The R package and the BiotreeDB (V3.0) were applied in metabolite identification.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - positive - hilic","Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["For polar metabolites, LC-MS/MS analyses were performed using an UHPLC system
(Vanquish, Thermo Fisher Scientific) with a Waters ACQUITY UPLC BEH Amide (2.1 mm × 50 mm,1.7 μm) coupled to Orbitrap Exploris 120 mass spectrometer (Orbitrap MS, Thermo). The mobile phase consisted of 25 mmol/L ammonium acetate and 25 ammonia hydroxide in water (pH =9.75)(A) and acetonitrile (B). The auto-sampler temperature was 4 , and the injection volume was 2 μL.
"],"publication":["PGM3-Driven Hexosamine Biosynthesis Facilitates Hepatocellular Carcinoma Progression through YBX1 O-GlcNAcylation (Untargeted metabolomics)."],"submitter_name":["Jiaqing Chen"],"submitter_affiliation":["The First Affiliated Hospital of Anhui Medical University"],"organism_part":["liver"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["For polar metabolites, LC-MS/MS analyses were performed using an UHPLC system (Vanquish, Thermo Fisher Scientific) with a Waters ACQUITY UPLC BEH Amide (2.1 mm × 50 mm, 1.7 μm) coupled to Orbitrap Exploris 120 mass spectrometer (Orbitrap MS, Thermo). The mobile phase consisted of 25 mmol/L ammonium acetate and 25 ammonia hydroxide in water (pH =9.75) (A) and acetonitrile (B). The auto-sampler temperature was 4 , and the injection volumewas 2 μL. The Orbitrap Exploris 120 mass spectrometer was used for its ability to acquire MS/MS spectra on information-dependent acquisition (IDA) mode in the control of the acquisition software (Xcalibur, Thermo). In this mode, the acquisition software continuously evaluates the full scan MS spectrum. The ESI source conditions were set as following: sheath gas flow rate as 50 Arb, Aux gas flow rate as 15 Arb, capillary temperature 320 , full MS resolution as 60000, MS/MS resolution as 15000, collision energy: SNCE 20/30/40, spray voltage as 3.8 kV (positive) or -3.4 kV (negative), respectively. The raw data were converted to the mzXML format using ProteoWizard and processed with an in-house program. which was developed using R and based on XCMS, for peak detection, extraction, alignment, and integration. The R package and the BiotreeDB (V3.0) were applied in metabolite identification.
"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15545"],"author":["Beicheng Sun. The First Affiliated Hospital of Anhui Medical University. sunbc@ahmu.edu.cn.","Jiaqing Chen. The First Affiliated Hospital of Anhui Medical University. 2345011394@stu.ahmu.edu.cn."],"data_transformation_protocol":["The raw data were converted to the mzXML format using ProteoWizard and processed withan in-house program. which was developed using R and based on XCMS, for peak detection,extraction, alignment, and integration.
