{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002202","ANALYSIS_ID":"AN003605","VERSION":"1","CREATED_ON":"June 29, 2022, 6:30 am"},

"PROJECT":{"PROJECT_TITLE":"Metabolic profiling of induced acute pancreatitis and pancreatic cancer progression in a mutant Kras mouse model","PROJECT_TYPE":"NMR-based metabolomics","PROJECT_SUMMARY":"Untargeted Nuclear Magnetic Resonance (NMR) metabolomics of polar extracts from the pancreata of a caerulin-induced mouse model of pancreatitis (Pt) and of a transgenic mouse model of pancreatic cancer (PCa) were used to find metabolic markers of Pt and to characterize the metabolic changes accompanying PCa progression. Using multivariate analysis a 10-metabolite metabolic signature specific to Pt tissue was found to distinguish the benign condition from both normal tissue and precancerous tissue (low grade pancreatic intraepithelial neoplasia, PanIN, lesions).","INSTITUTE":"University of Aveiro","DEPARTMENT":"Department of Chemistry and CICECO-Aveiro Institute of Materials","LABORATORY":"Metabolomics from Ana M. Gil","LAST_NAME":"Carneiro","FIRST_NAME":"Tatiana J.","ADDRESS":"Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal","EMAIL":"tatiana.joao@ua.pt","PHONE":"+351 234 370 200"},

