#METABOLOMICS WORKBENCH rkuna_20240813_140019 DATATRACK_ID:5101 STUDY_ID:ST003422 ANALYSIS_ID:AN005621 PROJECT_ID:PR002116
VERSION             	1
CREATED_ON             	August 20, 2024, 6:59 pm
#PROJECT
PR:PROJECT_TITLE                 	Bempedoic acid improves diet-induced steatosis independent of hepatic ACLY
PR:PROJECT_SUMMARY               	ATP citrate lyase (ACLY) synthesizes acetyl-CoA for de novo lipogenesis (DNL),
PR:PROJECT_SUMMARY               	which is elevated in metabolic dysfunction-associated steatotic liver disease.
PR:PROJECT_SUMMARY               	Hepatic ACLY is inhibited by the LDL-cholesterol lowering drug bempedoic acid
PR:PROJECT_SUMMARY               	(BPA), which also improves steatosis in mice. Indeed, BPA potently suppresses
PR:PROJECT_SUMMARY               	hepatic DNL and increases fat catabolism. However, it is unclear if ACLY is the
PR:PROJECT_SUMMARY               	relevant molecular target in reducing liver triglyceride, particularly since the
PR:PROJECT_SUMMARY               	acetyl-CoA synthetase ACSS2 can compensate for ACLY deficiency to provision
PR:PROJECT_SUMMARY               	acetyl-CoA for DNL. We show that on a Western diet, loss of hepatic ACLY alone
PR:PROJECT_SUMMARY               	or ACLY and ACSS2 together unexpectedly exacerbates steatosis, linked to reduced
PR:PROJECT_SUMMARY               	hepatic abundance of endogenous PPARa (Peroxisome proliferator-activated
PR:PROJECT_SUMMARY               	receptor alpha) ligands and lower expression of PPARa target genes controlling
PR:PROJECT_SUMMARY               	fatty acid oxidation. Importantly, BPA treatment ameliorates Western
PR:PROJECT_SUMMARY               	diet-mediated triglyceride accumulation in both WT and liver ACLY knockout mice,
PR:PROJECT_SUMMARY               	indicating that its primary effects on hepatic lipid metabolism are independent
PR:PROJECT_SUMMARY               	of ACLY. Together, these data indicate that hepatic ACLY plays an unexpected
PR:PROJECT_SUMMARY               	role in restraining diet-dependent lipid accumulation, and that BPA improves
PR:PROJECT_SUMMARY               	steatosis independent of ACLY.
PR:INSTITUTE                     	Salk Institute for Biological Studies
PR:LAST_NAME                     	Kuna
PR:FIRST_NAME                    	Ramya
PR:ADDRESS                       	10010 N Torrey Pines Rd, La Jolla, California, 92037, USA
PR:EMAIL                         	rkuna@salk.edu
PR:PHONE                         	8582038321
#STUDY
ST:STUDY_TITLE                   	Impact of ACLY and ACSS2 on the development of MASLD on longterm Western diet
ST:STUDY_SUMMARY                 	To further assess the impact of ACLY and ACSS2 on the development of MASLD on
ST:STUDY_SUMMARY                 	Western diet, we also carried out longer term experiments, in which mice
ST:STUDY_SUMMARY                 	remained on diet for 22 weeks. Prior work has shown that phosphatidylcholines
ST:STUDY_SUMMARY                 	(PCs) can serve as PPARa ligands, and specifically, PC 16:0/18:1 has been
ST:STUDY_SUMMARY                 	established as an endogenous ligand. PC 16:0/18:1 abundance has also been found
ST:STUDY_SUMMARY                 	to be regulated in a circadian manner dependent on the fatty acid synthesis
ST:STUDY_SUMMARY                 	pathway. Since PCs as a class are suppressed in the liver ACLY KO mice, we asked
ST:STUDY_SUMMARY                 	if PC 16:0/18:1 is specifically reduced, finding that it its abundance is lower
ST:STUDY_SUMMARY                 	in the ACLY and ACLY/ACSS2 KOs.
ST:INSTITUTE                     	Salk Institute for Biological Studies
ST:LAST_NAME                     	Kuna
ST:FIRST_NAME                    	Ramya
ST:ADDRESS                       	10010 N Torrey Pines Rd, La Jolla, California, 92037, USA
ST:EMAIL                         	rkuna@salk.edu
ST:PHONE                         	8582038321
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
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           	-	DF-1196_ACLY F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1196_1.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1207_ACLY F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1207_12.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1209_ACLY F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1209_14.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1214_ACLY F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1214_19.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1216_ACLY F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1216_21.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1224_ACLY F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1224_29.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1197_ACLY F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1197_2.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1208_ACLY F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1208_13.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1213_ACLY F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1213_18.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1215_ACLY F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1215_20.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1223_ACLY F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1223_28.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1225_ACLY F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1225_30.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1204_ACSS2F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1204_9.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1206_ACSS2F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1206_11.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1211_ACSS2F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1211_16.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1217_ACSS2F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1217_22.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1219_ACSS2F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1219_24.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1230_ACSS2F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1230_35.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1205_ACSS2F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1205_10.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1210_ACSS2F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1210_15.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1212_ACSS2F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1212_17.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1218_ACSS2F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1218_23.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1229_ACSS2F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1229_34.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1231_ACSS2F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1231_36.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1198_ACLY_ACSS2 F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1198_3.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1200_ACLY_ACSS2 F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1200_5.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1202_ACLY_ACSS2 F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1202_7.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1220_ACLY_ACSS2 F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1220_25.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1222_ACLY_ACSS2 F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1222_27.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1227_ACLY_ACSS2 F/F_GFP	Genotype:GFP | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1227_32.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1199_ACLY_ACSS2 F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1199_4.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1201_ACLY_ACSS2 F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1201_6.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1203_ACLY_ACSS2 F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1203_8.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1221_ACLY_ACSS2 F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1221_26.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1226_ACLY_ACSS2 F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1226_31.d
SUBJECT_SAMPLE_FACTORS           	-	DF-1228_ACLY_ACSS2 F/F_CRE	Genotype:CRE | Sample source:Mouse liver	RAW_FILE_NAME(Raw file name)=DF-1228_33.d
#COLLECTION
CO:COLLECTION_SUMMARY            	Liver samples were collected using Wollenberger clamps pre-cooled to the
CO:COLLECTION_SUMMARY            	temperature of liquid nitrogen and stored at -80 C until analysis.
