{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003504","ANALYSIS_ID":"AN005752","PROJECT_ID":"PR002150","VERSION":"1","CREATED_ON":"September 28, 2024, 8:37 pm"},

"PROJECT":{"PROJECT_TITLE":"Methionine-SAM metabolism-dependent ubiquinone synthesis is crucial for ROS accumulation in ferroptosis induction","PROJECT_SUMMARY":"Ferroptosis is a cell death modality in which iron-dependent lipid peroxides accumulate on cell membranes. Cysteine, a limiting substrate for the glutathione system that neutralizes lipid peroxidation and prevents ferroptosis, can be converted by cystine reduction or synthesized from methionine. However, accumulating evidence shows methionine-based cysteine synthesis fails to effectively rescue intracellular cysteine levels upon cystine deprivation and is unable to inhibit ferroptosis. Here, we report that methionine-based cysteine synthesis is tissue-specific. Unexpectedly, we find that rather than inhibiting ferroptosis, methionine in fact plays an essential role during cystine deprivation-induced ferroptosis. Methionine-derived S-adenosylmethionine (SAM) contributes to methylation-dependent ubiquinone synthesis, which leads to lipid peroxides accumulation and subsequent ferroptosis. Moreover, SAM supplementation synergizes with imidazole ketone erastin in a tumor growth suppression mouse model. Inhibiting the enzyme that converts methionine to SAM protects heart tissue from doxorubicin-induced and ferroptosis-driven cardiomyopathy. This study broadens our understanding about the intersection of amino acid metabolism and ferroptosis regulation, providing insight into the underlying mechanisms and suggesting the methionine-SAM axis is a promising therapeutic strategy to treat ferroptosis-related diseases.","INSTITUTE":"Northeast Normal University","LAST_NAME":"xia","FIRST_NAME":"chaoyi","ADDRESS":"5268 Renmin Street, changchun, ji lin, 130024, China","EMAIL":"xiacy834@nenu.edu.cn","PHONE":"18166850252"},

"STUDY":{"STUDY_TITLE":"Methionine-SAM metabolism-dependent ubiquinone synthesis is crucial for ROS accumulation in ferroptosis induction","STUDY_SUMMARY":"Ferroptosis is a cell death modality in which iron-dependent lipid peroxides accumulate on cell membranes. Cysteine, a limiting substrate for the glutathione system that neutralizes lipid peroxidation and prevents ferroptosis, can be converted by cystine reduction or synthesized from methionine. However, accumulating evidence shows methionine-based cysteine synthesis fails to effectively rescue intracellular cysteine levels upon cystine deprivation and is unable to inhibit ferroptosis. Here, we report that methionine-based cysteine synthesis is tissue-specific. Unexpectedly, we find that rather than inhibiting ferroptosis, methionine in fact plays an essential role during cystine deprivation-induced ferroptosis. Methionine-derived S-adenosylmethionine (SAM) contributes to methylation-dependent ubiquinone synthesis, which leads to lipid peroxides accumulation and subsequent ferroptosis. Moreover, SAM supplementation synergizes with imidazole ketone erastin in a tumor growth suppression mouse model. Inhibiting the enzyme that converts methionine to SAM protects heart tissue from doxorubicin-induced and ferroptosis-driven cardiomyopathy. This study broadens our understanding about the intersection of amino acid metabolism and ferroptosis regulation, providing insight into the underlying mechanisms and suggesting the methionine-SAM axis is a promising therapeutic strategy to treat ferroptosis-related diseases. To test, we firstly performed a metabolomics analysis of HT1080 cells that were cultured in medium lacking cystine or lacking both