, a Vanquish Horizon (Thermo Fisher Scientific, Waltham, MA) ultra-high liquid chromatography (LC) system coupled to a Thermo Q Exactive HF Orbitrap mass spectrometer (MS) was used. For separation, a Waters (Milford, MA) XBridge BEH Amide (2.5 μm, 2.1x150 mm) column fitted with a VanGuard (2.5 μm, 2.1x5 mm) guard column was used. The mobile phases were as follows: Phase A: 95% water/5% acetonitrile and Phase B: 20% water/80% acetonitrile with 10 mM ammonium acetate and 10 mM ammonium hydroxide in both phases. The flow rate was held constant at 0.3 ml/min and the following gradient conditions were used: 0 min, 100% B; 3 min, 100% B; 3.2 min, 90% B; 6.2 min, 90% B; 6.5 min, 80% B; 10.5 min, 80% B; 10.7 min, 70% B; 13.5 min, 70% B; 13.7 min, 45% B; 16 min, 45% B, 16.5 min, 100% B; and 22 min, 100% B. The samples were kept at 4°C, the injection volume was 5 μl and the column was maintained at 25°C. The separated metabolites were analyzed in both positive and negative ionization modes in the same run (switching mode). The mass spectra were acquired using a resolution of 120,000 in the 70 – 1,000 m/z range. The ElectroSpray Ionization source parameters for both modes were as follows: capillary temperature 300°C, spray voltage 3.5kV, sheath gas 40 (arbitrary units), auxiliary gas 10 (arbitrary units), probe heater temperature 30°C and S-Lens RF level 45 v. |
| Instrument Name: | Thermo Vanquish Horizon |
| Column Name: | Waters XBridge BEH Amide (150 x 2.1mm, 2.5um) with VanGuard (5 x 2.1mm, 2.5um) guard column |
| Column Temperature: | 25 |
| Flow Gradient: | 0 min, 100% B; 3 min, 100% B; 3.2 min, 90% B; 6.2 min, 90% B; 6.5 min, 80% B; 10.5 min, 80% B; 10.7 min, 70% B; 13.5 min, 70% B; 13.7 min, 45% B; 16 min, 45% B, 16.5 min, 100% B; and 22 min, 100% B |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 95% water/5% acetonitrile; 10 mM ammonium acetate; 10 mM ammonium hydroxide |
| Solvent B: | 20% water/80% acetonitrile; 10 mM ammonium acetate; 10 mM ammonium hydroxide |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN006320 |
| Laboratory Name: | Hui lab |
| Analysis Type: | MS |
| Operator Name: | Clement Rosique and Tony Shen Hui |
| Chromatography ID: | CH004795 |
| Num Factors: | 5 |
| Num Metabolites: | 138 |
| Rt Units: | Minutes |
| Units: | peak area |
| Analysis ID: | AN006321 |
| Laboratory Name: | Hui lab |
| Analysis Type: | MS |
| Operator Name: | Clement Rosique and Tony Shen Hui |
| Chromatography ID: | CH004795 |
| Num Factors: | 5 |
| Num Metabolites: | 37 |
| Rt Units: | Minutes |
| Units: | peak area |