CO:SAMPLE_TYPE                   	Liver
#TREATMENT
TR:TREATMENT_SUMMARY             	Male mice with deletion of hepatic ACLY (ACLY KO), ACLY and ACSS2 (double KO,
TR:TREATMENT_SUMMARY             	DKO), and respective controls (wildtype, WT) are on western diet for 22 weeks,
TR:TREATMENT_SUMMARY             	before sacrificing liver samples were collected using Wollenberger clamps
TR:TREATMENT_SUMMARY             	pre-cooled to the temperature of liquid nitrogen and stored at -80 C until
TR:TREATMENT_SUMMARY             	analysis.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Liver samples were collected using Wollenberger clamps pre-cooled to the
SP:SAMPLEPREP_SUMMARY            	temperature of liquid nitrogen and stored at -80 C until analysis.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Waters Acquity
CH:COLUMN_NAME                   	Waters Acquity BEH C18 (100 x 2mm, 1.7um)
CH:SOLVENT_A                     	100% water; 0.2% formic acid; 2 mM ammonium formate
CH:SOLVENT_B                     	100% methanol; 0.2% formic acid; 1 mM ammonium formate
CH:FLOW_GRADIENT                 	0 min, 82% B; 3 min, 82% B; 4 min, 90% B; 18 min, 99% B; 25 min, 99% B; 27 min,
CH:FLOW_GRADIENT                 	82% B; 30 min, 82% B
CH:FLOW_RATE                     	0.5 mL/min
CH:COLUMN_TEMPERATURE            	40˚C
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 6460 QQQ
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	PC 16:0/18:1 species were analyzed by multiple reaction monitoring of the
MS:MS_COMMENTS                   	transition from precursor to product ions at associated optimized collision
MS:MS_COMMENTS                   	energies, and fragmentor voltages using Agilent Masshunter. The m/z values of
MS:MS_COMMENTS                   	the
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	relative abundance/mg tissue
MS_METABOLITE_DATA_START
Samples	DF-1196_ACLY F/F_GFP	DF-1207_ACLY F/F_GFP	DF-1209_ACLY F/F_GFP	DF-1214_ACLY F/F_GFP	DF-1216_ACLY F/F_GFP	DF-1224_ACLY F/F_GFP	DF-1197_ACLY F/F_CRE	DF-1208_ACLY F/F_CRE	DF-1213_ACLY F/F_CRE	DF-1215_ACLY F/F_CRE	DF-1223_ACLY F/F_CRE	DF-1225_ACLY F/F_CRE	DF-1204_ACSS2F/F_GFP	DF-1206_ACSS2F/F_GFP	DF-1211_ACSS2F/F_GFP	DF-1217_ACSS2F/F_GFP	DF-1219_ACSS2F/F_GFP	DF-1230_ACSS2F/F_GFP	DF-1205_ACSS2F/F_CRE	DF-1210_ACSS2F/F_CRE	DF-1212_ACSS2F/F_CRE	DF-1218_ACSS2F/F_CRE	DF-1229_ACSS2F/F_CRE	DF-1231_ACSS2F/F_CRE	DF-1198_ACLY_ACSS2 F/F_GFP	DF-1200_ACLY_ACSS2 F/F_GFP	DF-1202_ACLY_ACSS2 F/F_GFP	DF-1220_ACLY_ACSS2 F/F_GFP	DF-1222_ACLY_ACSS2 F/F_GFP	DF-1227_ACLY_ACSS2 F/F_GFP	DF-1199_ACLY_ACSS2 F/F_CRE	DF-1201_ACLY_ACSS2 F/F_CRE	DF-1203_ACLY_ACSS2 F/F_CRE	DF-1221_ACLY_ACSS2 F/F_CRE	DF-1226_ACLY_ACSS2 F/F_CRE	DF-1228_ACLY_ACSS2 F/F_CRE
Factors	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:GFP | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver	Genotype:CRE | Sample source:Mouse liver
PC 16:0/18:1	12.88263626	21.63390204	18.34596543	18.96739093	20.2951672	21.01951499	17.13550752	18.69860606	16.60492939	18.19887723	16.84426003	17.35022754	19.69326321	23.72791842	25.05224714	24.3421084	24.9194635	23.99820791	21.24382204	24.6872998	23.39863058	21.19009341	26.15161669	25.88602248	24.53943556	21.60824879	21.55768495	23.70650753	25.15140592	21.36870694	14.66536524	13.67333472	14.89123924	17.47419864	16.02060465	18.98784824
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Precursor Ion m/z
PC 16:0/18:1	804.6
METABOLITES_END
#END