"],"study_factor":["Group"],"submitter_email":["2345011394@stu.ahmu.edu.cn"],"sample_collection_protocol":["For the chemically induced HCC model, two-week-old male C57BL/6 mice received a single intraperitoneal injection of diethylnitrosamine (DEN, 25 mg/kg), followed by weekly CCl4 administration (10%, 5 mL/kg) from 4 to 24 weeks of age. Concurrently, a control group was established, in which mice received intraperitoneal injections of PBS (n = 9 per group). After 20 weeks, all mice were euthanized under anesthesia; the livers were harvested and weighed, and a 0.5 g sample was taken from each liver for metabolomic profiling. After QC, a total of 16 samples were eligible for further analysis (n = 7 in the control group and n = 9 in the model group). The animal tissue samples (25 mg±1 mg) were taken, mixed with beads and 500 μL of extraction solution (MeOH:ACN:H2O, 2:2:1 (v/v)). The extraction solution contain deuterated internal standards. The mixed solution were vortexed for 30 s. Then the mixed samples were homogenized (35 Hz,4 min) and sonicated for 5 min in 4 water bath, the step repeat for three times. The samples were incubated for 1 h at -40 to precipitate proteins. Then the samples ware centrifuged at 12000 rpm (RCF=13800(×g),R= 8.6cm) for 15 min at 4 . The supernatant was transferred to a fresh glass vial for analysis. The quality control (QC) sample was prepared by mixing an equal aliquot of the supernatant of samples.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","Metabolomics","Mus musculus","FR054","liver","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","PGM3","Hepatocellular carcinoma","Hexosamine biosynthesis pathway","O-GlcNAcylation","YBX1"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","Metabolomics","Mus musculus","FR054","liver","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","PGM3","Hepatocellular carcinoma","Hexosamine biosynthesis pathway","O-GlcNAcylation","YBX1"],"mass_spectrometry_protocol":["The Orbitrap Exploris 120 mass spectrometer was used for its ability to acquire MS/MS
spectra on information-dependent acquisition (IDA) mode in the control of the acquisitionsoftware (Xcalibur, Thermo). In this mode, the acquisition software continuously evaluates the fullscan MS spectrum. The ESI source conditions were set as following: sheath gas flow rate as 50Arb, Aux gas flow rate as 15 Arb, capillary temperature 320 , full MS resolution as 60000,MS/MS resolution as 15000, collision energy: SNCE 20/30/40, spray voltage as 3.8 kV (positive) or-3.4 kV (negative),respectively.
"],"metabolite_name":["3-beta-Glucosylcellotriose","Thr-Phe","Phosphoglycolic acid","Riboflavin","Caprolactam","MeAIB","Ramipril","Cellopentaose","Mangiferdesmethylursanone","PC(14:1(9Z)/16:0)","SM(d18:1/14:0)","Deoxyinosine","Ectoine","Val-Met","Goralatide (acetate)","Hexanoylglycine","(25S)-26-Hydroxy-24-methylenecycloartan-3-one","Caplamin","Nipecotic acid","Citrulline","PI(18:1(11Z)/20:4(5Z,8Z,11Z,14Z))","LPC(20:5)","Glyzaglabrin","alpha-Muricholic acid","Isomalt","Octadecanedioic acid","Hyocholic acid","1-Hydroxy-2-naphthoic acid","N-Acetylaspartic acid","Rolofylline","cis-?9,?10-?Epoxystearic acid","Lamotrigine","4-Hydroxybenzaldehyde","N2-Acetylornithine","Griseofulvin","PE(20:1(11Z)/14:1(9Z))","Lauric diethanolamide","Glycine","Arabinono-1,4-lactone","3'3'-Cyclic