Summary of Study ST002123

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001347. The data can be accessed directly via it's Project DOI: 10.21228/M8M417 This work is supported by NIH grant, U2C- DK119886.


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 IDST002123
Study TitleGCN2 regulates mitochondrial OXPHOS in HSPCs under proliferation conditions.
Study SummaryOur results revealed that among all 273 metabolites detected, the levels of metabolites involved in glucose-related glycolysis and gluconeogenesis were elevated in GCN2 deleted HSPCs. Moreover, GCN2 deletion specifically increased mitochondrial OXPHOS and suppressed anaerobic glycolysis in HSPCs.
Sun Yat-sen University
Last NameZhao
First NameMeng
AddressZhongshan 2nd Road
Submit Date2022-04-05
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2022-11-01
Release Version1
Meng Zhao Meng Zhao application/zip

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Project ID:PR001347
Project DOI:doi: 10.21228/M8M417
Project Title:GCN2 deletion influenced the energy metabolism in HSPCs.
Project Summary:Hematopoietic stem cells (HSCs) adapt their metabolism to maintenance and proliferation, but the mechanism remains incompletely understood. Here, we demonstrated that homeostatic HSCs had high amino acid (AA) catabolism to reduce the cellular AA levels, which activated the GCN2-eIF2α axis, a protein-synthesis-inhibitory checkpoint to inhibit protein synthesis for maintenance. Furthermore, upon proliferation conditions, HSCs increased mitochondrial oxidative phosphorylation (OXPHOS) for higher energy production but decreased AA catabolism to accumulate cellular AAs, which inactivated the GCN2-eIF2α axis to increase protein synthesis and coupled with proteotoxic stress. Importantly, GCN2 deletion impaired HSC function in repopulation and regeneration. Mechanistically, GCN2 maintained proteostasis and inhibited Src mediated AKT activation to repress mitochondrial OXPHOS in HSCs. Moreover, glycolytic metabolite, NAD+ precursor nicotinamide riboside (NR), accelerated AA catabolism to activate GCN2 and sustain long-term function of HSCs. Overall, our study uncovers the direct links between metabolic alterations and translation control in HSCs during homeostasis and proliferation.
Institute:Sun Yat-sen University
Last Name:Zhao
First Name:Meng
Address:Zhongshan 2nd Road


Subject ID:SU002208
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090


Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Treatment Batch Source_Name[gating]
SA204260KO_3Mutant 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204261KO_4Mutant 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204262KO_6Mutant 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204263KO_2Mutant 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204264KO_5Mutant 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204265KO_1Mutant 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204266WT_3Wild-type 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204267WT_2Wild-type 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204268WT_4Wild-type 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204269WT_5Wild-type 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204270WT_6Wild-type 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
SA204271WT_1Wild-type 5 FU 2 weeks 1f Lin– Scal1+ c-Kit+ (LSK)
Showing results 1 to 12 of 12


Collection ID:CO002201
Collection Summary:2 million HSPCs (LSK cells) were sorted stored at -80 ℃.
Sample Type:Bone marrow


Treatment ID:TR002220
Treatment Summary:Wild-type and GCN2 knockout mice were intraperitoneally injected with 10 mg/kg 5FU (F6627-5G, Sigma-Aldrich) for 14 days. HSPCs were stained and sorted from treated mice.

Sample Preparation:

Sampleprep ID:SP002214
Sampleprep Summary:The cell samples were extracted with 800 µL of 80% methanol and vortexed for 1 min. Then, ultrasonicate for 30 min at 4℃ were performed, letting stand in -40℃ refrigerator for 1 h. After that, the samples were vortexed for 30s and set at 4℃ for 30 min. The samples were centrifuged at 12,000 rpm, 4℃ for 15 min. Taking all the supernatant in the centrifuge tube and concentrating to remove the organic reagents and water. 100 µL of 80% methanol would be used to reconstitute, vortex again for 1 min. The supernatant was transferred by centrifugation to the sample vial for liquid chromatography-mass spectrometry (LC-MS) analysis.

Combined analysis:

Analysis ID AN003476
Analysis type MS
Chromatography type HILIC
Chromatography system ACQUITY UPLC
Column Waters ACQUITY UPLC BEH Amide
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Units AU


Chromatography ID:CH002565
Instrument Name:ACQUITY UPLC
Column Name:Waters ACQUITY UPLC BEH Amide
Column Temperature:40
Flow Gradient:The gradient program started at 85% (B) and was reduced to 70% (B) over 9 min, then reduced from 70% (B) to 30% (B) over 3 min, followed by wash with 30% (B) for another 3 min, and finally 5 min re-equilibration with 85% (B).
Flow Rate:0.35ml/min
Solvent A:100% water; 10mM ammonium formate
Solvent B:100% acetonitrile
Chromatography Type:HILIC


MS ID:MS003237
Analysis ID:AN003476
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Comments:LC-MS data was acquired on SCIEX 5500 QQQ mass spectrometer (Applied Biosystems, Foster City, CA, USA) coupled with high-performance liquid chromatography (HPLC) system ACQUITY UPLC (Waters, Milford, MA, USA). Chromatographic separation was performed on a ACQUITY UPLC BEH Amide Column (1.7 µm, 2.1 mm x 100 mm, Waters, Milford, MA, USA). The mobile phase (A) was 10 mM ammonium formate and (B) acetonitrile. The gradient program started at 85% (B) and was reduced to 70% (B) over 9 min, then reduced from 70% (B) to 30% (B) over 3 min, followed by wash with 30% (B) for another 3 min, and finally 5 min re-equilibration with 85% (B). The flow rate was 0.35 mL/min and column compartment temperature was 40ºC. The total run time was 20 min with an injection sample volume of 5 µL.