"STUDY":{"STUDY_TITLE":"Metabolic profiling of induced acute pancreatitis and pancreatic cancer progression in a mutant Kras mouse model","STUDY_TYPE":"NMR-based metabolomics","STUDY_SUMMARY":"Untargeted Nuclear Magnetic Resonance (NMR) metabolomics of polar extracts from the pancreata of a caerulin-induced mouse model of pancreatitis (Pt) and of a transgenic mouse model of pancreatic cancer (PCa) were used to find metabolic markers of Pt and to characterize the metabolic changes accompanying PCa progression. Using multivariate analysis a 10-metabolite metabolic signature specific to Pt tissue was found to distinguish the benign condition from both normal tissue and precancerous tissue (low grade pancreatic intraepithelial neoplasia, PanIN, lesions). The mice pancreata showed significant changes in the progression from normal tissue, through low-grade and high-grade PanIN lesions to pancreatic ductal adenocarcinoma (PDA). These included increased lactate production, amino acid changes consistent with enhanced anaplerosis, decreased concentrations of intermediates in membrane biosynthesis (phosphocholine and phosphoethanolamine) and decreased glycosylated uridine phosphates, reflecting activation of the hexosamine biosynthesis pathway and protein glycosylation.","INSTITUTE":"University of Aveiro","DEPARTMENT":"Department of Chemistry and CICECO-Aveiro Institute of Materials","LABORATORY":"Metabolomics from Ana M. Gil","LAST_NAME":"Carneiro","FIRST_NAME":"Tatiana","ADDRESS":"Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal","EMAIL":"tatiana.joao@ua.pt","PHONE":"+351 234 370 200","NUM_GROUPS":"6","TOTAL_SUBJECTS":"40"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6 (WT); LSL-KrasG12D/+ - p48Cre/+; LSL-KrasG12/D+; LSL-Tpr53R172H/+; Pdx-1-Cre","AGE_OR_AGE_RANGE":"1.5 to 9 months","ANIMAL_LIGHT_CYCLE":"12h light/dark cycles (7.00 AM lights on)","ANIMAL_FEED":"ad libitum","ANIMAL_WATER":"ad libitum","ANIMAL_INCLUSION_CRITERIA":"Healthy animails","SPECIES_GROUP":"C57BL/6 (WT); LSL-KrasG12D/+ - p48Cre/+; LSL-KrasG12/D+; LSL-Tpr53R172H/+; Pdx-1-Cre"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"ES250414-N1",
"Factors":{"Treatment_group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-N1"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-N2",
"Factors":{"Treatment_group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-N2"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-N3",
"Factors":{"Treatment_group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-N3"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-N4",
"Factors":{"Treatment_group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-N4"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121016-22_N",
"Factors":{"Treatment_group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121016-22_N"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121016-24_N",
"Factors":{"Treatment_group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121016-24_N"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121016-40_N",
"Factors":{"Treatment_group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121016-40_N"}
},
{
"Subject ID":"-",
"Sample ID":"5848_HG",
"Factors":{"Treatment_group":"High-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"5848_HG"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-HG1",
"Factors":{"Treatment_group":"High-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-HG1"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-HG10",
"Factors":{"Treatment_group":"High-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-HG10"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-HG4",
"Factors":{"Treatment_group":"High-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-HG4"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-HG5",
"Factors":{"Treatment_group":"High-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-HG5"}
},
{
"Subject ID":"-",
"Sample ID":"HG14",
"Factors":{"Treatment_group":"High-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"HG14"}
},
{
"Subject ID":"-",
"Sample ID":"Pancreas46-HG",
"Factors":{"Treatment_group":"High-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"Pancreas46-HG"}
},
{
"Subject ID":"-",
"Sample ID":"LG11",
"Factors":{"Treatment_group":"Low-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"LG11"}
},
{
"Subject ID":"-",
"Sample ID":"LG14",
"Factors":{"Treatment_group":"Low-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"LG14"}
},
{
"Subject ID":"-",
"Sample ID":"LG15",
"Factors":{"Treatment_group":"Low-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"LG15"}
},
{
"Subject ID":"-",
"Sample ID":"ajw_eva5134_060616_LG",
"Factors":{"Treatment_group":"Low-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"ajw_eva5134_060616_LG"}
},
{
"Subject ID":"-",
"Sample ID":"ajw_eva5846_060614_LG",
"Factors":{"Treatment_group":"Low-grade PanIN lesion"},
"Additional sample data":{"RAW_FILE_NAME":"ajw_eva5846_060614_LG"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-PDA-KPC",
"Factors":{"Treatment_group":"Pancreatic ductal adenocarcinoma"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-PDA-KPC"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-PDA1",
"Factors":{"Treatment_group":"Pancreatic ductal adenocarcinoma"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-PDA1"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121016-48_PDA",
"Factors":{"Treatment_group":"Pancreatic ductal adenocarcinoma"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121016-48_PDA"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121102-31_PDA",
"Factors":{"Treatment_group":"Pancreatic ductal adenocarcinoma"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121102-31_PDA"}
},
{
"Subject ID":"-",
"Sample ID":"Pancreas57_PDA",
"Factors":{"Treatment_group":"Pancreatic ductal adenocarcinoma"},
"Additional sample data":{"RAW_FILE_NAME":"Pancreas57_PDA"}
},
{
"Subject ID":"-",
"Sample ID":"Pancreas58_PDA",
"Factors":{"Treatment_group":"Pancreatic ductal adenocarcinoma"},
"Additional sample data":{"RAW_FILE_NAME":"Pancreas58_PDA"}
},
{
"Subject ID":"-",
"Sample ID":"Pt2",
"Factors":{"Treatment_group":"Pancreatitis"},
"Additional sample data":{"RAW_FILE_NAME":"Pt2"}
},
{
"Subject ID":"-",
"Sample ID":"Pt3",
"Factors":{"Treatment_group":"Pancreatitis"},
"Additional sample data":{"RAW_FILE_NAME":"Pt3"}
},
{
"Subject ID":"-",
"Sample ID":"Pt4",
"Factors":{"Treatment_group":"Pancreatitis"},
"Additional sample data":{"RAW_FILE_NAME":"Pt4"}
},
{
"Subject ID":"-",
"Sample ID":"Pt5",
"Factors":{"Treatment_group":"Pancreatitis"},
"Additional sample data":{"RAW_FILE_NAME":"Pt5"}
},
{
"Subject ID":"-",
"Sample ID":"Pt6",
"Factors":{"Treatment_group":"Pancreatitis"},
"Additional sample data":{"RAW_FILE_NAME":"Pt6"}
},
{
"Subject ID":"-",
"Sample ID":"Pt7",
"Factors":{"Treatment_group":"Pancreatitis"},
"Additional sample data":{"RAW_FILE_NAME":"Pt7"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-S2-sarc",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-S2-sarc"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-S3-sarc",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-S3-sarc"}
},
{
"Subject ID":"-",
"Sample ID":"ES250414-S4-sarc",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"ES250414-S4-sarc"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121016-30_SARC",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121016-30_SARC"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121016-50_SARC",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121016-50_SARC"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121016-53_SARC",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121016-53_SARC"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121102-34_SARC",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121102-34_SARC"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121102-37_SARC",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121102-37_SARC"}
},
{
"Subject ID":"-",
"Sample ID":"MB-ES-121102-38_SARC",
"Factors":{"Treatment_group":"Sarcomatoid"},
"Additional sample data":{"RAW_FILE_NAME":"MB-ES-121102-38_SARC"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mice were sacrificed by cervical dislocation and pancreatic tissue rapidly excised and freeze-clamped using liquid nitrogen-cooled tongs.","SAMPLE_TYPE":"Pancreas"},