guanosine monophosphate-adenosine monophosphate (cGAMP)","Valyl-Glycine","lactitol","3-Hydroxyisobutyric acid","PC(20:3(5Z,8Z,11Z)/14:0)","Arginine","Oleic acid","Glu-Arg","Glutaric acid","[12]-Gingerol","Glutathione","Adenylsuccinic acid","4-Hydroxyglutamic acid","N-Acetylglutamic acid","DMPO","Lamivudine","Pseudouridine","Butyrylcarnitine (Car(4:0))","Maltopentaose","Tetrabenazine","2-Acetylthiophene","Terephthalic-Acid","PC(14:1(9Z)/15:0)","Ginkgolide A","Lindleyin","PC(18:0/14:0)","3'-Sialyllactose","Pyrazine","Dihydrocapsaicin","Pyridoxal (Vitamin B6)","Posaconazole","N-Acetylneuraminic acid","Nicotinamide riboside (NR)","LysoPE(22:0/0:0)","Pantothenic acid","Octocrylene","Dehydroaporheine","3-Hydroxyhexadecanoylcarnitine","(S)-3,4-Dihydroxybutyric acid (lithium hydrate)","Hygric acid","Mintsulfide","Threoninyl-Serine","Tyrosylalanine","5,6-Dihydroxyindole","Guanosine","Protopine","3-Hydroxydecanoic acid","Leu-Val","Ursocholic acid","8Z,11Z,14Z-eicosatrienoyl-CoA","Erucic acid","1-O-Hexadecyl-sn-glycero-3-phosphocholine (LPC(O-16:0/0:0))","Cytochalasin B","3-Oxocholic acid","Isoleucyl-Phenylalanine","Succinyladenosine","Acetylglycine","PA(18:0/20:4(5Z,8Z,11Z,14Z))","Biliverdin","N6-Acetyl-5S-hydroxy-L-lysine","5-Methoxytryptamine","2-Aminoisobutyric acid","Prolylalanine","Montecristin","Homocitric acid","Palmitoyl sphingomyelin","S-(Formylmethyl)glutathione","PS(20:3(8Z,11Z,14Z)/20:4(5Z,8Z,11Z,14Z))","2-Phenyllactic acid","PC(10:0/10:0)","L-Thyronine","1-Methylguanine","Pyrophosphate","Uridine","Cycasin","Asparaginyl-Valine","N6-Methyllysine","Ornithine","Chenodeoxycholic acid","Enterodiol","4-Acetamidobutyric acid","Octadienedioylcarnitine","PS(18:0/18:2)","1-oleoyl-2-myristoyl-sn-glycero-3-phosphocholine","Carbidopa","Serine","2-Hydroxyadenine","Proline","cis-11.14-Eicosadienoic acid","PC(18:2(9Z,12Z)/15:0)","LPE(P-16:0)","3-Methyl-4-phenyl-3-buten-2-one","Trandolapril","Sambutoxin","Nelarabine","Chlorambucil","Phenylsulfate","Isocitric acid","Marimastat","Tetradecyl sulfate (sodium)","Tagatose","Malonyl-CoA","LPC(18:1)","Gly-His","Thiamine","13-OxoODE","(Cyclohexylmethyl)pyrazine","Adenosine","Glucuronic acid","PC(16:0/18:1(9Z))","PC(18:1(9E)/18:1(9E))","Allopurinol","7-Methylrosmanol","Etoposide","Phe-Lys","2,4-Dihydroxybutanoic acid","L-tyrosine-methyl-ester","Linoleic acid","Allose","CPA(16:0/0:0)","Occidentoside","Cyclic adenosine diphosphate-ribose (cADPR)","Oligomycin A","Argininosuccinic acid","PC(18:0/18:1(9Z))","Adenosine 3',5'-diphosphate (PAP)","Hypotaurine","3-Hydroxybutyric acid","Glucoiberin","Benzoic acid","Betonicine","Phe-Pro","Ascorbic acid","Phenylalanylphenylalanine","PA(16:0/18:1(9Z))","dTDP-4-acetamido-4,6-dideoxy-D-galactose","Argatroban","Daltogen","Methylsuccinic acid","Mannose","PI(16:0/16:0)","Glucose","Glycolithocholic acid 3-sulfate","N6-Acetyllysine","Azimsulfuron","O-Acetylserine","3'-O-Methylguanosine","Chromone","PC(16:0/16:0)","Sphingosine","(2R)-6-Oxo-2-piperidinecarboxylic acid","Cytidine monophosphate N-acetylneuraminic acid","Taurocholic acid","Folinic