Summary of Study ST003985

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 PR002491. The data can be accessed directly via it's Project DOI: 10.21228/M8NN8C This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST003985
Study Title	Glucose-activated JMJD1A drives visceral adipogenesis via α-ketoglutarate-dependent chromatin remodeling (Study part 6 of 5)
Study Summary	Understanding how extracellular glucose regulates adipose tissue remodeling is key to decoding metabolic health. Here, we show that the histone demethylase JMJD1A senses glucose availability via α-ketoglutarate (α-KG), a TCA cycle metabolite derived from glycolysis. Upon glucose stimulation, α-KG accumulates in the nucleus and activates JMJD1A to remove repressive H3K9me2 marks at glycolytic and adipogenic gene loci, including Pparg. This initiates a transcriptional feedforward loop that amplifies glycolysis and de novo adipogenesis. Mechanistically, JMJD1A is pre-recruited to chromatin by NFIC, and glucose-induced demethylation enables subsequent ChREBP binding. In vivo, mice lacking JMJD1A in adipocyte precursors exhibit impaired adipose tissue hyperplasia and compensatory hypertrophic expansion selectively in visceral fat, resulting in metabolically unfavorable remodeling. These findings uncover a glucose-sensing α-KG-JMJD1A pathway that regulates histone demethylation and de novo adipogenesis, enabling adaptive expansion of visceral adipose tissue under nutrient excess conditions.
Institute	Tohoku University
Last Name	Sakai
First Name	Juro
Address	2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
Email	juro.sakai.b6@tohoku.ac.jp
Phone	+81-22-717-8117
Submit Date	2025-06-11
Study Comments	Figure S1H
Raw Data Available	Yes
Raw Data File Type(s)	d, mzML
Analysis Type Detail	CE-MS
Release Date	2025-07-07
Release Version	1

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Project:

Project ID:	PR002491
Project DOI:	doi: 10.21228/M8NN8C
Project Title:	Glucose-activated JMJD1A drives visceral adipogenesis via α-ketoglutarate-dependent chromatin remodeling
Project Summary:	Understanding how extracellular glucose regulates adipose tissue remodeling is key to decoding metabolic health. Here, we show that the histone demethylase JMJD1A senses glucose availability via α-ketoglutarate (α-KG), a TCA cycle metabolite derived from glycolysis. Upon glucose stimulation, α-KG accumulates in the nucleus and activates JMJD1A to remove repressive H3K9me2 marks at glycolytic and adipogenic gene loci, including Pparg. This initiates a transcriptional feedforward loop that amplifies glycolysis and de novo adipogenesis. Mechanistically, JMJD1A is pre-recruited to chromatin by NFIC, and glucose-induced demethylation enables subsequent ChREBP binding. In vivo, mice lacking JMJD1A in adipocyte precursors exhibit impaired adipose tissue hyperplasia and compensatory hypertrophic expansion selectively in visceral fat, resulting in metabolically unfavorable remodeling. These findings uncover a glucose-sensing α-KG-JMJD1A pathway that regulates histone demethylation and de novo adipogenesis, enabling adaptive expansion of visceral adipose tissue under nutrient excess conditions.
Institute:	Tohoku University
Last Name:	Sakai
First Name:	Juro
Address:	2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
Email:	juro.sakai.b6@tohoku.ac.jp
Phone:	+81-22-717-8117

Subject:

Subject ID:	SU004122
Subject Type:	Cultured cells
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

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

mb_sample_id	local_sample_id	Sample source	Treatment
SA454648	3T3-L1_0h	3T3-L1	13C6-Glucose
SA454649	3T3-L1_1h	3T3-L1	13C6-Glucose
SA454650	3T3-L1_2h	3T3-L1	13C6-Glucose
SA454651	3T3-L1_4h	3T3-L1	13C6-Glucose

Showing results 1 to 4 of 4

Showing results 1 to 4 of 4

Collection:

Collection ID:	CO004115
Collection Summary:	3T3-L1 cells were washed twice with 5% mannitol before metabolite extraction. Aqueous metabolites were extracted with 400 µL of methanol containing three internal standards (3ISs; methionine sulfone, 2-(N-morpholino)ethanesulfonic acid [MES] and D-camphol-10-sulfonic acid [CSA]; 25 µM each) at room temperature for 10 min. Then 400 µL chloroform and 200 µL of water were added, and the solution was centrifuged at 10,000 × g for 3 min at 4ºC. The upper aqueous layer (400 µL) was filtered through a 5 kDa cutoff filter (Millipore), and the filtrate was stored at -80ºC until analysis. At the time of analysis, the filtrate was thawed and centrifugally concentrated and dissolved in 25 µL of water containing reference compounds (3-aminopyrrolidine and 1,3,5-benzenetricarboxylic acid; 200 µM each).
Sample Type:	Cultured cells

Treatment:

Treatment ID:	TR004131
Treatment Summary:	3T3-L1 preadipocytes were differentiated with MDI mixture until day 4 and treated with 25 mM 13C glucose.

