{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002122","ANALYSIS_ID":"AN003474","VERSION":"1","CREATED_ON":"March 30, 2022, 9:10 pm"},

"PROJECT":{"PROJECT_TITLE":"Functional metabolomics analysis of pancreatic cancer cells Aspc-1 with gemcitabine treatment","PROJECT_TYPE":"Targeted MS quantitative analysis","PROJECT_SUMMARY":"Characteristics of pancreatic cancer cells Aspc-1 metabolomics with gemcitabine and inhibitor IBMX treatment","INSTITUTE":"Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University","DEPARTMENT":"Shanghai Center for Systems Biomedicine","LABORATORY":"Lu Group","LAST_NAME":"Lu","FIRST_NAME":"Haitao","ADDRESS":"800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China","EMAIL":"haitao_lu@sjtu.edu.cn","PHONE":"15221478139"},

"STUDY":{"STUDY_TITLE":"Functional metabolic molecules were identified as novel therapeutic targets to facilitate gemcitabine treatment against pancreatic cancer (Cells metabolomics)","STUDY_SUMMARY":"With the development of frontier technologies in system biology, traditional omics-drove phenotypic studies are insufficient to decipher the diseases. Therefore, for a thorough understanding of the molecular mechanisms of diseases to investigate novel drug targets, traditional phenotypic studies must be broken through to the functional exploration of molecules. Meanwhile, the intuitive role of small molecule compounds (metabolites) in pathogenesis, precision diagnosis and therapy are gradually recognized compared to macromolecules such as DNA, RNA and proteins. Therefore, we pioneeringly proposed Spatial Temporal Operative Real Metabolomics (STORM) strategy that established a relationship between metabolic phenotypes and functions to accurately character abnormal metabolisms and further identify operative functional molecules as novel therapeutic targets. Here, given the difficulty of pancreatic cancer (PC) treatment and the high resistance of clinical drugs, we were committed to explore new targets and drugs of pancreatic cancer from a small molecular functional perspective via STORM strategy. Fortunately, based on targeted metabolomics, we found that gemcitabine, one of the most effective clinical anti-PC drugs, served as a dual modulator that promote the accumulation of functional metabolic molecules in purine metabolism to activate down-streamed kinases. And the quantitative consequences of related enzymes annotated the unique molecular mechanisms of purine metabolism regulations by gemcitabine. Collectively, we broadened the cognitions of gemcitabine in tumor inhibition, providing potential strategies for treating PC with small molecules modification. Even more importantly, with the integration of multiple frontier technologies, the STORM strategy has proven to be well adapted to the phenotypic era of functional molecules devoted to innovate molecule mechanism annotation and therapeutic discovery.","INSTITUTE":"Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University","DEPARTMENT":"Shanghai Center for Systems Biomedicine","LABORATORY":"Lu Group","LAST_NAME":"Lu","FIRST_NAME":"Haitao","ADDRESS":"800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China","EMAIL":"haitao_lu@sjtu.edu.cn","PHONE":"15221478139"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"ASPC-C-1",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-C-1"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-C-2",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-C-2"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-C-3",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-C-3"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-C-4",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-C-4"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-C-5",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-C-5"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-G-1-r002",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-G-1-r002"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-G-2",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-G-2"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-G-3",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-G-3"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-G-4",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-G-4"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-G-5",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-G-5"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-GI-1",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-GI-1"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-GI-2",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-GI-2"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-GI-3",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-GI-3"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-GI-4",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-GI-4"}
},
{
"Subject ID":"-",
"Sample ID":"ASPC-GI-5",
"Factors":{"Treatment":"After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h"},
"Additional sample data":{"RAW_FILE_NAME":"ASPC-GI-5"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After 72 hours of drug treatment, the cells were washed twice with ice PBS and scraped in 80% ice methanol","SAMPLE_TYPE":"Tumor cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were evenly divided into 3 groups of 6 discs each. 24h after cell inoculation, gemcitabine administration group was treated with gemcitabine with final concentration of 50μM for 72h, while the GI group was supplemented with an additional 200μM 3-isobutyl-1-methylxanthine (IBMX) in the culture medium. Meanwhile, the control group was given the same volume of DMSO. One plate of cells was taken from each group for counting, and the rest were collected for metabolite extraction"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The cells were cultured as described above and fixed with 1 ml of 80% ice-cold menthol after being washed twice with ice-cold PBS. The cells were scraped from the plates, and 0.5-mm beads were added to process the cells by grinding and shaking. The supernatants were collected after centrifugation and deproteinized by mixing with 800μL acetonitrile on ice. Then, the supernatants collected and spun down under nitrogen at room temperature. The samples were resuspended in 100 μL of distilled H2O, and 5 μL was used for LC-TQ-MS-based metabolome assay."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Waters Acquity HSS T3 column (100 mm×2.1, 1.8 μm)"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6495 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Agilent MassHunter Workstation Data Acquisition Agilent MassHunter"},