acid","Imazalil","2-Deoxyribose 5-phosphate","Isodeoxycholic acid","N-Acetyl-arginine","Neouralenol","Amentoflavone","Imidafenacin","Nitrofurazone","Lysine","Fagomine","Cyclobenzaprine","Entacapone","Linoleoylcarnitine","Tolmetin","4-Nitroaniline","N-Acetylglucosamine","Nicotinamide adenine dinucleotide (NAD)","5-Methylcytidine","N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole","Tetraethylene glycol","Ceftriaxone","Betanidin","Guanine","SM(d18:0/18:0)","Nivalenol","LPS(18:1)","Aminomalonic acid","5'-Methylthioadenosine","Cer(d18:1/16:0)","1-Methylnicotinamide","Menadione bisulfite (sodium)","1-(sn-Glycero-3-phospho)-1D-myo-inositol","Dihydroberberine","N-Acetylphenylalanine","Creatinine","Cytidine 5'-monophosphate (CMP)","Xanthosine","GlcCer(d18:1/16:0)","Cysteine-glutathione disulfide","2,2-Dimethylsuccinic acid","Desaminotyrosine","Glycylleucine","His-Gly","Mannose 1-phosphate","6-Phosphogluconic acid","Citric acid","LPS(18:0)","7-Methylguanine","4-Deoxycohumulone","5-Aminopentanoic acid","PC(15:0/22:5(7Z,10Z,13Z,16Z,19Z))","Valine","Stachydrine","Denticetic-acid","Mardepodect","Hydroxyisocaproic acid","Glutathione disulfide","Succinyl-CoA","Galangin","LysoPC(22:6(4Z,7Z,10Z,13Z,16Z,19Z))","Nadolol","Tauroursodeoxycholic acid","Inosine 5'-monophosphate (IMP)","Zaltoprofen","SM(d18:0/16:0)","Glycocholic acid","Phe-Val","Pipecolic acid","Gynocardin","Fulvestrant","2-Hexyl-5-[2-(4-hydroxy-3-methoxyphenyl)ethyl]furan","L-Urobilinogen","5-Fluorouridine","Betaine","Glucose 6-phosphate","2'-Deoxyuridine","N-Methylhydantoin","Phenacetin","S-Nitrosoglutathione","Glutethimide","7,8-Dihydrobiopterin","Ethyl 4-hydroxybenzoate","Daminozide","Indapamide","Lotaustralin","Uridine diphosphate glucose (UDP-glucose)","Glyco-gamma-muricholic acid","Glutamate","Terbinafine","Cytidine","Carnitine","gamma-Glutamylalanine","Candoxatril","MES","LPC(16:0)","Besifovir","Taurochenodeoxycholic acid","Mangiferin","AG 1295","2-Aminoadipic acid","Karanjin","5-Methyl DL-glutamate","H-Val-Ala-OH","Trimethylamine N-oxide","(22E,24R)-Stigmasta-4,22-diene-3,6-dione","Cafestol","Alanylalanine (Ala-Ala)","1-Methylhistidine","Triflupromazine","Isoleucyl-Threonine","PC(20:4(8Z,11Z,14Z,17Z)/15:0)","PC(18:1(9Z)/18:1(9Z))","6-Methoxy-alpha-pyrufuran","Isobutyrylcarnitine (Car(4:0))","N6,N6,N6-Trimethyllysine","3-Hydroxybutyrylcarnitine (Car(4:0-O))","Nabilone","LPC(17:0/0:0)","Glycerophosphoethanolamine","PS(18:3(9Z,12Z,15Z)/20:3(8Z,11Z,14Z))","N6,N6-Dimethyllysine","2-Hydroxyethanesulfonic acid","2-Naphthalenethiol","Clofarabine","Stercobilin","Pelargonic acid","2-Hydroxyglutaric acid","13(S)-HODE","Hyodeoxycholic acid","N-Acetylglucosamine 1-phosphate","Ligustilide","Amphotericin B","(S)-2-acetamido-4-amino-4-oxobutanoic acid","4-Hydroxyisoleucine","Maltol","Sarcosine","N-Acetylalanine","Galactose","Taurine","1-Methylhistamine","N-Acetylgalactosamine","LysoPE(0:0/18:0)","PC(22:5(7Z,10Z,13Z,16Z,19Z)/20:5(5Z,8Z,11Z,14Z,17Z))","Xanthohumol","Allantoin","Embelin","1,5-Anhydroglucitol","LPG(18:1(9Z))","Tetradecenedioylcarnitine","Bistris","Car(18:1)","2-methylcitrate","O-Phosphoethanolamine","SM(d18:1/20:0)","Syringin","Mannose 