Summary of Study ST002202
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001405. The data can be accessed directly via it's Project DOI: 10.21228/M83T37 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002202 |
| 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 |
| tatiana.joao@ua.pt | |
| Phone | +351 234 370 200 |
| Submit Date | 2022-05-09 |
| Num Groups | 6 |
| Total Subjects | 40 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | 1r |
| Analysis Type Detail | NMR |
| Release Date | 2022-09-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001405 |
| Project DOI: | doi: 10.21228/M83T37 |
| 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 |
Subject:
| Subject ID: | SU002288 |
| 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 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment_group |
|---|---|---|
| SA211320 | MB-ES-121016-40_N | Control |
| SA211321 | ES250414-N1 | Control |
| SA211322 | MB-ES-121016-22_N | Control |
| SA211323 | MB-ES-121016-24_N | Control |
| SA211324 | ES250414-N2 | Control |
| SA211325 | ES250414-N3 | Control |
| SA211326 | ES250414-N4 | Control |
| SA211327 | HG14 | High-grade PanIN lesion |
| SA211328 | Pancreas46-HG | High-grade PanIN lesion |
| SA211329 | ES250414-HG5 | High-grade PanIN lesion |
| SA211330 | ES250414-HG4 | High-grade PanIN lesion |
| SA211331 | ES250414-HG1 | High-grade PanIN lesion |
| SA211332 | 5848_HG | High-grade PanIN lesion |
| SA211333 | ES250414-HG10 | High-grade PanIN lesion |
| SA211334 | ajw_eva5846_060614_LG | Low-grade PanIN lesion |
| SA211335 | ajw_eva5134_060616_LG | Low-grade PanIN lesion |
| SA211336 | LG15 | Low-grade PanIN lesion |
| SA211337 | LG11 | Low-grade PanIN lesion |
| SA211338 | LG14 | Low-grade PanIN lesion |
| SA211339 | Pancreas58_PDA | Pancreatic ductal adenocarcinoma |
| SA211340 | Pancreas57_PDA | Pancreatic ductal adenocarcinoma |
| SA211341 | ES250414-PDA1 | Pancreatic ductal adenocarcinoma |
| SA211342 | MB-ES-121102-31_PDA | Pancreatic ductal adenocarcinoma |
| SA211343 | ES250414-PDA-KPC | Pancreatic ductal adenocarcinoma |
| SA211344 | MB-ES-121016-48_PDA | Pancreatic ductal adenocarcinoma |
| SA211345 | Pt7 | Pancreatitis |
| SA211346 | Pt5 | Pancreatitis |
| SA211347 | Pt6 | Pancreatitis |
| SA211348 | Pt3 | Pancreatitis |
| SA211349 | Pt2 | Pancreatitis |
| SA211350 | Pt4 | Pancreatitis |
| SA211351 | MB-ES-121102-34_SARC | Sarcomatoid |
| SA211352 | MB-ES-121102-37_SARC | Sarcomatoid |
| SA211353 | MB-ES-121102-38_SARC | Sarcomatoid |
| SA211354 | MB-ES-121016-53_SARC | Sarcomatoid |
| SA211355 | ES250414-S2-sarc | Sarcomatoid |
| SA211356 | ES250414-S3-sarc | Sarcomatoid |
| SA211357 | ES250414-S4-sarc | Sarcomatoid |
| SA211358 | MB-ES-121016-30_SARC | Sarcomatoid |
| SA211359 | MB-ES-121016-50_SARC | Sarcomatoid |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO002281 |
| 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 ID: | TR002300 |
| 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. |
Sample Preparation:
| Sampleprep ID: | SP002294 |
| 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 ID: | AN003605 |
| Laboratory Name: | Metabolomics Ana M. Gil |
| Analysis Type: | NMR |
| Software Version: | Topspin 3.2 |
| Results File: | ST002202_AN003605_Results.txt |
| Units: | ppmn |
NMR:
| NMR ID: | NM000242 |
| Analysis ID: | AN003605 |
| 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) |