"MS_METABOLITE_DATA":{
"Units":"counts",

"Data":[{"Metabolite":"ATP","ASPC-C-1":"434250.62","ASPC-C-2":"532911.1446","ASPC-C-3":"732486.0849","ASPC-C-4":"808356.5781","ASPC-C-5":"732246.1247","ASPC-G-1-r002":"1015876.132","ASPC-G-2":"887428.432","ASPC-G-3":"1183220.652","ASPC-G-4":"984235.0784","ASPC-G-5":"1101187.344","ASPC-GI-1":"512948.1636","ASPC-GI-2":"595094.365","ASPC-GI-3":"520935.9288","ASPC-GI-4":"580656.959","ASPC-GI-5":"776794.4286"},{"Metabolite":"2-Deoxyadenosine","ASPC-C-1":"145437.3938","ASPC-C-2":"169201.3123","ASPC-C-3":"229617.277","ASPC-C-4":"242758.5989","ASPC-C-5":"407183.5824","ASPC-G-1-r002":"42753.73781","ASPC-G-2":"48477.56265","ASPC-G-3":"48142.98339","ASPC-G-4":"43080.46573","ASPC-G-5":"45986.01672","ASPC-GI-1":"30676.76336","ASPC-GI-2":"39035.97638","ASPC-GI-3":"35478.03218","ASPC-GI-4":"42307.79709","ASPC-GI-5":"36866.22579"},{"Metabolite":"Adenosine","ASPC-C-1":"19087600.76","ASPC-C-2":"24806280.95","ASPC-C-3":"26892679","ASPC-C-4":"27345577.11","ASPC-C-5":"35756956.32","ASPC-G-1-r002":"44918786.15","ASPC-G-2":"33957890.42","ASPC-G-3":"46181003.71","ASPC-G-4":"44650736.47","ASPC-G-5":"43876717.79","ASPC-GI-1":"30121152.48","ASPC-GI-2":"38235586.8","ASPC-GI-3":"39487687.38","ASPC-GI-4":"46218488.82","ASPC-GI-5":"38356066.45"},{"Metabolite":"Inosine-5'-monophosphate","ASPC-C-1":"27795.78179","ASPC-C-2":"19612.13356","ASPC-C-3":"36237.27931","ASPC-C-4":"26397.07759","ASPC-C-5":"38044.14573","ASPC-G-1-r002":"64821.40863","ASPC-G-2":"172997.0716","ASPC-G-3":"103011.6829","ASPC-G-4":"119583.6483","ASPC-G-5":"94267.21935","ASPC-GI-1":"73926.92734","ASPC-GI-2":"81257.60205","ASPC-GI-3":"59902.42506","ASPC-GI-4":"51103.60011","ASPC-GI-5":"55609.26732"},{"Metabolite":"Adenosine 5'-monophosphate","ASPC-C-1":"803614.0528","ASPC-C-2":"566254.7464","ASPC-C-3":"1082537.32","ASPC-C-4":"811667.4394","ASPC-C-5":"1138038.398","ASPC-G-1-r002":"1328055.516","ASPC-G-2":"3019003.309","ASPC-G-3":"1970622.656","ASPC-G-4":"2342649.518","ASPC-G-5":"1950667.963","ASPC-GI-1":"1611003.677","ASPC-GI-2":"1602068.921","ASPC-GI-3":"1431925.071","ASPC-GI-4":"1237743.025","ASPC-GI-5":"1175629.464"},{"Metabolite":"3-Isobutyl-1-methylxanthine","ASPC-C-1":"6007.267394","ASPC-C-2":"3623.849061","ASPC-C-3":"1983.157593","ASPC-C-4":"1493.337642","ASPC-C-5":"1514.176238","ASPC-G-1-r002":"130590.6731","ASPC-G-2":"2419559.715","ASPC-G-3":"9495.494113","ASPC-G-4":"13400.81694","ASPC-G-5":"10904537.66","ASPC-GI-1":"28728742.99","ASPC-GI-2":"25251453.52","ASPC-GI-3":"26224885.33","ASPC-GI-4":"23519451.31","ASPC-GI-5":"28944874.09"},{"Metabolite":"cAMP","ASPC-C-1":"34259.0578","ASPC-C-2":"32323.87926","ASPC-C-3":"30644.01852","ASPC-C-4":"30385.77372","ASPC-C-5":"26978.38562","ASPC-G-1-r002":"50691.97382","ASPC-G-2":"54543.89698","ASPC-G-3":"53023.34764","ASPC-G-4":"49548.39595","ASPC-G-5":"53173.87645","ASPC-GI-1":"33155.10858","ASPC-GI-2":"29973.76835","ASPC-GI-3":"32542.06815","ASPC-GI-4":"31658.97033","ASPC-GI-5":"32597.64737"},{"Metabolite":"Inosine","ASPC-C-1":"1113371.124","ASPC-C-2":"1552869.981","ASPC-C-3":"1760874.816","ASPC-C-4":"1801967.859","ASPC-C-5":"2724419.13","ASPC-G-1-r002":"2573613.509","ASPC-G-2":"1950981.21","ASPC-G-3":"2720401.945","ASPC-G-4":"2529655.388","ASPC-G-5":"2544227.103","ASPC-GI-1":"1771833.954","ASPC-GI-2":"2350199.824","ASPC-GI-3":"2440117.107","ASPC-GI-4":"2904926.202","ASPC-GI-5":"2290984.068"}],

"Metabolites":[{"Metabolite":"ATP","m/z":"508.01","RT":"1.94"},{"Metabolite":"2-Deoxyadenosine","m/z":"252.1","RT":"3.03"},{"Metabolite":"Adenosine","m/z":"268.25","RT":"2.7"},{"Metabolite":"Inosine-5'-monophosphate","m/z":"349.06","RT":"1.32"},{"Metabolite":"Adenosine 5'-monophosphate","m/z":"348.07","RT":"1.32"},{"Metabolite":"3-Isobutyl-1-methylxanthine","m/z":"223.25","RT":"9.08"},{"Metabolite":"cAMP","m/z":"330.22","RT":"3.13"},{"Metabolite":"Inosine","m/z":"269.09","RT":"2.7"}]
}

}