6-phosphate","Maltobionate","Fructose 1,6-bisphosphate","N2-Acetyllysine","Trifluoroacetic acid","4-Guanidinobutyric acid","Ceanothic acid","Adenosine 3'-monophosphate","Phe-Trp","Sph(d18:0)","Trigonelline","Thiamine monophosphate","His-Phe","Succinate","Methionine","Carboxytolbutamide","Cholic acid 7-sulfate","Ganoderic acid H","Nalbuphine","Ganoderic acid B","PI(18:1(9Z)/18:3(9Z,12Z,15Z))","9-Oxooctadecanoic acid","Ganoderic acid A","PC(18:1(11Z)/15:0)","Salicin","trans-Vaccenic acid","9-Methylxanthine","cis-11-Eicosenoic acid","1-Methylguanosine","6-(alpha-D-Glucosaminyl)-1D-myo-inositol","Cholesteryl sulfate","CMP-N-glycoloylneuraminate","Cryptotanshinone","Isovalerylcarnitine (Car(5:0))","Ethyl glucuronide","Citrinin","N-Acetylglutamine","Fructose 1-phosphate","PC(22:4(7Z,10Z,13Z,16Z)/20:4(5Z,8Z,11Z,14Z))","gamma-Glutamylglutamic acid","Na-Hexanoyl-Nb-inosityltryptophan","Val-Ile","2-Aminobutyric acid","Lincomycin","Phosphate","H-Val-Tyr-OH","Hexamethylquercetagetin","PI(18:1/18:1)","Glucosamine 1-phosphate","Pentadecanoic acid","Papaverine","S-Formylglutathione","5-Aminopentanal","PC(16:0/16:1(9Z))","Phenylalanine","Serotonin","Sph(d18:2)","Phenylacetylglycine","UDP-galactose","Car(18:0)","Prolylhydroxyproline","3-methylcytidine","17-ODYA","Guanosine 5'-monophosphate (GMP)","6,11-Dihydroxy-2,2-dimethylpyrano[3,2-c]xanthen-7(2H)-one","Dhurrin","Nitazoxanide","Pentaethylene glycol","PI(18:1(9Z)/16:0)","Persicachrome","N-Acetylmannosamine","2-Hydroxy-3-methyl-9H-carbazole","Uracil","Eicosapentaenoic acid","Oxooctanoylcarnitine","Glu-Glu","11-Dehydrocorticosterone","Pentadecadienoylcarnitine","D-4'-Phosphopantothenate","Ile-Pro-Ile","Norleucine","LysoPE(18:1(11Z)/0:0)","Maltotetraose","Creatine","Xanthotoxol","Caprylic acid","Tetradecenoylcarnitine","Arachidonoylcarnitine (Car(20:4))","Maraviroc","Lactodifucotetraose","SM(d18:1/18:0)","Formoterol","2-Acetylthiazole","beta-Muricholic acid","Tyrosine","Pro-Phe","L-Cystine","1-Oleoyl-sn-glycerol 3-phosphate","Ile-Leu","Harderoporphyrinogen","Acetylcarnitine (Car(2:0))","Stevioside","Pantetheine 4'-phosphate","Guanidinosuccinic acid","Taurocyamine","3-Hydroxylauric acid","N,N-Dimethylarginine (ADMA)","Acadesine","Hypoxanthine","Bathophenanthroline","Dephospho-CoA","Homoserine","4-Hydroxyestrone","gamma-Linolenic acid","2'-Deoxyguanosine 5'-diphosphate (dGDP)","5Z,8Z,11Z-Eicosatrienoic acid","Hippuric acid","PE(P-36:4)","alpha-Linolenic acid","LysoPC(0:0/18:0)","Uridine 5'-monophosphate (UMP)","1-Palmitoyllysophosphatidate","LPE(18:1(9Z)/0:0)","S-(2,2-Dichloro-1-hydroxy)ethyl glutathione","beta-Guanidinopropionic acid","Val-Val","LPC(18:0/0:0)","Tauro-gamma-muricholic acid","2-Propanoylthiazole","Isoleucyl-Cysteine","UDP-N-acetylglucosamine","2-Hydroxybutyric acid","cis-8,11,14-Eicosatrienoic acid","gamma-Glutamyllysine","3-Hydroxymethylantipyrine","Ophthalmic acid","PC(18:4(6Z,9Z,12Z,15Z)/20:3(8Z,11Z,14Z))","Vaccinoside","Isoleucine","Theogallin","Alanyl-Proline","LPI(20:4)","Xanthone","Phe-Tyr","S-(Hydroxymethyl)glutathione","3,3',4,4'-Tetrahydroxy-5,5'-diisopropyl-2,2'-dimethylbiphenyl","2-Ethyl-2-hydroxybutyric