Summary of Study ST004126
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 PR002594. The data can be accessed directly via it's Project DOI: 10.21228/M8BN8K 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 | ST004126 |
| Study Title | Glyc3P, hexose phosphates, and pentose phosphates measurements in citrin deficiency. |
| Study Type | Metabolomics |
| Study Summary | Citrin Deficiency (CD) is caused by inactivation of SLC25A13, a mitochondrial membrane protein required to move electrons from cytosolic NADH to the mitochondrial matrix in hepatocytes. In this study we used the mutant mouse models, with deletions of NADH shuttle systems, Slc25a13-/-, Gpd2-/-, and Slc25a13-/- Gpd2-/- to further characterize CD and ChREBP activation by measuring the liver levels of hexose phosphates, pentose phosphates, and glycerol-3-phosphate. The pentose phosphate xylulose-5-phosphate and hexose phosphates: glucose-6-phosphate and fructose-6-phosphate, were previously proposed activators of ChREBP. We provided ad libitum glycerol (5% w/v) to these mutant mice and compared the levels of these metabolites to determine their ability to activate ChREBP. Here we show that only G3P is elevated and accumulates in the liver of the mouse model of CD, and that ChREBP is activated in this model with transcription of FGF21 and activation of a lipogenic transcriptional program. Our data further show that G3P is a specific ligand of the ChREBP GSM, and suggest that features of the G3P-ChREBP activation mechanism can account for why fructose is more lipogenic than glucose, provide a unifying mechanism for nonalcoholic and alcoholic hepatic steatogenesis, resolve paradoxes of FGF21 expression, and explain key aspects of CD pathogenesis including lean MASLD, the favorable effects of MCTs, and severe urea cycle dysfunction. |
| Institute | Beckman Research Institute of City of Hope |
| Last Name | Brenner |
| First Name | Charles |
| Address | 1500 E. Duarte Road, Duarte, California, 91010, USA |
| cbrenner@coh.org | |
| Phone | 626-218-2750 |
| Submit Date | 2025-08-14 |
| Num Groups | 8 |
| Total Subjects | 35 |
| Num Males | 35 |
| Publications | Tiwari, V. et al Glycerol-3-phosphate activates ChREBP, FGF21 transcription and lipogenesis in Citrin Deficiency doi: 10.1101/2024.12.27.630525 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-08-21 |
| Release Version | 1 |
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Project:
| Project ID: | PR002594 |
| Project DOI: | doi: 10.21228/M8BN8K |
| Project Title: | Glycerol-3-phosphate activates ChREBP, FGF21 transcription and lipogenesis in Citrin Deficiency |
| Project Type: | MS quantitative analysis |
| Project Summary: | Citrin Deficiency (CD) is caused by inactivation of SLC25A13, a mitochondrial membrane protein required to move electrons from cytosolic NADH to the mitochondrial matrix in hepatocytes. People with CD do not like sweets. We discovered that SLC25A13 loss causes accumulation of glycerol-3-phosphate (G3P), which activates carbohydrate response element binding protein (ChREBP) to transcribe FGF21, which acts in the brain to restrain intake of sweets and alcohol, and to transcribe key genes of de novo lipogenesis. Mouse and human data establish G3P-ChREBP as a new mechanistic component of the Randle Cycle that contributes to metabolic dysfunction-associated steatotic liver disease (MASLD) and forms part of a system that communicates metabolic states from liver to brain in a manner that alters food and alcohol choices. The data provide a framework for understanding FGF21 induction in varied conditions, suggest ways to develop FGF21-inducing drugs, and drug candidates for both lean MASLD and support of urea cycle function in CD. |
| Institute: | Beckman Research Institute of City of Hope |
| Last Name: | Brenner |
| First Name: | Charles |
| Address: | 1500 E. Duarte Road, Duarte, California, 91010, USA |
| Email: | cbrenner@coh.org |
| Phone: | 626-218-2750 |
| Funding Source: | National Institute of Health grant R01HL147545 |
