#METABOLOMICS WORKBENCH Kaori_20250611_221809 DATATRACK_ID:6030 STUDY_ID:ST003987 ANALYSIS_ID:AN006568 PROJECT_ID:PR002491
VERSION             	1
CREATED_ON             	June 17, 2025, 1:08 am
#PROJECT
PR:PROJECT_TITLE                 	Glucose-activated JMJD1A drives visceral adipogenesis via
PR:PROJECT_TITLE                 	α-ketoglutarate-dependent chromatin remodeling
PR:PROJECT_SUMMARY               	Understanding how extracellular glucose regulates adipose tissue remodeling is
PR:PROJECT_SUMMARY               	key to decoding metabolic health. Here, we show that the histone demethylase
PR:PROJECT_SUMMARY               	JMJD1A senses glucose availability via α-ketoglutarate (α-KG), a TCA cycle
PR:PROJECT_SUMMARY               	metabolite derived from glycolysis. Upon glucose stimulation, α-KG accumulates
PR:PROJECT_SUMMARY               	in the nucleus and activates JMJD1A to remove repressive H3K9me2 marks at
PR:PROJECT_SUMMARY               	glycolytic and adipogenic gene loci, including Pparg. This initiates a
PR:PROJECT_SUMMARY               	transcriptional feedforward loop that amplifies glycolysis and de novo
PR:PROJECT_SUMMARY               	adipogenesis. Mechanistically, JMJD1A is pre-recruited to chromatin by NFIC, and
PR:PROJECT_SUMMARY               	glucose-induced demethylation enables subsequent ChREBP binding. In vivo, mice
PR:PROJECT_SUMMARY               	lacking JMJD1A in adipocyte precursors exhibit impaired adipose tissue
PR:PROJECT_SUMMARY               	hyperplasia and compensatory hypertrophic expansion selectively in visceral fat,
PR:PROJECT_SUMMARY               	resulting in metabolically unfavorable remodeling. These findings uncover a
PR:PROJECT_SUMMARY               	glucose-sensing α-KG-JMJD1A pathway that regulates histone demethylation and de
PR:PROJECT_SUMMARY               	novo adipogenesis, enabling adaptive expansion of visceral adipose tissue under
PR:PROJECT_SUMMARY               	nutrient excess conditions.
PR:INSTITUTE                     	Tohoku University
PR:LAST_NAME                     	Sakai
PR:FIRST_NAME                    	Juro
PR:ADDRESS                       	2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
PR:EMAIL                         	juro.sakai.b6@tohoku.ac.jp
PR:PHONE                         	+81-22-717-8117
#STUDY
ST:STUDY_TITLE                   	Glucose-activated JMJD1A drives visceral adipogenesis via
ST:STUDY_TITLE                   	α-ketoglutarate-dependent chromatin remodeling (Study part 6 of 6)
ST:STUDY_SUMMARY                 	Understanding how extracellular glucose regulates adipose tissue remodeling is
ST:STUDY_SUMMARY                 	key to decoding metabolic health. Here, we show that the
ST:INSTITUTE                     	Tohoku University
ST:LAST_NAME                     	Sakai
ST:FIRST_NAME                    	Juro
ST:ADDRESS                       	2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
ST:EMAIL                         	juro.sakai.b6@tohoku.ac.jp
ST:PHONE                         	+81-22-717-8117
ST:STUDY_COMMENTS                	Figure S1I
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	16	3T3-L1_0h	Sample source:3T3-L1 | Treatment:13C6-Glucose	RAW_FILE_NAME(Lipid)=TSOGA038_p_20241106_Sample_16.mzML
SUBJECT_SAMPLE_FACTORS           	17	3T3-L1_1h	Sample source:3T3-L1 | Treatment:13C6-Glucose	RAW_FILE_NAME(Lipid)=TSOGA038_p_20241106_Sample_17.mzML
SUBJECT_SAMPLE_FACTORS           	18	3T3-L1_2h	Sample source:3T3-L1 | Treatment:13C6-Glucose	RAW_FILE_NAME(Lipid)=TSOGA038_p_20241106_Sample_18.mzML
SUBJECT_SAMPLE_FACTORS           	19	3T3-L1_4h	Sample source:3T3-L1 | Treatment:13C6-Glucose	RAW_FILE_NAME(Lipid)=TSOGA038_p_20241106_Sample_19.mzML
#COLLECTION
CO:COLLECTION_SUMMARY            	3T3-L1 cells were washed twice with 5% mannitol before metabolite extraction.
