{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002529","ANALYSIS_ID":"AN004163","VERSION":"1","CREATED_ON":"March 28, 2023, 10:11 am"},

"PROJECT":{"PROJECT_TITLE":"Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress","PROJECT_SUMMARY":"Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs to maintain survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of murine pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors (Sullivan et al., 2019a). Here, we develop Tumor Interstitial Fluid Medium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling study of PDAC metabolism under physiological nutrition. We show that PDAC cells cultured in TIFM, compared to standard laboratory models, adopt a cellular state more similar to PDAC cells in tumors. Further, using the TIFM model we identified arginine biosynthesis as a metabolic adaptation PDAC cells engage to cope with microenvironmental arginine starvation driven by myeloid cells in PDAC tumors. Altogether, these data show that nutrient availability in tumors is an important determinant of cancer cell metabolism and behavior, and cell culture models that incorporate physiological nutrient availability have improved fidelity and enable the discovery of novel cancer metabolic phenotypes.","INSTITUTE":"University of Chicago","LAST_NAME":"Apiz Saab","FIRST_NAME":"Juan","ADDRESS":"929 E. 57th St.","EMAIL":"japizsaab@uchicago.edu","PHONE":"7738346506"},

"STUDY":{"STUDY_TITLE":"In vivo 15N2-glutamine tracing by jugular vein infusion in PDAC-tumor bearing Lyz2-Arg1 and control mice","STUDY_SUMMARY":"We assessed the relative levels of urea cycle related metabolites in PDAC tumors in Lyz2-Cre+/+; Arg1fl/fl compared to Arg1fl/fl control host animals.","INSTITUTE":"University of Chicago","LAST_NAME":"Apiz Saab","FIRST_NAME":"Juan","ADDRESS":"929 E. 57th St.","EMAIL":"japizsaab@uchicago.edu","PHONE":"7738346506"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"0785-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0785-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0785-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0785-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0785-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0785-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0785-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0785-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0787-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0787-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0787-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0787-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0787-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0787-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0787-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0787-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0788-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0788-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0788-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0788-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0788-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0788-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0788-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0788-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0789-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0789-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0789-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0789-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0789-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0789-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0789-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_0789-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35066-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35066-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35066-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35066-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35066-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35066-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35066-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35066-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35089-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35089-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35089-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35089-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35089-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35089-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35089-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35089-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35096-0",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35096-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35096-120",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35096-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35096-240",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35096-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35096-30",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35096-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35097-0",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35097-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35097-120",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35097-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35097-240",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35097-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35097-30",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35097-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35098-0",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35098-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35098-120",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35098-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35098-240",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35098-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35098-30",
"Factors":{"Sample type":"Plasma","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35098-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35465-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35465-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35465-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35465-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35465-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35465-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35465-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35465-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35469-0",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35469-0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35469-120",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35469-120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35469-240",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35469-240.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35469-30",
"Factors":{"Sample type":"Plasma","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"Plasma_A35469-30.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0785_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"0785_tumor_Arg1_KO.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0787_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"0787_tumor_Arg1_KO.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0788_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"0788_tumor_Arg1_KO.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"0789_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"0789_tumor_Arg1_KO.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35089_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"A35089_tumor_Arg1_KO.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35096_tumor_Control",
"Factors":{"Sample type":"Tumor","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"A35096_tumor_Control.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35097_tumor_Control",
"Factors":{"Sample type":"Tumor","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"A35097_tumor_Control.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35098_tumor_Control",
"Factors":{"Sample type":"Tumor","Condition":"Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"A35098_tumor_Control.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35465_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"A35465_tumor_Arg1_KO.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35466_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"A35466_tumor_Arg1_KO.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A35469_tumor_Arg1_KO",
"Factors":{"Sample type":"Tumor","Condition":"Lyz2-Cre+/+; Arg1fl/fl"},
"Additional sample data":{"RAW_FILE_NAME":"A35469_tumor_Arg1_KO.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"6~8-month-old female & male Lyz2-Cre +/+; Arg1fl/fl and litter mate control Arg1fl/fl mice with murine PDAC orthotopic tumors underwent dual jugular vein & carotid artery catheterization surgery. On day 5 of post recovery, mice received a 0.28 mg/g 10 min. bolus followed by a continuous 4 hr. infusion 0.005 mg/g/min infusion of 15N2-glutamine (Cambridge Isotope Laboratory #NLM-1328-PK). Plasma samples were taken at time points: 0' 15' 30' 60' 120' 180’ 240’. Tumors and tissues were harvested at 240’ and immediately snap frozen with liquid nitrogen stored at -80°C prior to analysis.","SAMPLE_TYPE":"Tumor, plasma"},