| Publications: | Tiwari, V. et al Glycerol-3-phosphate activates ChREBP, FGF21 transcription and lipogenesis in Citrin Deficiency doi: 10.1101/2024.12.27.630525 |
| Contributors: | Edwin Lopez Gonzalez, Vinod Tiwari and Olivia Sun |
Subject:
| Subject ID: | SU004275 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 8-16 Weeks |
| Gender: | Male |
| Animal Animal Supplier: | Dr. Saheki and the Citrin Foundation |
| Animal Housing: | Single-sex group-housed |
| Animal Light Cycle: | 12:12-hour light-dark cycle |
| Animal Feed: | ad libitim LabDiet irradiated PicoLab Rodent Diet 20, 5053 |
| Animal Water: | ad libitim water |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Treatment |
|---|---|---|---|---|
| SA476497 | M095 | Liver | Gpd2 -/- | 2 days 5% glycerol |
| SA476498 | M093 | Liver | Gpd2 -/- | 2 days 5% glycerol |
| SA476499 | M092 | Liver | Gpd2 -/- | 2 days 5% glycerol |
| SA476500 | M040 | Liver | Gpd2 -/- | 2 days 5% glycerol |
| SA476501 | M039 | Liver | Gpd2 -/- | 2 days 5% glycerol |
| SA476502 | M036 | Liver | Gpd2 -/- | 2 days water |
| SA476503 | M094 | Liver | Gpd2 -/- | 2 days water |
| SA476504 | M091 | Liver | Gpd2 -/- | 2 days water |
| SA476505 | M090 | Liver | Gpd2 -/- | 2 days water |
| SA476506 | M035 | Liver | Gpd2 -/- | 2 days water |
| SA476507 | M186 | Liver | Slc25a13 -/- Gpd2 -/- | 2 days 5% glycerol |
| SA476508 | M195 | Liver | Slc25a13 -/- Gpd2 -/- | 2 days 5% glycerol |
| SA476509 | M118 | Liver | Slc25a13 -/- Gpd2 -/- | 2 days 5% glycerol |
| SA476510 | M119 | Liver | Slc25a13 -/- Gpd2 -/- | 2 days 5% glycerol |
| SA476511 | M191 | Liver | Slc25a13 -/- Gpd2 -/- | 2 days 5% glycerol |
| SA476512 | M124 | Liver | Slc25a13 -/- Gpd2 -/- | 2 days water |
| SA476513 | M105 | Liver | Slc25a13 -/- Gpd2 -/- | 2 days water |
| SA476514 | M009 | Liver | Slc25a13 -/- | 2 days 5% glycerol |
| SA476515 | M010 | Liver | Slc25a13 -/- | 2 days 5% glycerol |
| SA476516 | M011 | Liver | Slc25a13 -/- | 2 days 5% glycerol |
| SA476517 | M025 | Liver | Slc25a13 -/- | 2 days 5% glycerol |
| SA476518 | M026 | Liver | Slc25a13 -/- | 2 days 5% glycerol |
| SA476519 | M190/20 | Liver | Slc25a13 -/- | 2 days water |
| SA476520 | M191/20 | Liver | Slc25a13 -/- | 2 days water |
| SA476521 | M187 | Liver | Slc25a13 -/- | 2 days water |
| SA476522 | M188 | Liver | Slc25a13 -/- | 2 days water |
| SA476523 | M189 | Liver | Slc25a13 -/- | 2 days water |
| SA476524 | M004 | Liver | Wild Type | 2 days 5% glycerol |
| SA476525 | M001 | Liver | Wild Type | 2 days 5% glycerol |
| SA476526 | M002 | Liver | Wild Type | 2 days 5% glycerol |
| SA476527 | M003 | Liver | Wild Type | 2 days 5% glycerol |
| SA476528 | M005 | Liver | Wild Type | 2 days 5% glycerol |
| SA476529 | M4 | Liver | Wild Type | 2 days water |
| SA476530 | M3 | Liver | Wild Type | 2 days water |
| SA476531 | M2 | Liver | Wild Type | 2 days water |
| Showing results 1 to 35 of 35 |
Collection:
| Collection ID: | CO004268 |
| Collection Summary: | All mouse breeding and experiments were performed with protocols approved by the City of Hope Institutional Animal Care and Use Committee and Institutional Biosafety Committee. Sperm from a male Slc25a13 -/- Gpd2 -/- C57BL6/J mouse were a kind gift of Dr. Saheki and the Citrin Foundation. In vitro fertilization was performed with C57BL6/J eggs and a pseudopregnant C57BL6/J female recipient by Walter Tsark in the City of Hope Transgenic Mouse Core. Resulting diheterozygous offspring were intercrossed to generate wild-type, Slc25a13 -/-, Gpd2 -/-, and Slc25a13 -/- Gpd2 -/- mice of both sexes. At weaning, genotypes were determined by PCR of tail tissues (Transnetyx, Cordova, TN), and mice were single-sex group-housed until experimental use. Mice were maintained at 21°C under a standard 12:12-hour light-dark cycle and provided with ad libitim access to food and water. Mice were then euthanized by decapitation via guillotine without sedation, exsanguinated with a funnel for blood collection into 1.5 mL microcentrifuge tubes on ice, and livers were freeze-clamped in liquid nitrogen immediately after harvest. Sera were obtained by centrifuging blood at 8,000 g for 10 minutes at 4°C. Liver samples were pulverized with a mortar and pestle cooled by liquid nitrogen. |