Sample Preparation:

Sampleprep ID:	SP004128
Sampleprep Summary:	For metabolite extraction, the 3T3-L1 cells were washed twice with ice-cold 5% mannitol solution and covered with 1 mL of methanol containing 25 µM internal standards for 10 min. 400 µL of the resulting extracts were mixed with 200 µL of Milli-Q water and 400 µL of chloroform. 400 µL of the aqueous solution was centrifugally filtered through a 5-kDa cut-off filter (Human Metabolome Technologies, Tsuruoka, Japan) to remove proteins. The filtrate was centrifugally concentrated and dissolved in 50 µL of Milli-Q water that contained reference compounds (200 µM each of 3-aminopyrrolidine and trimesate) immediately prior to metabolome analysis.

Sampleprep ID:

SP004128

Sampleprep Summary:

For metabolite extraction, the 3T3-L1 cells were washed twice with ice-cold 5% mannitol solution and covered with 1 mL of methanol containing 25 µM internal standards for 10 min. 400 µL of the resulting extracts were mixed with 200 µL of Milli-Q water and 400 µL of chloroform. 400 µL of the aqueous solution was centrifugally filtered through a 5-kDa cut-off filter (Human Metabolome Technologies, Tsuruoka, Japan) to remove proteins. The filtrate was centrifugally concentrated and dissolved in 50 µL of Milli-Q water that contained reference compounds (200 µM each of 3-aminopyrrolidine and trimesate) immediately prior to metabolome analysis.

Combined analysis:

Analysis ID	AN006563	AN006564	AN006565
Chromatography ID	CH004981	CH004982	CH004983
MS ID	MS006262	MS006263	MS006264
Analysis type	MS	MS	MS
Chromatography type	CE	CE	CE
Chromatography system	Agilent 7100 CE	Agilent 7100 CE	Agilent 7100 CE
Column	COSMO(+) capillary i. d. 50 µm x 105 cm	Fused silica capillary i. d. 50 µm x 100 cm	Fused silica capillary i. d. 50 µm x 100 cm
MS Type	ESI	ESI	ESI
MS instrument type	TOF	TOF	Triple quadrupole
MS instrument name	Agilent 6230 TOF	Agilent 6230 TOF	Agilent 6410 QQQ
Ion Mode	NEGATIVE	POSITIVE	NEGATIVE
Units	fmol / cell	fmol / cell	fmol/cell

Chromatography:

Chromatography ID:	CH004981
Instrument Name:	Agilent 7100 CE
Column Name:	COSMO(+) capillary i. d. 50 µm x 105 cm
Column Temperature:	N/A
Flow Gradient:	N/A
Flow Rate:	N/A
Solvent A:	100% Water; 50 mM deuterated ammonium acetate (CD3COOND4), pH 8.5
Solvent B:	N/A
Chromatography Type:	CE

Chromatography ID:	CH004982
Instrument Name:	Agilent 7100 CE
Column Name:	Fused silica capillary i. d. 50 µm x 100 cm
Column Temperature:	N/A
Flow Gradient:	N/A
Flow Rate:	N/A
Solvent A:	100% Water; 1 M formic acid
Solvent B:	N/A
Chromatography Type:	CE

Chromatography ID:	CH004983
Instrument Name:	Agilent 7100 CE
Column Name:	Fused silica capillary i. d. 50 µm x 100 cm
Column Temperature:	N/A
Flow Gradient:	N/A
Flow Rate:	N/A
Solvent A:	100% Water; 300 mM diethylamine
Solvent B:	N/A
Chromatography Type:	CE

MS:

MS ID:	MS006262
Analysis ID:	AN006563
Instrument Name:	Agilent 6230 TOF
Instrument Type:	TOF
MS Type:	ESI
MS Comments:	ESI-TOFMS was performed in the negative ion mode. The capillary voltage was set at 3.5 kV, and a nitrogen gas flow rate (heater temperature 300°C) was set at 10 L/min. The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using the automatic integration software MasterHands (Keio University, Tsuruoka, Japan)(Sugimoto et al., Metabolomics, 2009). Based on the in-house library, metabolites were identified from migration time and m/z. Quantification was performed using the standard mixture measured in the same run.
Ion Mode:	NEGATIVE

MS ID:	MS006263
Analysis ID:	AN006564
Instrument Name:	Agilent 6230 TOF
Instrument Type:	TOF
MS Type:	ESI
MS Comments:	ESI-TOFMS was performed in the positive ion mode. The capillary voltage was set at 4 kV, and a flow rate of nitrogen gas (heater temperature 300°C) was set at 10 L/min. The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using the automatic integration software MasterHands (Keio University, Tsuruoka, Japan)(Sugimoto et al., Metabolomics, 2009). Based on the in-house library, metabolites were identified from migration time and m/z. Quantification was performed using the Standard mixture measured in the same run.
Ion Mode:	POSITIVE

MS ID:	MS006264
Analysis ID:	AN006565
Instrument Name:	Agilent 6410 QQQ
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Agilent jet stream-ESI-MS/MS analysis was performed in negative ion mode using the following source parameters: dry gas temperature, 300°C; dry gas flow rate, 10 L/min; nebulizer pressure, 10 psi. Data were acquired using dynamic multiple reaction monitoring (MRM) mode, and the MRM transition setting was based on the in-house MRM library. Peaks were extracted using automatic integration software MasterHands (Keio University, Tsuruoka, Japan)(Sugimoto et al., Metabolomics, 2009).
Ion Mode:	NEGATIVE