CO:COLLECTION_SUMMARY            	Aqueous metabolites were extracted with 400 µL of methanol containing three
CO:COLLECTION_SUMMARY            	internal standards (3ISs; methionine sulfone, 2-(N-morpholino)ethanesulfonic
CO:COLLECTION_SUMMARY            	acid [MES] and D-camphol-10-sulfonic acid [CSA]; 25 µM each) at room
CO:COLLECTION_SUMMARY            	temperature for 10 min. Then 400 µL chloroform and 200 µL of water were added,
CO:COLLECTION_SUMMARY            	and the solution was centrifuged at 10,000 × g for 3 min at 4 ºC. The upper
CO:COLLECTION_SUMMARY            	aqueous layer (400 µL) was filtered through a 5 kDa cutoff filter (Millipore),
CO:COLLECTION_SUMMARY            	and the filtrate was stored at -80 ºC until analysis. At the teime of analysis,
CO:COLLECTION_SUMMARY            	the filtrate was thawed and centrifugally concentrated and dissolved in 25 µL
CO:COLLECTION_SUMMARY            	of water containing reference compounds (3-aminopyrrolidine and
CO:COLLECTION_SUMMARY            	1,3,5-benzenetricarboxylic acid; 200 µM each).
CO:SAMPLE_TYPE                   	Cultured cells
#TREATMENT
TR:TREATMENT_SUMMARY             	3T3-L1 preadipocytes were differentiated with MDI mixture until day 4 and
TR:TREATMENT_SUMMARY             	treated with 25 mM 13C glucose.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	containing 25 µM internal standards for 10 min. 400 µL of the resulting
SP:SAMPLEPREP_SUMMARY            	extracts were mixed with 200 µL of Milli-Q water and 400 µL of
SP:SAMPLEPREP_SUMMARY            	chloroform.After centrifuge at 10,000xg for 3 min at 4°C, the upper 400 µL
SP:SAMPLEPREP_SUMMARY            	water layer was used for CE-MS analysis and 600 µL of methanol containing 2 µM
SP:SAMPLEPREP_SUMMARY            	reserpine was added to the remaining chloroform layer and vortex for 10 min.