| Sample Type: | Liver |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004284 |
| Treatment Summary: | 8-16 week old mice were single-housed with chow (LabDiet irradiated PicoLab Rodent Diet 20, 5053) and a single bottle of either water or 5% (w/v) glycerol for two days. |
| Treatment Compound: | Glycerol |
| Treatment Dose: | ad libitim 5% (w/v) glycerol solution |
Sample Preparation:
| Sampleprep ID: | SP004281 |
| Sampleprep Summary: | For Glycerol-3-Phosphate quantification, 2.0 mg samples of pulverized frozen liver were spiked with 13C3-Glycerol-3-Phosphate (2.28 µM final concentration, Sigma Aldrich). Frozen samples were immediately processed with a boiling buffered ethanol extraction (600 µL of 25% 10 mM HEPES Buffer and 75% Ethanol) followed by vigorous vortexing. Samples were placed on a thermomixer for 5 min at 55°C with shaking at 1,200 rpm, then cooled on ice for 30 seconds. Samples were then placed in a water bath sonicator for 1 minute followed by an additional 30 seconds on ice. Samples were clarified by centrifugation at 16,100 g in a prechilled centrifuge at 4°C; the supernatant was transferred to a clean tube followed by a second round of centrifugation. Clarified supernatants were transferred to new tubes and dried for 5 hours in a vacuum centrifuge at 4°C. Dried samples were resuspended in 80 µL of LC-MS water. Twenty-fold diluted samples were transferred to MS vials for analysis on LC-MS/MS. For analysis of hexose phosphates and pentose phosphates, 2.0 mg samples of pulverized frozen liver were spiked with a 13C glucose-grown yeast extract (ISO101, Cambridge Isotope Laboratories) as an internal standard and the same workup was performed. |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | Described in summary |
Chromatography:
| Chromatography ID: | CH005195 |
| Chromatography Summary: | Samples were analyzed on a Vanquish Horizon UHPLC with a tandem Thermo Scientific Orbitrap Fusion mass spectrometer. Vials were maintained in autosampler at 4°C. Instrument source parameters were held at 3 kV negative ion spray voltage, 300°C ion transfer tube temperature, 250°C vaporizer temperature, sheath gas of 20, auxiliary gas of 10, and sweep gas of 3. Liquid chromatography separation was carried out using an Acquity Premier HSS T3 column with VanGuard FIT, 1.8 µm, 2.1 x 150 mm with mobile phases A (5 mM tributylamine and 10 mM acetic acid with 5% v/v methanol in LC-MS grade water) and B (LC-MS grade methanol) at a constant flow rate of 0.5 ml/min. Separation was carried out with starting condition of 0% B; 0-10 min, 10.5% B; 10-18 min, 52.6% B; 18-19 min 52.6% B; 19-20 min, 0% B; 20-26 min, 0% B. Spectra for G3P were acquired using a targeted MS2 scan with parent ion of m/z 171.0058 with collision energy 25. Spectra for 13C3-G3P were acquired with parent ion m/z of 174.0165 with collision energy 25 with primary fragment ion of m/z 78.9588. Hexose phosphate spectra were acquired using a targeted MS2 scan of parent ion m/z 259.0198. 13C6-hexose phosphate spectra were acquired with a parent ion of m/z 265.0426 with collision energy of 20 and primary fragment ion m/z 96.9690. Pentose phosphate spectra were acquired using targeted MS2 scan for the parent ion m/z 229.0124 at collision energy 30 with a primary fragment ion m/z of 78.9588. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Acquity Premier HSS T3 column with VanGuard FIT (150 x 2.1 mm, 1.8 µm) |
| Column Temperature: | 45°C |
| Flow Gradient: | Starting condition of 0% B; 0-10 min, 10.5% B; 10-18 min, 52.6% B; 18-19 min 52.6% B; 19-20 min, 0% B; 20-21, 0.5-0.8 mL/min; 21-23.9, 0.8 mL/min, 0% B; 23.9-24 min, 0.8-0.5 mL/min, 0% B. |
| Flow Rate: | 0.5 mL/min (unless specified in gradient) |
| Solvent A: | 95% Water/5% Methanol; 5 mM tributylamine; 10 mM acetic acid |
| Solvent B: | 100% Methanol |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006839 |
| Analysis Type: | MS |
| Chromatography ID: | CH005195 |
| Num Factors: | 8 |
| Num Metabolites: | 3 |
| Units: | millimoles/liter |