"TREATMENT":{"TREATMENT_SUMMARY":"The control group (N, normal tissue, n=7) comprised animals that did not develop lesions or tumors (C57BL/6 wt mice); the pancreatitis group (Pt, n=6) comprised C57BL/6 wt mice in which acute pancreatitis was induced by six hourly intraperitoneal 50 ug/kg caerulein (Sigma-Aldrich, Dorset, UK) injections; the low grade lesion group (LG, n=5) comprised 4-month old KC (LSL-KrasG12D/+ - p48Cre/+) mice with predominant LG PanIN lesions (mPanIN 1 and 1A); the high grade lesion group (HG, n=7) comprised 9-month old KC mice with predominant HG PanIN lesions (mPanIN 2 and 3); the spontaneous pancreatic ductal adenocarcinoma (PDA, n=6) and sarcomatoid (Sarc., n=9) groups corresponded to 3-6 month old KPC (LSL-KrasG12/D+;LSL-Tpr53R172H/+;Pdx-1-Cre) mice. Tumors were studied when they were less than 5 mm in diameter."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Tissues (weights in the 60-120 mg range) were homogenized (ca. 200mg/mL) in 50 mM HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), 1 mM EDTA (ethylenediaminetetraacetic acid), 0.7% sodium deoxy- cholate, 1% Nonidet P-40, 0.5 M lithium chloride, pH 7.6, using a Precellys 24 homogeniser (Stretton Scientific, Stretton, UK) and then extracted in methanol:chloroform:water.","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACTION_METHOD":"Biphasic method (methanol/ chloroform/ water)","EXTRACT_STORAGE":"-80℃"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR","LABORATORY_NAME":"Metabolomics Ana M. Gil","SOFTWARE_VERSION":"Topspin 3.2"},

"NM":{"INSTRUMENT_NAME":"Bruker 600 MHz NMR spectrometer","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","NMR_COMMENTS":"1st subfolder contains raw spectra; 2nd subfolder contains manually processed spectra","FIELD_FREQUENCY_LOCK":"H2O+D2O for 2H","SPECTROMETER_FREQUENCY":"600MHz","NMR_SOLVENT":"D2O","NMR_TUBE_SIZE":"5mm","SHIMMING_METHOD":"Topshim","RECEIVER_GAIN":"724.1","CHEMICAL_SHIFT_REF_CPD":"3-(trimethylsilyl)-2,2’,3,3’-tetradeuteropropionic acid (TSP)","TEMPERATURE":"298K","NUMBER_OF_SCANS":"512","ACQUISITION_TIME":"4.5 s","RELAXATION_DELAY":"12.5 s","SPECTRAL_WIDTH":"7.3 kHz","NUM_DATA_POINTS_ACQUIRED":"32 k","REAL_DATA_POINTS":"64 k","ZERO_FILLING":"64 k (and multiplied by a 0.3 Hz exponential function prior to Fourier transformation)","BASELINE_CORRECTION_METHOD":"Manual","CHEMICAL_SHIFT_REF_STD":"3-(trimethylsilyl)-2,2’,3,3’-tetradeuteropropionic acid (TSP)","NMR_RESULTS_FILE":"ST002202_AN003605_Results.txt UNITS:ppmn"}

}