SP:SAMPLEPREP_SUMMARY            	After centrifuge at 10,000xg for 20 min at 4°C again, the supernatant was
SP:SAMPLEPREP_SUMMARY            	transferred to a sample vial for LC-MS measurement.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Agilent 1290 Infinity
CH:COLUMN_NAME                   	Waters ACQUITY UPLC HSS T3 (50 x 2.1mm,1.8um)
CH:SOLVENT_A                     	5 mM Ammonium Formate / Water : Methanol : Acetonitrile = 3:1:1
CH:SOLVENT_B                     	5 mM Ammonium Formate / 2-propanol
CH:FLOW_GRADIENT                 	0.0 min 0 % B, 5.0 min 40% B, 7.5-12.0 min 64% B, 12.5 min 82.5% B, 19.0 min 85
CH:FLOW_GRADIENT                 	% B, 20.0 min 95% B
CH:FLOW_RATE                     	0.3 mL/min
CH:COLUMN_TEMPERATURE            	45℃
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent G6530A
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	ESI- Quadrupole-TOFMS was performed in the positive ion mode. The capillary
MS:MS_COMMENTS                   	voltage was set at 3.5 kV, and a nitrogen gas flow rate (heater temperature
MS:MS_COMMENTS                   	350°C) was set at 10 L/min. The Fragmentor voltage was set at 150 V. The
MS:MS_COMMENTS                   	spectrometer was scanned from m/z 100 to 1,700. Peaks were extracted using the
MS:MS_COMMENTS                   	automatic integration software MasterHands (Keio University, Tsuruoka,
MS:MS_COMMENTS                   	Japan)(Sugimoto et al., Metabolomics, 2009). Based on the in-house library,
MS:MS_COMMENTS                   	lipids were identified based on retention time and m/z. The relative area was
MS:MS_COMMENTS                   	calculated by dividing the area value of each lipid by the area value of
MS:MS_COMMENTS                   	Reserpine.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	Relative Area
MS_METABOLITE_DATA_START
Samples	3T3-L1_0h	3T3-L1_1h	3T3-L1_2h	3T3-L1_4h
Factors	Sample source:3T3-L1 | Treatment:13C6-Glucose	Sample source:3T3-L1 | Treatment:13C6-Glucose	Sample source:3T3-L1 | Treatment:13C6-Glucose	Sample source:3T3-L1 | Treatment:13C6-Glucose
TG 46:3_m+0	1.03	7.95	15.66	3.70
TG 46:3_m+1	1.73	1.62	3.37	7.12
TG 46:3_m+2	1.55	1.51	3.01	2.20
TG 46:3_m+3	0.27	1.46	3.81	3.07
TG 46:3_m+4	N.D.	0.68	1.73	1.63
TG 46:3_m+5	N.D.	0.31	0.88	0.91
TG 46:3_m+6	N.D.	0.16	0.36	0.27
TG 46:3_m+7	N.D.	0.16	0.40	0.65
TG 46:3_m+8	N.D.	0.11	0.33	0.48
TG 46:3_m+9	N.D.	0.11	0.29	0.35
TG 46:3_m+10	N.D.	0.07	0.24	0.33
TG 46:3_m+11	N.D.	0.10	0.27	0.32
TG 46:3_m+12	N.D.	0.08	0.20	0.24
TG 46:3_m+13	N.D.	N.D.	0.16	0.19
TG 48:1_m+0	127.57	141.96	196.78	144.92
TG 48:1_m+1	77.81	70.82	100.60	69.82
TG 48:1_m+2	11.11	12.29	22.14	14.68
TG 48:1_m+3	1.15	4.98	9.11	7.93
TG 48:1_m+4	0.13	1.61	3.77	4.18
TG 48:1_m+5	N.D.	0.82	1.86	2.36
TG 48:1_m+6	N.D.	0.53	1.39	2.14
TG 48:1_m+7	N.D.	0.53	1.40	2.02
TG 48:1_m+8	N.D.	0.36	0.96	1.47
TG 48:1_m+9	N.D.	0.40	0.98	1.43
TG 48:1_m+10	N.D.	0.23	0.66	1.03
TG 48:1_m+11	N.D.	0.25	0.67	0.97
TG 48:1_m+12	N.D.	N.D.	N.D.	N.D.
TG 48:1_m+13	N.D.	N.D.	N.D.	N.D.
TG 48:1_m+14	N.D.	N.D.	N.D.	0.55
TG 48:1_m+15	N.D.	N.D.	N.D.	N.D.
TG 48:1_m+16	N.D.	N.D.	N.D.	N.D.
TG 48:1_m+17	N.D.	N.D.	N.D.	N.D.