acid","Arachidonic acid (AA)","Pyruvate","Canrenone","Adenine","6-Acetamidohexanoic acid","2-Methylhippuric acid","Leucyl-Lysine","N-Lactoyl-Phenylalanine","Threonic acid","Fructose","trans-3,4-Dihydro-3,4-dihydroxy-7,12-dimethylbenz[a]anthracene","2,2'-Iminodiacetic acid","Gly-Phe","Niflumic acid","12alpha-Hydroxy-13,18-dehydroparain","Heptadecanoic acid","Alloimperatorin","Citraconic acid","Dehydroascorbic acid (Oxidized vitamin C)","Inosine","Cytidine 5'-diphosphocholine (CDP-choline)","Dimethylglycine","Glutamine","MOPS","Methylimidazoleacetic acid","Caproic acid","Delphinidin","Leu-Ile","3-Hydroxy-4-aminopyridine","Adenosine 5'-diphosphate (ADP)","LPC(18:2/0:0)","Thiamine pyrophosphate (TPP)","Cholic acid","Methylprednisolone","omega-Muricholic acid","Carnosol","sn-Glycerol 3-phosphate","N-Acetylmethionine","2-Methylbutylamine","3-AMINO-2-PIPERIDONE","Histidine","Melibiose","Cellobiose","Ala-Glu","Anserine","Saccharopine","Lysyl-Glycine","Pachyrrhizin","3-Methylhistidine","SM(d16:1/24:1(15Z))","Ala-Gln","Acetylleucine","Galactosamine","Myristoylcarnitine","Tetradecadienedioylcarnitine","Palmitoylcarnitine (Car(16:0))","Propionic acid","Allocholic acid","Allopurinol-1-ribonucleoside","PE(14:0/22:5(7Z,10Z,13Z,16Z,19Z))","Glyco-beta-muricholic acid","12-Hydroxydodecanoic acid","Maltotriose","Propionylcarnitine (Car(3:0))","Gly-Val","Valproic acid","N5-acetyl-l-ornithine","CDP-Ethanolamine","Ser-Ala","D-erythro-D-galacto-octitol","Theaflavin","2-Hydroxystearic acid","N-Acetylhistamine","L-Valyl-L-phenylalanine","Nicotinamide","Cysteinylglycine","Glycerophosphocholine","Gaylussacin","N-Glycolylneuraminic acid","Ergothioneine","Flavin mononucleotide (FMN)","Ferulic acid 4-O-glucuronide","7-Ketodeoxycholic acid","Hydroxyprolyl-Threonine","Castamollissin","Hexenoylcarnitine","PE(18:0/18:2)","PC(34:3)","myo-Inositol","Sorbose","Pyroglutamic acid","Kynurenine","Glucose 1-phosphate","Desbenzyl donepezil","3-Pyridylacetic acid","N-Methylglutamic acid","Uridine 5'-diphosphate (UDP)","SM(d17:1/24:1(15Z))","Betaine aldehyde","1-Myristoyl-sn-glycero-3-phosphocholine (LPC(14:0/0:0))","Hydroxyphenyllactic acid","L-Alanyl-L-leucine","N-Lactoylphenylalanine","Alanine","N-Acetylhistidine","gamma-Glutamylglutamine","2-Methylguanosine","Isomaltose","5-O-Desmethyldonepezil","PG(18:1/18:1(9Z))","Prulifloxacin","Xanthine","Piperundecalidine","EDTA","Ethoxyacetic acid","S-Adenosylmethionine","Fructose 6-phosphate","ADP-ribose","Deoxyguanosine","Nobiletin","PC(16:0/20:4)","Choline","Asparagine","Tauro-beta-muricholic acid","Acteoside","Valerylcarnitine","LPC(20:0)","Sph(t18:0)","PG(16:0/18:1)","Arg-Phe","Thymidine","S-Methylmethionine","2-Hydroxyhexanoic acid","Ursodeoxycholic acid","3-Methylglutarylcarnitine","Isocaproic acid","Orotic acid","Aniline","Adenosine monophosphate (AMP)","N-Tigloylglycine","3'-Deoxyoleacein","Nicotinamide N-oxide","Malic acid","Flavin adenine dinucleotide (FAD)","3-Phosphoglyceric acid","Miconazole","Cotinine","Phenylpropionylglycine","PC(14:0/16:0)","Docebenone","Gluconic