Summary of Study ST004125
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 PR002593. The data can be accessed directly via it's Project DOI: 10.21228/M8GG2T This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004125 |
| Study Title | Metabolite profiling in the glycerol kinase (GK), GPD1 and GAPDH genes into the reconstituted ChREBPα-MLX HEK293T system alongside green fluorescent protein (GFP). |
| Study Summary | To distinguish between potential ChREBP-activating ligands, we introduced glycerol kinase (GK), GPD1 and GAPDH genes into the reconstituted ChREBP MLX HEK293T system alongside green fluorescent protein (GFP).Relative quantification of 137 metabolites showed that in these cells, GPD1 strongly depressed levels of GA3P and DHAP, while elevating G3P. |
| Institute | University of Chicago |
| Last Name | Shah |
| First Name | Hardik |
| Address | 900 E 57th street, Chicago IL 60637. USA. |
| hardikshah@uchicago.edu | |
| Phone | 7738348830 |
| Submit Date | 2025-08-13 |
| Num Groups | 2 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-08-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002593 |
| Project DOI: | doi: 10.21228/M8GG2T |
| Project Title: | Glycerol-3-phosphate activates ChREBP, FGF21 transcription and lipogenesis 2 in Citrin Deficiency |
| 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 driving 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 lean MASLD and support of urea cycle function in CD. |
| Institute: | University of Chicago |
| Laboratory: | UCCC-Metabolomics Platform |
| Last Name: | Shah |
| First Name: | Hardik |
| Address: | 900 E 57th street, Chicago IL 60637. USA. |
| Email: | hardikshah@uchicago.edu |
| Phone: | 7738348830 |
Subject:
| Subject ID: | SU004274 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA476485 | GAPDH_11 | HEK293T | GAPDH |
| SA476486 | GAPDH_10 | HEK293T | GAPDH |
| SA476487 | GAPDH_12 | HEK293T | GAPDH |
| SA476494 | GPD1_07 | HEK293T | Genotype |
| SA476495 | GPD1_08 | HEK293T | Genotype |
| SA476496 | GPD1_09 | HEK293T | Genotype |
| SA476488 | GFP_01 | HEK293T | GFP |
| SA476489 | GFP_02 | HEK293T | GFP |
| SA476490 | GFP_03 | HEK293T | GFP |
| SA476491 | GK_04 | HEK293T | GK |
| SA476492 | GK_05 | HEK293T | GK |
| SA476493 | GK_06 | HEK293T | GK |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO004267 |
| Collection Summary: | 48 hours after transfection with the specified plasmid, cells were washed with room-temperature PBS, immediately quenched with dry-ice-cold 80% methanol |
| Sample Type: | Human embryonic kidney cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004283 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP004280 |
| Sampleprep Summary: | Cells were washed with room-temperature PBS, immediately quenched with dry-ice-cold 80% methanol.Samples were centrifuged at 20,000 g for 20 minutes at 4°C, the supernatant was dried down on a Genvevac EZ-2 4.0 elite evaporator, and the samples were resuspended in 100 µL of 60/40 acetonitrile-water. |
Combined analysis:
| Analysis ID | AN006838 |
|---|---|
| Chromatography ID | CH005194 |
| MS ID | MS006537 |
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | HILICON iHILIC-(P) Classic (150 x 2.1 mm, 5 µm) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Scientific IQ-X tribrid |
| Ion Mode | UNSPECIFIED |
| Units | A.U. |
Chromatography:
| Chromatography ID: | CH005194 |
| Chromatography Summary: | The chromatography separation was performed using Thermo Scientific Vanquish Horizon UHPLC system and iHILIC-(P) Classic (2.1 x 150 mm, 5 µm; part # 160.152.0520; HILICON AB) column. The mobile phase A(MPA) was 20 mM ammonium bicarbonate at pH 9.6, adjusted by ammonium hydroxide addition and MPB was acetonitrile. The column temperature, injection volume, and the flow rate were 40°C, 2 µL, and 0.2 mL/minute, respectively. The chromatographic gradient was 0 minutes: 85% B, 0.5 minutes: 85% B, 18 minutes: 20% B, 20 minutes: 20% B, 20.5 minutes: 85% B and 28 minutes: 85% B. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | HILICON iHILIC-(P) Classic (150 x 2.1 mm, 5 µm) |
| Column Temperature: | 40°C |
| Flow Gradient: | The chromatographic gradient was 0 minutes: 85% B, 0.5 minutes: 85% B, 18 minutes: 20% B, 20 minutes: 20% B, 20.5 minutes: 85% B and 28 minutes: 85% B |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | 100% Water; 20 mM ammonium bicarbonate; ammonium hydroxide 0.2% |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS006537 |
| Analysis ID: | AN006838 |
| Instrument Name: | Thermo Scientific IQ-X tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The high-resolution Orbitrap IQ-X Tribrid mass spectrometer (Thermo Scientific) with a H-ESI probe operating in switch polarity was used to detect and quantify the metabolite levels. MS parameters were as follows: Acquisition range of 70-1000 m/z at 60K resolution, spray voltage:3600V for positive ionization and 2800 for negative ionization modes, sheath gas: 35, auxiliary gas: 5, sweep gas: 1, ion transfer tube temperature: 250°C, vaporizer temperature: 350°C, AGC target: 100%, and a maximum injection time of 118 ms. AcquireX workflow was used to collect the MS/MS data in negative and positive separately using the assisted HCD collision energy 20,35,50,75,100 as well as targeted MS/MS with a defined retention time window for the in-house retention time database. Data acquisition was done using the Xcalibur software (Thermo Scientific) and data analysis was performed using Compound Discoverer 3.3 (± 5 ppm) & Tracefinder 5.1 software (Thermo Scientific). Metabolite identification was done by matching the retention time and MS/MS fragmentation to the in-house database generated using the commercially available reference standards. In the data table, the “RT+MS/MS” indicates the matching retention time & MS/MS, “RT”-indicates the only matching retention time and doesn’t have MS/MS while the MS/MS is for carnitine species identified based on the 85.0281 fragment. |
| Ion Mode: | UNSPECIFIED |
