Summary of Study ST002528
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 PR001627. The data can be accessed directly via it's Project DOI: 10.21228/M8D434 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 | ST002528 |
| Study Title | Concentrations of amino acids in interstitial fluid and whole tumor samples of a murine PDAC orthotopic tumor model, measured by LC-MS |
| Study Summary | We extracted polar metabolites from the interstitial fluid and whole tumor samples of orthotopic murine PDAC tumors. Weused LC-MS to measure the concentration of amino acids in the interstitial fluid of orthotopic murine PDAC tumors and compared this to the intratumoral concentrations. |
| Institute | University of Chicago |
| Last Name | Apiz Saab |
| First Name | Juan |
| Address | 929 E. 57th St. |
| japizsaab@uchicago.edu | |
| Phone | 7738346506 |
| Submit Date | 2023-03-23 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001627 |
| Project DOI: | doi: 10.21228/M8D434 |
| 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 |
Subject:
| Subject ID: | SU002628 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample type |
|---|---|---|
| SA254624 | TIF_01 | PDAC_TIF |
| SA254625 | TIF_03 | PDAC_TIF |
| SA254626 | TIF_02 | PDAC_TIF |
| SA254627 | Tumor_04 | PDAC_Tumor |
| SA254628 | Tumor_01 | PDAC_Tumor |
| SA254629 | Tumor_02 | PDAC_Tumor |
| SA254630 | Tumor_03 | PDAC_Tumor |
| Showing results 1 to 7 of 7 |
Collection:
| Collection ID: | CO002621 |
| Collection Summary: | Briefly, tumors were rapidly dissected after euthanizing animals. Tumors were weighed and rinsed in blood bank saline solution (150 mM NaCl) and blotted on filter paper (VWR, Radnor, PA, 28298–020). The process of dissection and tumor preparation took < 3min. Tumors were cut in half and put onto 20µm nylon mesh filters (Spectrum Labs, Waltham, MA, 148134) on top of 50 mL conical tubes, and centrifuged for 10min. at 4°C at 400xg. IF was then collected, snap-frozen in liquid nitrogen and stored at -80°C until further analysis. Tumors were then immediately snap frozen using a BioSqueezer (BioSpec) cooled with liquid nitrogen and stored at -80°F until further analysis. |
| Sample Type: | Tumor, Interstitial fluid |
Treatment:
| Treatment ID: | TR002640 |
| Treatment Summary: | Orthotopic tumors were implanted in C57BL6J mice at 8-12 weeks of age. 4 weeks after induction interstitial fluid and tumors were collected. |
Sample Preparation:
| Sampleprep ID: | SP002634 |
| 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. For TIF 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. |
Combined analysis:
| Analysis ID | AN004162 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | Peak area (m/z) |
Chromatography:
| Chromatography ID: | CH003081 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um) |
| Column Temperature: | 25 |
| Flow Gradient: | linear gradient from 80% to 20% B; 20–20.5 min: linear gradient from 20% to 80% B; 20.5–28 min: hold at 80% B |
| Flow Rate: | 0.150 mL/min |
| Solvent A: | 20 mM ammonium carbonate, 0.1% ammonium hydroxide |
| Solvent B: | acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003909 |
| Analysis ID: | AN004162 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | XCalibur 965 2.2 software (Thermo 966 Fisher Scientific) was used for identification and quantification of metabolites. |
| Ion Mode: | UNSPECIFIED |
