Summary of Study ST002526

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	ST002526
Study Title	Stable isotope tracing of 15N2-glutamine in orthotopic pancreatic ductal adenocarcinoma tumor bearing mice and non tumor-bearing controls
Study Summary	Stable isotope tracing by bolus intravenous injections of 15N2-glutamine in orthotopic PDAC tumor bearing mice and non tumor-bearing controls followed by plasma sampling and tumor extraction for analysis of intratumoral metabolite labeling during the period of kinetic labeling
Institute	University of Chicago
Last Name	Apiz Saab
First Name	Juan
Address	929 E. 57th St.
Email	japizsaab@uchicago.edu
Phone	7738346506
Submit Date	2022-08-05
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:	SU002626
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
SA254575	Tissue 8	Healthy_Mouse_Pancreas_Tissue
SA254576	Tissue 11	Healthy_Mouse_Pancreas_Tissue
SA254577	Tissue 13	Healthy_Mouse_Pancreas_Tissue
SA254578	Tissue 1	Healthy_Mouse_Pancreas_Tissue
SA254579	Tissue 7	Healthy_Mouse_Pancreas_Tissue
SA254580	Tissue 3	Healthy_Mouse_Pancreas_Tissue
SA254581	Tissue 5	Healthy_Mouse_Pancreas_Tissue
SA254582	Plasma 5	Healthy_Mouse_Plasma
SA254583	Plasma 3	Healthy_Mouse_Plasma
SA254584	Plasma 7	Healthy_Mouse_Plasma
SA254585	Plasma 8	Healthy_Mouse_Plasma
SA254586	Plasma 11	Healthy_Mouse_Plasma
SA254587	Plasma 13	Healthy_Mouse_Plasma
SA254588	Plasma 1	Healthy_Mouse_Plasma
SA254589	Plasma 2	Tumor_Bearing_Mouse_Plasma
SA254590	Plasma 9	Tumor_Bearing_Mouse_Plasma
SA254591	Plasma 10	Tumor_Bearing_Mouse_Plasma
SA254592	Plasma 12	Tumor_Bearing_Mouse_Plasma
SA254593	Plasma 6	Tumor_Bearing_Mouse_Plasma
SA254594	Plasma 4	Tumor_Bearing_Mouse_Plasma
SA254595	Plasma 14	Tumor_Bearing_Mouse_Plasma
SA254596	Tissue 2	Tumor_Bearing_Mouse_Tumor_Tissue
SA254597	Tissue 4	Tumor_Bearing_Mouse_Tumor_Tissue
SA254598	Tissue 9	Tumor_Bearing_Mouse_Tumor_Tissue
SA254599	Tissue 14	Tumor_Bearing_Mouse_Tumor_Tissue
SA254600	Tissue 12	Tumor_Bearing_Mouse_Tumor_Tissue
SA254601	Tissue 10	Tumor_Bearing_Mouse_Tumor_Tissue
SA254602	Tissue 6	Tumor_Bearing_Mouse_Tumor_Tissue

Showing results 1 to 28 of 28

Showing results 1 to 28 of 28

Collection:

Collection ID:	CO002619
Collection Summary:	~100uL of blood were be obtained by submandibular sampling as described previously (Parasuraman et al., 2010) and centrifuged at 845 x g for 10 minutes at 4°C to separate plasma. Plasma was frozen in liquid nitrogen and stored at -80°C until further analysis animals. Mice were then immediately euthanized and tumor or pancreas from each animal was then harvested and immediately snap frozen using a BioSqueezer (BioSpec) cooled with liquid nitrogen and stored at -80°F until further analysis.
Sample Type:	Tumor, Pancreas & Plasma

Treatment:

Treatment ID:	TR002638
Treatment Summary:	Orthotopic tumors were implanted in C57BL6J mice at 8-12 weeks of age. 4 weeks after induction tumor-bearing mice and healthy littermate controls were treated with 15N2-glutamine (Cambridge Isotope Laboratory #NLM-1328-PK) dissolved in sterile phosphate buffered saline at 7.2mg/animal by tail vein injection as previously described (Lane et al., 2015). Briefly, animals were dosed three times at 15-minute intervals.

Treatment ID:

TR002638

Treatment Summary:

Orthotopic tumors were implanted in C57BL6J mice at 8-12 weeks of age. 4 weeks after induction tumor-bearing mice and healthy littermate controls were treated with 15N2-glutamine (Cambridge Isotope Laboratory #NLM-1328-PK) dissolved in sterile phosphate buffered saline at 7.2mg/animal by tail vein injection as previously described (Lane et al., 2015). Briefly, animals were dosed three times at 15-minute intervals.

Sample Preparation:

Sampleprep ID:	SP002632
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.

Sampleprep ID:

SP002632

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.

Combined analysis:

Analysis ID	AN004160
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	POSITIVE
Units	Fractional labelling

Chromatography:

Chromatography ID:	CH003079
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:	MS003907
Analysis ID:	AN004160
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 identification and relative quantification for metabolites. Natural abundance correction was performed using the IsoCor (Millard et al., 2019).
Ion Mode:	POSITIVE