TG 48:2_m+0	220.10	167.33	230.34	173.86
TG 48:2_m+1	109.68	84.23	117.82	85.24
TG 48:2_m+2	18.35	18.02	28.97	23.01
TG 48:2_m+3	2.06	10.67	21.44	19.68
TG 48:2_m+4	N.D.	3.78	9.10	10.67
TG 48:2_m+5	N.D.	1.69	0.06	6.05
TG 48:2_m+6	N.D.	0.88	2.69	4.52
TG 48:2_m+7	N.D.	0.95	2.85	4.21
TG 48:2_m+8	N.D.	0.64	1.92	3.25
TG 48:2_m+9	N.D.	0.78	2.17	3.22
TG 48:2_m+10	N.D.	0.45	1.25	2.05
TG 48:2_m+11	N.D.	0.54	1.36	1.94
TG 48:2_m+12	N.D.	0.39	0.84	1.33
TG 48:2_m+13	N.D.	0.29	0.74	1.08
TG 48:2_m+14	N.D.	0.33	0.60	0.98
TG 48:2_m+15	N.D.	0.27	0.49	0.66
TG 48:2_m+16	N.D.	N.D.	N.D.	0.45
TG 48:2_m+17	N.D.	N.D.	0.23	0.30
TG 48:2_m+18	N.D.	N.D.	N.D.	N.D.
TG 48:3_m+0	106.54	80.11	121.86	89.39
TG 48:3_m+1	51.30	40.50	64.60	45.11
TG 48:3_m+2	9.17	8.89	16.14	12.71
TG 48:3_m+3	0.91	8.14	18.45	15.06
TG 48:3_m+4	0.24	3.10	7.83	7.46
TG 48:3_m+5	N.D.	1.27	3.37	3.80
TG 48:3_m+6	N.D.	0.45	1.73	2.54
TG 48:3_m+7	N.D.	0.30	0.93	1.22
TG 48:3_m+8	N.D.	0.17	1.27	1.87
TG 48:3_m+9	N.D.	0.52	1.54	1.58
TG 48:3_m+10	N.D.	0.26	0.86	1.24
TG 48:3_m+11	N.D.	0.33	0.66	0.86
TG 48:3_m+12	N.D.	0.22	0.55	0.76
TG 48:3_m+13	N.D.	0.20	0.55	0.73
TG 48:3_m+14	N.D.	0.20	0.38	0.47
TG 48:3_m+15	N.D.	0.18	0.35	0.31
TG 48:3_m+16	N.D.	0.17	0.27	0.31
TG 48:3_m+17	N.D.	0.14	0.24	0.30
TG 50:1_m+0	70.12	65.53	90.57	60.99
TG 50:1_m+1	32.12	31.97	45.03	28.79
TG 50:1_m+2	5.61	6.61	10.09	7.25
TG 50:1_m+3	0.75	2.78	4.74	4.06
TG 50:1_m+4	0.15	0.40	2.14	2.15
TG 50:1_m+5	0.05	0.56	1.17	1.44
TG 50:1_m+6	0.14	0.32	0.73	0.90
TG 50:1_m+7	0.06	0.28	0.66	0.88
TG 50:1_m+8	N.D.	0.17	0.39	0.60
TG 50:1_m+9	N.D.	0.18	0.42	0.57
TG 50:1_m+10	N.D.	0.09	0.23	0.42
TG 50:1_m+11	N.D.	0.11	0.21	0.34
TG 50:1_m+12	N.D.	N.D.	N.D.	N.D.
TG 50:1_m+13	N.D.	N.D.	N.D.	N.D.
TG 50:1_m+14	N.D.	N.D.	N.D.	N.D.
TG 50:1_m+15	N.D.	N.D.	N.D.	N.D.
