{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002115","ANALYSIS_ID":"AN003513","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"A ferroptosis defense mechanism mediated by glycerol 3-phosphate dehydrogenase 2 in mitochondria","PROJECT_SUMMARY":"Mechanisms of defense against ferroptosis (an iron-dependent form of cell death induced by lipid peroxidation) in cellular organelles remain poorly understood, hindering our ability to target ferroptosis in disease treatment. In this study, metabolomic analyses revealed that treatment of cancer cells with glutathione peroxidase 4 (GPX4) inhibitors results in intracellular glycerol 3-phosphate (G3P) depletion. We further showed that supplementation of cancer cells with G3P attenuates ferroptosis induced by GPX4 inhibitors in a G3P dehydrogenase 2 (GPD2)-dependent manner; GPD2 deletion sensitizes cancer cells to GPX4 inhibition-induced mitochondrial lipid peroxidation and ferroptosis, and combined deletion of GPX4 and GPD2 synergistically suppresses tumor growth by inducing ferroptosis in vivo. Mechanistically, inner mitochondrial membrane-localized GPD2 couples G3P oxidation with ubiquinone reduction to ubiquinol, which acts as a radical-trapping antioxidant to suppress ferroptosis in mitochondria. Taken together, these results reveal that GPD2 participates in ferroptosis defense in mitochondria by generating ubiquinol.","INSTITUTE":"University of Texas MD Anderson Cancer Center","LAST_NAME":"Gan","FIRST_NAME":"Boyi","ADDRESS":"6565 MD Anderson Blvd, Houston, TX 77030","EMAIL":"bgan@mdanderson.org","PHONE":"713-792-8653","DOI":"http://dx.doi.org/10.21228/M8HD8Q"},

"STUDY":{"STUDY_TITLE":"LC-MS analysis of metabolic changes induced by GPX4 inhibitor treatment in cultured HT1080 cells","STUDY_SUMMARY":"HT1080 cells were treated with vehicle (DMSO), RSL3 (10 micromolar), ML210 (10 micromolar), or ML162 (10 micromolar) for 2 hours. Cellular metabolites were then extracted and analyzed by LC-MS.","INSTITUTE":"University of Texas MD Anderson Cancer Center","LAST_NAME":"Gan","FIRST_NAME":"Boyi","ADDRESS":"6565 MD Anderson Blvd, Houston TX, 77030","EMAIL":"bgan@mdanderson.org","PHONE":"713-792-8653","SUBMIT_DATE":"2022-03-02"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","CELL_STRAIN_DETAILS":"HT1080"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"HT1080_DMSO_01",
"Factors":{"Treatment":"DMSO"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_DMSO_01.mzXML","RAW_FILE_NAME":"HT1080_DMSO_01_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_DMSO_02",
"Factors":{"Treatment":"DMSO"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_DMSO_02.mzXML","RAW_FILE_NAME":"HT1080_DMSO_02_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_DMSO_03",
"Factors":{"Treatment":"DMSO"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_DMSO_03.mzXML","RAW_FILE_NAME":"HT1080_DMSO_03_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_ML162_01",
"Factors":{"Treatment":"ML162"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_ML162_01.mzXML","RAW_FILE_NAME":"HT1080_ML162_01_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_ML162_02",
"Factors":{"Treatment":"ML162"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_ML162_02.mzXML","RAW_FILE_NAME":"HT1080_ML162_02_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_ML162_03",
"Factors":{"Treatment":"ML162"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_ML162_03.mzXML","RAW_FILE_NAME":"HT1080_ML162_03_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_ML210_01",
"Factors":{"Treatment":"ML210"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_ML210_01.mzXML","RAW_FILE_NAME":"HT1080_ML210_01_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_ML210_02",
"Factors":{"Treatment":"ML210"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_ML210_02.mzXML","RAW_FILE_NAME":"HT1080_ML210_02_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_ML210_03",
"Factors":{"Treatment":"ML210"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_ML210_03.mzXML","RAW_FILE_NAME":"HT1080_ML210_03_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_RSL3_01",
"Factors":{"Treatment":"RSL3"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_RSL3_01.mzXML","RAW_FILE_NAME":"HT1080_RSL3_01_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_RSL3_02",
"Factors":{"Treatment":"RSL3"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_RSL3_02.mzXML","RAW_FILE_NAME":"HT1080_RSL3_02_HILIC.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"HT1080_RSL3_03",