acid","PE(18:1(9Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z))","o-Tyrosine","PC(15:0/22:4(7Z,10Z,13Z,16Z))","2-Aminopurine","Indoxyl sulfate","3-Amino-4-methylpentanoic acid","Eupatorin","N1-Methyl-2-pyridone-5-carboxamide","Maltose","Phosphorylcholine","Theanine","S-Adenosylhomocysteine","Tetracycline","Aflatoxin B1exo-8,9-epoxide-GSH","Histamine","2-Hydroxy-2-methylbutyric acid","2-Methoxy-3-methyl-9H-carbazole","Indole-3-butyric acid","Nornantenine","Hexanoylcarnitine (Car(6:0))","sn-Glycerol 1-phosphate","Oxypurinol","Gulono-1,4-lactone","Protoporphyrin IX","Azathioprine","12-Hydroxystearic acid","3'-Hydroxystanozolol","Diglycine","Isovalerylglycine","N-cis-Caffeoyltyramine","2-Oxoadipic acid","Fenamiphos","Erianin","GDP-mannose","SM(d18:1/22:0)","Leucine","beta-D-Galactopyranosyl-(1->4)-2-amino-2-deoxy-beta-D-glucopyranosyl-(1->6)-D-mannose","Aspartyl-Tryptophan","Taurodeoxycholic acid","L-isoleucyl-L-proline","Maltoheptaose","4-Aminobutyric acid (GABA)","Lorazepam glucuronide","N1-Methyl-4-pyridone-3-carboxamide","Piperidine","Pyrrolidine","gamma-Crocetin","2-Hydroxyhexanedioic acid","Uridine 5'-diphosphoglucuronic acid (UDP-glucuronate)","Arg-Ala","L-?Leucyl-?L-?alanine","Ziprasidone","Imidazoleacetic acid","12-Methoxy-8,11,13-abietatrien-20,11-olide","Maltohexaose","PC(14:0/14:1(9Z))","2-Linoleoyl-1-palmitoyl-sn-glycero-3-phosphoethanolamine","Rosmaricine","LPI(18:0)","2,5-Furandicarboxylic acid","PC(20:1(11Z)/15:0)","Deoxycholic acid","Lactose","Neogrifolin","Isopentenyladenine-9-N-glucoside","Phe-Ala","Biopterin","AG126","2'-Deoxyguanosine 5'-monophosphate (dGMP)"],"additional_accession":[]},"is_claimable":false,"name":"PGM3-Driven Hexosamine Biosynthesis Facilitates Hepatocellular Carcinoma Progression through YBX1 O-GlcNAcylation (Untargeted metabolomics)","description":"Phosphoglucomutase 3 (PGM3) is one of the rate-limiting enzymes in the hexosamine biosynthesis pathway (HBP) and a key regulator of HBP metabolic flux. Despite the functional role of PGM3 has been validated in various tumors, its function and molecular mechanism in hepatocellular carcinoma (HCC) remain to be elucidated. This study found that PGM3 expression is upregulated in HCC tissues, and high PGM3 expression is closely associated with poor prognosis in HCC patients. In vitro and in vivo results demonstrated that PGM3 enhances UDP-GlcNAc synthesis and protein O-GlcNAcylation, thereby promoting HCC proliferation, migration, and invasion. Further O-GlcNAcylomic sequencing of HCC cells identified Y-box binding protein 1 (YBX1) as a key substrate for PGM3-mediated O-GlcNAcylation. Notably, O-GlcNAcylation of YBX1 at a specific serine residue (Ser165) enhances its nuclear translocation. Additionally, we validated that FR054, a novel reported PGM3 inhibitor, retards HCC progression by diminishing PGM3-mediated O-GlcNAcylation. These interventions effectively inhibit HCC malignant progression. Collectively, our findings reveal the potential therapeutic value of targeting the PGM3-HBP-YBX1 signaling axis in HCC 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