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Average m/z	Retention Time (min)
TG 46:3_m+0	790.7418	14.76
TG 46:3_m+1	791.7398	14.76
TG 46:3_m+2	792.7045	14.76
TG 46:3_m+3	793.7066	14.76
TG 46:3_m+4	794.7081	14.76
TG 46:3_m+5	795.7213	14.76
TG 46:3_m+6	796.7262	14.76
TG 46:3_m+7	797.7278	14.76
TG 46:3_m+8	798.7182	14.76
TG 46:3_m+9	799.7340	14.76
TG 46:3_m+10	800.7221	14.76
TG 46:3_m+11	801.7313	14.76
TG 46:3_m+12	802.7296	14.77
TG 46:3_m+13	803.7387	14.75
TG 48:1_m+0	822.7557	16.02
TG 48:1_m+1	823.7546	16.02
TG 48:1_m+2	824.7649	16.02
TG 48:1_m+3	825.7624	16.02
TG 48:1_m+4	826.7652	16.02
TG 48:1_m+5	827.7556	16.02
TG 48:1_m+6	828.7709	16.01
TG 48:1_m+7	829.7855	16.01
TG 48:1_m+8	830.7704	16.02
TG 48:1_m+9	831.7825	16.01
TG 48:1_m+10	832.7845	16.02
TG 48:1_m+11	833.7908	16.02
TG 48:1_m+12	834.7921	16.01
TG 48:1_m+13	835.7959	16.02
TG 48:1_m+14	836.7879	16.01
TG 48:1_m+15	837.7995	16.01
TG 48:1_m+16	838.8097	16.02
TG 48:1_m+17	839.8145	16.02
TG 48:2_m+0	820.7318	15.57
TG 48:2_m+1	821.7386	15.58
TG 48:2_m+2	822.7420	15.56
TG 48:2_m+3	823.7514	15.57
TG 48:2_m+4	824.7544	15.57
TG 48:2_m+5	825.7561	15.59
TG 48:2_m+6	826.7566	15.57
TG 48:2_m+7	827.7694	15.57
TG 48:2_m+8	828.7638	15.57
TG 48:2_m+9	829.7665	15.58
TG 48:2_m+10	830.7739	15.57
TG 48:2_m+11	831.7754	15.57
TG 48:2_m+12	832.7840	15.57
TG 48:2_m+13	833.7910	15.57
TG 48:2_m+14	834.7745	15.57
TG 48:2_m+15	835.7798	15.56
TG 48:2_m+16	836.7879	15.56
TG 48:2_m+17	837.7909	15.57
TG 48:2_m+18	838.7888	15.56
TG 48:3_m+0	818.7229	15.18
TG 48:3_m+1	819.7271	15.18
TG 48:3_m+2	820.7365	15.17
TG 48:3_m+3	821.7455	15.18
TG 48:3_m+4	822.7441	15.18
TG 48:3_m+5	823.7430	15.17
TG 48:3_m+6	824.7393	15.17
TG 48:3_m+7	825.7674	15.17
TG 48:3_m+8	826.7575	15.17
TG 48:3_m+9	827.7647	15.17
TG 48:3_m+10	828.7597	15.17
TG 48:3_m+11	829.7734	15.17
TG 48:3_m+12	830.7622	15.16
TG 48:3_m+13	831.7699	15.17
TG 48:3_m+14	832.7683	15.17
TG 48:3_m+15	833.7697	15.17
TG 48:3_m+16	834.7766	15.16
TG 48:3_m+17	835.7798	15.17
TG 50:1_m+0	850.7874	16.64
TG 50:1_m+1	851.7834	16.64
TG 50:1_m+2	852.7904	16.64
TG 50:1_m+3	853.7969	16.63
TG 50:1_m+4	854.7972	16.63
TG 50:1_m+5	855.7947	16.63
TG 50:1_m+6	856.7953	16.63
TG 50:1_m+7	857.7989	16.63
TG 50:1_m+8	858.8090	16.64
TG 50:1_m+9	859.8130	16.64
TG 50:1_m+10	860.8124	16.62
TG 50:1_m+11	861.8165	16.63
TG 50:1_m+12	862.8250	16.64
TG 50:1_m+13	863.8263	16.63
TG 50:1_m+14	864.8249	16.63
TG 50:1_m+15	865.8337	16.64
METABOLITES_END
#END