cystine and methionine. The metabolomics results containing full profile of the metabolites was subjected to cluster assay, and the triplicates of each group were automatically clustered together, indicating better homogeneity of the data in each condition. Then, we filtrated the metabolomics data with the threshold fold change (FC) ≥2 and P≤ 0.05.Only the RP Pos method results are used/reported in this study. The results showed that the cellular cysteine and GSH levels were expectedly depressed upon cystine limitation; meanwhile, once methionine was restricted, cellular SAM level was significantly reduced. This highlights the decisive regulatory role of methionine on the metabolite levels of SAM.","INSTITUTE":"Northeast Normal University","LAST_NAME":"xia","FIRST_NAME":"chaoyi","ADDRESS":"5268 Renmin Street, changchun, ji lin, 130024, China","EMAIL":"xiacy834@nenu.edu.cn","PHONE":"18166850252"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Male"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"+CC+Met_2",
"Sample ID":"XiaChaoYi_A4_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"+CC+Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A4_RP pos.mzML"}
},
{
"Subject ID":"-CC+Met_3",
"Sample ID":"XiaChaoYi_A5_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"-CC+Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A5_RP pos.mzML"}
},
{
"Subject ID":"-CC-Met_1",
"Sample ID":"XiaChaoYi_A6_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"-CC-Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A6_RP pos.mzML"}
},
{
"Subject ID":"+CC+Met_1",
"Sample ID":"XiaChaoYi_A7_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"+CC+Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A7_RP pos.mzML"}
},
{
"Subject ID":"-CC+Met_2",
"Sample ID":"XiaChaoYi_A8_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"-CC+Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A8_RP pos.mzML"}
},
{
"Subject ID":"-CC-Met_3",
"Sample ID":"XiaChaoYi_A9_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"-CC-Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A9_RP pos.mzML"}
},
{
"Subject ID":"+CC+Met_3",
"Sample ID":"XiaChaoYi_A10_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"+CC+Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A10_RP pos.mzML"}
},
{
"Subject ID":"-CC+Met_1",
"Sample ID":"XiaChaoYi_A11_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"-CC+Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A11_RP pos.mzML"}
},
{
"Subject ID":"-CC-Met_2",
"Sample ID":"XiaChaoYi_A12_RP pos",
"Factors":{"Sample source":"HT1080 human epithelial cancer cells","Treatment":"-CC-Met"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME(Raw file name)":"XiaChaoYi_A12_RP pos.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were seeded at a density of 2×106 per well in a 10 cm glass bottom cell culture dish and grown for 12 h in DMEM supplemented with 10% Fetal Bovine Serum（FBS）, 1% Penicillin-Streptomycin(P/S).","COLLECTION_PROTOCOL_FILENAME":"2024-NC.pdf","SAMPLE_TYPE":"HT1080 Human epithelial cancer cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"HT1080 cells were cultured in the medium ± cystine or ± methionine as indicated for 10 h. The metabolites levels were measured by UHPLC-HRMS."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cells were trypsinized, washed and resuspended in methanol: acetonitrile: ddH2O2 (2:2:1, v/v) after indicated treatment. Then subjected to LC/MS analysis at LipidALL Technologies (Changzhou, China). Briefly, polar metabolites were extracted using 1000 µl of ice-cold methanol: H2O (4:1, v/v), and incubated at 2000 × g for 30 min at 4oC. At the end of the incubation, samples were centrifuged for 10 min at 13,000 × g at 4oC. Clean supernatant was transferred to a new tube. Extracts were dried in a centrifugal concentrator.","SAMPLEPREP_PROTOCOL_FILENAME":"2024-NC.