"TREATMENT":{"TREATMENT_SUMMARY":"6~8-month-old female & male Lyz2-Cre +/+; Arg1fl/fl and litter mate control Arg1fl/fl mice with murine PDAC orthotopic tumors underwent dual jugular vein & carotid artery catheterization surgery. On day 5 of post recovery, mice received a 0.28 mg/g 10 min. bolus followed by a continuous 4 hr. infusion 0.005 mg/g/min infusion of 15N2-glutamine (Cambridge Isotope Laboratory #NLM-1328-PK). Plasma samples were taken at time points: 0' 15' 30' 60' 120' 180’ 240’. Tumors and tissues were harvested at 240’ and immediately snap frozen with liquid nitrogen stored at -80°C prior to analysis."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cryogenically frozen tumor pieces were ground to a fine homogenous powder with a liquid nitrogen cooled mortar and pestle. ~30mg of tissue powder was weighed into sample tubes, and metabolites were extracted with 600µL HPLC grade methanol, 300µL HPLC grade water, and 400µL chloroform. Samples were vortexed for 10min at 4°C, centrifuged 21,000xg at 4°C for 10 min. 400µL of the aqueous top layer was removed into a new tube and dried under nitrogen. Dried tumor extracts were resuspended in 100µL HPLC grade water and LC-MS analysis was performed as described before(Sullivan et al., 2019b, 2019a). For plasma samples, we extracted polar metabolites from 5µL of sample using 45µL of a 75:25:0.1 HPLC grade acetonitrile:methanol:formic acid extraction mix. Samples in extraction mix were vortexed for 10 min at 4°C and centrifugated at 15,000x rpm for 10 min at 4°C to pellet insoluble material. 20µL of the soluble polar metabolite supernatant was moved to sample vials for analysis by LC-MS."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Atlantis BEH Z-HILIC (2.1x150 mm, 2.5 µM; part # 186009990; Waters Corporation)","SOLVENT_A":"20 mM ammonium bicarbonate at pH 9.6, adjusted by ammonium hydroxide addition","SOLVENT_B":"100% Acetonitrile","FLOW_GRADIENT":"0 minute: 85% B, 0.5 minute: 85% B, 18 minutes: 20% B, 20 minutes: 20% B, 20.5 minutes: 85% B and 28 minutes: 85% B","FLOW_RATE":"0.2 mL/minute","COLUMN_TEMPERATURE":"30°C"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap IQ-X Tribrid","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"Data acquisition was done using the Xcalibur software (Thermo Scientific) in full-scan mode with a range of 70-1000 m/z at 60K. Metabolite identification was done by matching the retention time and MS/MS fragmentation to the reference standards. Data analysis was performed using Tracefinder 5.1 software (Thermo Scientific)."},

"MS_METABOLITE_DATA":{
"Units":"Natural abundance corrected percentages",

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"Metabolites":[{"metabolite_name":"Glutamine_M+0"},{"metabolite_name":"Glutamine_M+1"},{"metabolite_name":"Glutamine_M+2"},{"metabolite_name":"Aspartate_M+0"},{"metabolite_name":"Aspartate_M+1"},{"metabolite_name":"Citrulline _M+0"},{"metabolite_name":"Citrulline _M+1"},{"metabolite_name":"Citrulline _M+2"},{"metabolite_name":"Citrulline _M+3"},{"metabolite_name":"Glutamate _M+0"},{"metabolite_name":"Glutamate _M+1"},{"metabolite_name":"Argininosuccinate _M+0"},{"metabolite_name":"Argininosuccinate _M+1"},{"metabolite_name":"Argininosuccinate _M+2"},{"metabolite_name":"Argininosuccinate _M+3"},{"metabolite_name":"Argininosuccinate _M+4"},{"metabolite_name":"Arginine _M+0"},{"metabolite_name":"Arginine _M+1"},{"metabolite_name":"Arginine _M+2"},{"metabolite_name":"Arginine _M+3"},{"metabolite_name":"Ornithine _M+0"},{"metabolite_name":"Ornithine _M+1"},{"metabolite_name":"Ornithine _M+2"},{"metabolite_name":"Carbamoyl_aspartate _M+0"},{"metabolite_name":"Carbamoyl_aspartate _M+1"},{"metabolite_name":"Carbamoyl_aspartate _M+2"},{"metabolite_name":"Dihydroorotate _M+0"},{"metabolite_name":"Dihydroorotate _M+1"},{"metabolite_name":"Dihydroorotate _M+2"},{"metabolite_name":"Orotate _M+0"},{"metabolite_name":"Orotate _M+1"},{"metabolite_name":"Orotate _M+2"},{"metabolite_name":"UMP _M+0"},{"metabolite_name":"UMP _M+1"},{"metabolite_name":"UMP _M+2"},{"metabolite_name":"UDP _M+0"},{"metabolite_name":"UDP _M+1"},{"metabolite_name":"UDP _M+2"},{"metabolite_name":"UTP _M+0"},{"metabolite_name":"UTP _M+1"},{"metabolite_name":"UTP _M+2"},{"metabolite_name":"Putrescine _M+0"},{"metabolite_name":"Putrescine _M+1"},{"metabolite_name":"Putrescine _M+2"}]
}

}