Summary of Study ST003978

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

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	ST003978
Study Title	Glucose-activated JMJD1A drives visceral adipogenesis via α-ketoglutarate-dependent chromatin remodeling (Study part 6 of 3)
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 2I
Raw Data Available	Yes
Raw Data File Type(s)	d, mzML
Analysis Type Detail	CE-MS
Release Date	2025-07-07
Release Version	1

Select appropriate tab below to view additional metadata details:

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:	SU004115
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
SA454294	si-Ctr_D0	3T3-L1	si-Ctr
SA454295	si-Ctr_D2	3T3-L1	si-Ctr
SA454296	si-Ctr_D4	3T3-L1	si-Ctr
SA454297	si-Ctr_D6	3T3-L1	si-Ctr
SA454298	si-Ctr_D8	3T3-L1	si-Ctr
SA454299	si-Idh3b_D0	3T3-L1	si-Idh3b
SA454300	si-Idh3b_D2	3T3-L1	si-Idh3b
SA454301	si-Idh3b_D4	3T3-L1	si-Idh3b
SA454302	si-Idh3b_D6	3T3-L1	si-Idh3b
SA454303	si-Idh3b_D8	3T3-L1	si-Idh3b

Showing results 1 to 10 of 10

Showing results 1 to 10 of 10

Collection:

Collection ID:	CO004108
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:	TR004124
Treatment Summary:	3T3-L1 preadipocytes were transfected with si-Ctr or si-Idh3b and differentiated with MDI mixture.

Sample Preparation:

Sampleprep ID:	SP004121
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:

SP004121

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.

Chromatography:

Chromatography ID:	CH004971
Instrument Name:	Agilent 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 ammonium acetate, pH 8.5
Solvent B:	N/A
Chromatography Type:	CE

Chromatography ID:	CH004972
Instrument Name:	Agilent 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

Analysis:

Analysis ID:	AN006552
Analysis Type:	MS
Chromatography ID:	CH004971
Num Factors:	2
Num Metabolites:	120
Units:	fmol / cell

Analysis ID:	AN006553
Analysis Type:	MS
Chromatography ID:	CH004972
Num Factors:	2
Num Metabolites:	127
Units:	fmol / cell