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)","SOLVENT_A":"100% water; 0.1% formic acid","SOLVENT_B":"100% acetonitrile","FLOW_GRADIENT":"0 - 1.0 min with 2% B, 1.0 - 6.0 min with 2% - 42% B, 6.0 - 8.0 min with 42% - 65% B, 8.0 - 10.0 min with 65% - 76% B, 10.0 - 11.0 min with 76% - 100% B, 11.0 - 14.0 min with 100% - 100% B.","FLOW_RATE":"0.35 mL/min","COLUMN_TEMPERATURE":"40","METHODS_FILENAME":"2024-NC.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"2024-NC.pdf"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex 5600+ TripleTOF","INSTRUMENT_TYPE":"Triple TOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"MS parameters for detection were: ESI source voltage positive ion mode 5.5 kV, negative ion mode -4.5 kV; vaporizer temperature, 450°C; drying gas (N2) pressure, 50 psi; nebulizer gas (N2) pressure, 50 psi; curtain gas (N2) pressure, 35 psi; The scan range was m/z 60-800. Information-dependent acquisition mode was used for MS/MS analyses of the metabolites. Collision energy was set at (±) 35 ± 15 eV. Data acquisition and processing were performed using Analyst® TF 1.7.1 Software (AB Sciex, Concord, ON, Canada)."},

"MS_METABOLITE_DATA":{
"Units":"Peak area",

"Data":[{"Metabolite":"Butyrylcarnitine","XiaChaoYi_A7_RP pos":"26427.9476","XiaChaoYi_A4_RP pos":"27155.77889","XiaChaoYi_A10_RP pos":"22194.91525","XiaChaoYi_A11_RP pos":"23267.92453","XiaChaoYi_A8_RP pos":"25663.7931","XiaChaoYi_A5_RP pos":"27419.64286","XiaChaoYi_A6_RP pos":"30495.41284","XiaChaoYi_A12_RP pos":"32775","XiaChaoYi_A9_RP pos":"32104"},{"Metabolite":"Dodecanoylcarnitine","XiaChaoYi_A7_RP pos":"2872.489083","XiaChaoYi_A4_RP pos":"4478.39196","XiaChaoYi_A10_RP pos":"2461.864407","XiaChaoYi_A11_RP pos":"1956.981132","XiaChaoYi_A8_RP pos":"2376.724138","XiaChaoYi_A5_RP pos":"2844.642857","XiaChaoYi_A6_RP pos":"3096.330275","XiaChaoYi_A12_RP pos":"3588.333333","XiaChaoYi_A9_RP pos":"2982.4"},{"Metabolite":"Isobutyrylcarnitine","XiaChaoYi_A7_RP pos":"26323.1441","XiaChaoYi_A4_RP pos":"27125.62814","XiaChaoYi_A10_RP pos":"22127.11864","XiaChaoYi_A11_RP pos":"23207.54717","XiaChaoYi_A8_RP pos":"25603.44828","XiaChaoYi_A5_RP pos":"27375","XiaChaoYi_A6_RP 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pos":"87075.37688","XiaChaoYi_A10_RP pos":"67186.44068","XiaChaoYi_A11_RP pos":"62958.49057","XiaChaoYi_A8_RP pos":"76637.93103","XiaChaoYi_A5_RP pos":"81089.28571","XiaChaoYi_A6_RP pos":"109816.5138","XiaChaoYi_A12_RP pos":"85166.66667","XiaChaoYi_A9_RP pos":"91120"},{"Metabolite":"Phosphorylcholine","XiaChaoYi_A7_RP pos":"2096943.231","XiaChaoYi_A4_RP pos":"1934673.367","XiaChaoYi_A10_RP pos":"1691525.424","XiaChaoYi_A11_RP pos":"1512452.83","XiaChaoYi_A8_RP pos":"2015517.241","XiaChaoYi_A5_RP pos":"2042857.143","XiaChaoYi_A6_RP pos":"2071559.633","XiaChaoYi_A12_RP pos":"2007500","XiaChaoYi_A9_RP pos":"2541600"},{"Metabolite":"3-methyl-2-Quinoxalinone","XiaChaoYi_A7_RP pos":"66043.66812","XiaChaoYi_A4_RP pos":"96492.46231","XiaChaoYi_A10_RP pos":"93220.33898","XiaChaoYi_A11_RP pos":"56415.09434","XiaChaoYi_A8_RP pos":"65163.7931","XiaChaoYi_A5_RP pos":"69026.78571","XiaChaoYi_A6_RP pos":"88458.7156","XiaChaoYi_A12_RP pos":"118333.3333","XiaChaoYi_A9_RP pos":"78448"}],