"Factors":{"Treatment":"RSL3"},
"Additional sample data":{"RAW_FILE_NAME":"HT1080_RSL3_03.mzXML","RAW_FILE_NAME":"HT1080_RSL3_03_HILIC.mzXML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Metabolites were extracted from cells in 35 mm culture plates by rapidly aspirating the culture medium and incubating the plates with 0.6 ml of an 80% methanol: 20% water mixture on a cold block on dry ice for 15 min. Next, the cell material was scraped into Eppendorf tubes pre-chilled on ice. After centrifugation at 13,000 RCF for 5 min at 4 °C, the supernatant was collected into a fresh tube and stored on dry ice until analysis.","SAMPLE_TYPE":"Cultured cells","STORAGE_CONDITIONS":"-80?"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were seeded in 35-mm culture plates. When the cell confluence reached 70-80%, cells were treated with RSL3, ML210, or ML162 for 2 hours."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"For analysis by reverse phase chromatography, just before analysis, 500 µL of extract was dried under a nitrogen gas flow and then resuspended in 100 µL of water. For analysis by HILIC chromatography, the extracts were analyzed directly.","PROCESSING_STORAGE_CONDITIONS":"4?","EXTRACT_STORAGE":"4?"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The gradient was 0 min, 0% B; 2.5 min, 0% B; 5 min, 20% B; 7.5 min, 20% B; 13 min, 55% B; 15.5 min, 95% B; 18.5 min, 95% B; 19 min, 0% B; and 25 min, 0% B. Solvent A was 10 mM tributylamine and 15 mm acetic acid in water; Solvent B was methanol. The injection volume was 10 µL.","INSTRUMENT_NAME":"Thermo Accela 1250","COLUMN_NAME":"Phenomenex Synergi Hydro RP 100 A (100 x 2mm,2.5um)","COLUMN_TEMPERATURE":"40","FLOW_RATE":"200","SOLVENT_A":"100% water; 15 mM acetic acid; 10 mM tributylamine","SOLVENT_B":"100% methanol","CHROMATOGRAPHY_TYPE":"Reversed phase"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"The scan range was 80-1000 m/z. Raw data files were converted to mzXML format using msconvert (ProteoWizard). Data was analyzed in the MAVEN software suite and metabolite assignments were made using a previously generated list of retention times derived from pure standard solutions.","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"Peak area (top)",

"Data":[{"Metabolite":"2-dehydro-D-gluconate","HT1080_DMSO_01":"1681.0630","HT1080_DMSO_02":"1000.0000","HT1080_DMSO_03":"1358.5650","HT1080_ML162_01":"3551.6600","HT1080_ML162_02":"1550.7230","HT1080_ML162_03":"1381.7440","HT1080_ML210_01":"1581.9170","HT1080_ML210_02":"1045.4550","HT1080_ML210_03":"1585.8620","HT1080_RSL3_01":"2785.9410","HT1080_RSL3_02":"1380.2460","HT1080_RSL3_03":"1501.7760"},{"Metabolite":"2-hydroxy-2-methylbutanedioate","HT1080_DMSO_01":"6353728.0000","HT1080_DMSO_02":"5788824.0000","HT1080_DMSO_03":"6473928.0000","HT1080_ML162_01":"5649644.0000","HT1080_ML162_02":"6078020.0000","HT1080_ML162_03":"5790394.0000","HT1080_ML210_01":"6842502.0000","HT1080_ML210_02":"6451418.0000","HT1080_ML210_03":"6515564.0000","HT1080_RSL3_01":"5665662.0000","HT1080_RSL3_02":"6206106.0000","HT1080_RSL3_03":"6323622.0000"},{"Metabolite":"2-keto-isovalerate","HT1080_DMSO_01":"89396.9300","HT1080_DMSO_02":"52462.9800","HT1080_DMSO_03":"93677.7300","HT1080_ML162_01":"163184.0000","HT1080_ML162_02":"73002.4500","HT1080_ML162_03":"72975.5900","HT1080_ML210_01":"72392.2900","HT1080_ML210_02":"80587.6500","HT1080_ML210_03":"85590.5900","HT1080_RSL3_01":"158797.7000","HT1080_RSL3_02":"89711.1500","HT1080_RSL3_03":"93519.4700"},{"Metabolite":"3-phosphoglycerate","HT1080_DMSO_01":"82959.7000","HT1080_DMSO_02":"66399.7500","HT1080_DMSO_03":"61797.7700","HT1080_ML162_01":"14526.6600","HT1080_ML162_02":"55861.2300","HT1080_ML162_03":"55704.5700","HT1080_ML210_01":"52988.5300","HT1080_ML210_02":"32311.1400","HT1080_ML210_03":"49360.6700","HT1080_RSL3_01":"10274.2500","HT1080_RSL3_02":"54527.7500","HT1080_RSL3_03":"45729.1800"},{"Metabolite":"4-aminobutyrate","HT1080_DMSO_01":"1051829.0000","HT1080_DMSO_02":"751368.5000","HT1080_DMSO_03":"940448.7000","HT1080_ML162_01":"458982.6000","HT1080_ML162_02":"791705.6000","HT1080_ML162_03":"712483.8000","HT1080_ML210_01":"919933.8000","HT1080_ML210_02":"863733.8000","HT1080_ML210_03":"787778.1000","HT1080_RSL3_01":"485094.7000","HT1080_RSL3_02":"704948.9000","HT1080_RSL3_03":"704682.7000"},{"Metabolite":"4-pyridoxic 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