#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