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(min)":"1.59","Database ID":"HMDB0004827","Formula":"C7H13NO2"},{"Metabolite":"Prolylhydroxyproline","Experimental m/z":"229.1173","Retention time (min)":"1.69","Database ID":"HMDB0006695","Formula":"C10H16N2O4"},{"Metabolite":"Pyroglutamic acid","Experimental m/z":"130.0498","Retention time (min)":"2.66","Database ID":"HMDB0000267","Formula":"C5H7NO3"},{"Metabolite":"Pyroglutamine","Experimental m/z":"129.0656","Retention time (min)":"1.46","Database ID":"HMDB0062558","Formula":"C5H8N2O2"},{"Metabolite":"S-Methyl-L-cysteinesulfoxide","Experimental m/z":"152.0313","Retention time (min)":"1.33","Database ID":"HMDB0029432","Formula":"C4H9NO3S"},{"Metabolite":"Symmetric dimethylarginine","Experimental m/z":"203.1517","Retention time (min)":"1.49","Database ID":"HMDB0001539","Formula":"C8H18N4O2"},{"Metabolite":"Taurine","Experimental m/z":"126.0214","Retention time (min)":"1.33","Database ID":"HMDB0000251","Formula":"C2H7NO3S"},{"Metabolite":"4-Hydroxyproline","Experimental 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m/z":"138.0545","Retention time (min)":"5.86","Database ID":"HMDB0001123","Formula":"C7H7NO2"},{"Metabolite":"Hippuric acid","Experimental m/z":"180.0649","Retention time (min)":"5.87","Database ID":"HMDB0000714","Formula":"C9H9NO3"},{"Metabolite":"1-(beta-D-Ribofuranosyl)-1,4-dihydronicotinamide","Experimental m/z":"257.1149","Retention time (min)":"3.9","Database ID":"HMDB0011648","Formula":"C11H16N2O5"},{"Metabolite":"2-Deoxygalactopyranose","Experimental m/z":"165.0708","Retention time (min)":"1.54","Database ID":"HMDB0012327","Formula":"C6H12O5"},{"Metabolite":"D-Fructofuranose 1,2'':2,3''-dianhydride","Experimental m/z":"325.1125","Retention time (min)":"1.57","Database ID":"KEGG C04420","Formula":"C12H20O10"},{"Metabolite":"Trehalose","Experimental m/z":"343.1241","Retention time (min)":"1.58","Database ID":"HMDB0000975","Formula":"C12H22O11"},{"Metabolite":"4-Trimethylammoniobutanoic acid","Experimental m/z":"146.1172","Retention time (min)":"4.89","Database ID":"HMDB0001161","Formula":"C7H15NO2"},{"Metabolite":"Glycerophosphocholine","Experimental m/z":"258.1094","Retention time (min)":"1.36","Database ID":"HMDB0000086","Formula":"C8H20NO6P"},{"Metabolite":"LysoPC(14:0)","Experimental m/z":"468.308","Retention time (min)":"10.33","Database ID":"HMDB0010379","Formula":"C22H46NO7P"},{"Metabolite":"LysoPC(16:0)","Experimental m/z":"497.3435","Retention time (min)":"11.69","Database ID":"HMDB0010382","Formula":"C24H50NO7P"},{"Metabolite":"LysoPC(P-16:0/0:0)","Experimental m/z":"480.3433","Retention time (min)":"12.11","Database ID":"HMDB0010407","Formula":"C24H50NO6P"},{"Metabolite":"PC (16:0)","Experimental m/z":"482.3585","Retention time (min)":"12.14","Database ID":"METLIN40386","Formula":"C24H52NO6P"},{"Metabolite":"LysoPE(16:0)","Experimental m/z":"454.2916","Retention time (min)":"11.62","Database ID":"HMDB0011473","Formula":"C21H44NO7P"},{"Metabolite":"LysoPE(18:1)","Experimental m/z":"480.3054","Retention time (min)":"11.95","Database ID":"HMDB0011505","Formula":"C23H46NO7P"},{"Metabolite":"LysoPE(18:2)","Experimental m/z":"478.2915","Retention time (min)":"11.07","Database ID":"HMDB0011507","Formula":"C23H44NO7P"},{"Metabolite":"SAH","Experimental m/z":"385.1299","Retention time (min)":"3.31","Database ID":"HMDB0000939","Formula":"C14H20N6O5S"},{"Metabolite":"5''-Methylthioadenosine","Experimental m/z":"298.0969","Retention time (min)":"4.77","Database ID":"HMDB0001173","Formula":"C11H15N5O3S"},{"Metabolite":"SAM","Experimental m/z":"399.1452","Retention time (min)":"1.36","Database ID":"HMDB0001185","Formula":"C15H22N6O5S"},{"Metabolite":"2-Acetylpyrazine","Experimental m/z":"123.055","Retention time (min)":"2.14","Database ID":"HMDB0031861","Formula":"C6H6N2O"},{"Metabolite":"L-Kynurenine","Experimental m/z":"209.0919","Retention time (min)":"4.34","Database ID":"HMDB0000684","Formula":"C10H12N2O3"},{"Metabolite":"2-Piperidinone","Experimental m/z":"100.0754","Retention time (min)":"4.44","Database ID":"HMDB0011749","Formula":"C5H9NO"},{"Metabolite":"Lumichrome","Experimental m/z":"243.0882","Retention time (min)":"7.08","Database ID":"KEGG C01727","Formula":"C12H10N4O2"},{"Metabolite":"1-Methyladenosine","Experimental m/z":"282.1196","Retention time (min)":"2.29","Database ID":"HMDB0003331","Formula":"C11H15N5O4"},{"Metabolite":"Adenosine","Experimental m/z":"268.1043","Retention time (min)":"3.69","Database ID":"HMDB0000050","Formula":"C10H13N5O4"},{"Metabolite":"N2,N2-Dimethylguanosine","Experimental m/z":"312.1289","Retention time (min)":"4.39","Database ID":"HMDB0004824","Formula":"C12H17N5O5"},{"Metabolite":"Succinyladenosine","Experimental m/z":"384.1149","Retention time (min)":"4.37","Database ID":"HMDB0000912","Formula":"C14H17N5O8"},{"Metabolite":"Guanosine monophosphate","Experimental m/z":"364.0642","Retention time (min)":"2.13","Database ID":"HMDB0001397","Formula":"C10H14N5O8P"},{"Metabolite":"1-Methylguanine","Experimental m/z":"166.0719","Retention time (min)":"2.38","Database ID":"HMDB0003282","Formula":"C6H7N5O"},{"Metabolite":"Allopurinol","Experimental m/z":"137.0447","Retention time (min)":"3.82","Database ID":"HMDB0014581","Formula":"C5H4N4O"},{"Metabolite":"Guanine","Experimental m/z":"152.0564","Retention time (min)":"3.77","Database ID":"HMDB0000132","Formula":"C5H5N5O"},{"Metabolite":"Hypoxanthine","Experimental m/z":"137.0445","Retention time (min)":"2.42","Database ID":"HMDB00157","Formula":"C5H4N4O"},{"Metabolite":"1-methylnicotinamide","Experimental m/z":"173.0478","Retention time (min)":"1.09","Database ID":"PubChem 1005-24-9","Formula":"C7H9ClN2O"},{"Metabolite":"2-Methylnicotinamide","Experimental m/z":"137.0703","Retention time (min)":"8.17","Database ID":"HMDB0059711","Formula":"C7H8N2O"},{"Metabolite":"N1-Methyl-2-pyridone-5-carboxamide","Experimental m/z":"153.0653","Retention time (min)":"3.88","Database ID":"HMDB0004193","Formula":"C7H8N2O2"},{"Metabolite":"Niacinamide","Experimental m/z":"123.0553","Retention time (min)":"2.31","Database ID":"HMDB0001406","Formula":"C6H6N2O"},{"Metabolite":"Cytidine","Experimental m/z":"244.0907","Retention time (min)":"1.92","Database ID":"HMDB0000089","Formula":"C9H13N3O5"},{"Metabolite":"CDP-ethanolamine","Experimental m/z":"447.0676","Retention time (min)":"1.42","Database ID":"HMDB0001564","Formula":"C11H20N4O11P2"},{"Metabolite":"Cytosine","Experimental m/z":"112.0497","Retention time (min)":"1.91","Database ID":"HMDB0000630","Formula":"C4H5N3O"},{"Metabolite":"Thymine","Experimental m/z":"127.0498","Retention time (min)":"4","Database ID":"HMDB0000262","Formula":"C5H6N2O2"},{"Metabolite":"Uracil","Experimental m/z":"113.0338","Retention time (min)":"3.4","Database ID":"HMDB0000300","Formula":"C4H4N2O2"},{"Metabolite":"Pyrrolidine","Experimental m/z":"72.0806","Retention time (min)":"1.94","Database ID":"HMDB0031641","Formula":"C4H9N"},{"Metabolite":"Acetylcholine","Experimental m/z":"146.1174","Retention time (min)":"1.5","Database ID":"HMDB0000895","Formula":"C7H15NO2"},{"Metabolite":"Choline","Experimental m/z":"104.1066","Retention time (min)":"1.32","Database ID":"HMDB00097","Formula":"C5H13NO"},{"Metabolite":"L-Carnitine","Experimental m/z":"162.1111","Retention time (min)":"1.38","Database ID":"HMDB0000062","Formula":"C7H15NO3"},{"Metabolite":"Phosphorylcholine","Experimental m/z":"184.0724","Retention time (min)":"1.34","Database ID":"HMDB0001565","Formula":"C5H14NO4P"},{"Metabolite":"3-methyl-2-Quinoxalinone","Experimental m/z":"161.0717","Retention time (min)":"8.16","Database ID":"PubChem 26384","Formula":"C9H8N2O"}]
}

}