Summary of Study ST003714
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 PR002307. The data can be accessed directly via it's Project DOI: 10.21228/M8F244 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 | ST003714 |
| Study Title | Lipidomics analysis of mouse PDAC cell lines treated with alpha-eleostearic acid |
| Study Type | Lipidomics |
| Study Summary | Mouse pancreatic cancer epithelial cells (mPDAC1) were cultured in RPMI, TIFM (tumor interstitial fluid medium), or TIFM + arginine and treated with 50 uM alpha-Eleostearic acid (a-ESA) or vehicle for 24 hours and analyzed for lipidomic changes. Cells that were arginine-deprived (TIFM) were found to exhibit a greater increase in alpha-eleostearic acid incorporation, particularly in triglycerides and phosphatidylethanolamines. Arginine deprived cells also showed a strong decrease in the abundance of monounsaturated fatty acids in triglycerides and phosaphtidylethanolamines, whereas these changes were not observed in cells cultured in RPMI or TIFM + arginine. |
| Institute | University of Chicago |
| Department | Ben May Department of Cancer Research |
| Laboratory | Muir Lab |
| Last Name | Jonker |
| First Name | Patrick |
| Address | 929 E 57th St. Chicago IL, 60637 |
| pbjonker@uchicago.edu | |
| Phone | 6162884547 |
| Submit Date | 2025-02-08 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-02-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002307 |
| Project DOI: | doi: 10.21228/M8F244 |
| Project Title: | Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis |
| Project Type: | Lipidomics |
| Project Summary: | Nutrient limitation is a characteristic feature of poorly perfused tumors. These changes in nutrient availability impose metabolic constraints and perturb metabolic pathways in cancer cells, in contrast to cells in well-perfused tissues. Consequently, targeting the metabolic dependencies created by tumor microenvironmental constraints may be a promising antineoplastic therapeutic approach. To identify these adaptations, we challenged pancreatic cancer cell lines (mouse Pancreatic Ductal Adenocarcinoma - PDAC) with pathophysiological nutrient levels and analyzed changes to cell metabolism. Here, we report that arginine limitation in pancreatic cancer perturbs saturated and monounsaturated fatty acid synthesis by suppressing the lipogenic transcription factor SREBP1. Synthesis of these acyl species is critical to maintaining a balance of saturated, monounsaturated, and polyunsaturated fatty acids in cellular membranes. We found that, as a consequence of the loss of fatty acid synthesis, pancreatic cancer cells were unable to maintain balanced lipidomes when exposed to polyunsaturated fatty acids, leading to cell death by ferroptosis. Importantly, we found orally administering oils rich in polyunsaturated fats reduces tumor burden in mice with pancreatic cancer. In sum, this study illustrates that arginine restriction in the tumor microenvironment alters pancreatic cancer cells by perturbing lipid synthesis, making them sensitive to supplementation with polyunsaturated fats. |
| Institute: | University of Chicago |
| Last Name: | Jonker |
| First Name: | Patrick |
| Address: | 929 E 57th St. Chicago IL, 60637 |
| Email: | pbjonker@uchicago.edu |
| Phone: | 6162884547 |
Subject:
| Subject ID: | SU003846 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Media | Treatment |
|---|---|---|---|---|
| SA406629 | S12_RPMI-NoArg-ESA_3 | Mouse PDAC cell line | RPMI | 50 uM ESA |
| SA406630 | S10_RPMI-NoArg-ESA_1 | Mouse PDAC cell line | RPMI | 50 uM ESA |
| SA406631 | S11_RPMI-NoArg-ESA_2 | Mouse PDAC cell line | RPMI | 50 uM ESA |
| SA406632 | S08_RPMI-NoArg-BSA_2 | Mouse PDAC cell line | RPMI | Fatty acid free BSA |
| SA406633 | S07_RPMI-NoArg-BSA_1 | Mouse PDAC cell line | RPMI | Fatty acid free BSA |
| SA406634 | S09_RPMI-NoArg-BSA_3 | Mouse PDAC cell line | RPMI | Fatty acid free BSA |
| SA406635 | S17_TIFM-Arg-ESA_2 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | 50 uM ESA |
| SA406636 | S18_TIFM-Arg-ESA_3 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | 50 uM ESA |
| SA406637 | S16_TIFM-Arg-ESA_1 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | 50 uM ESA |
| SA406638 | S13_TIFM-Arg-BSA_1 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Fatty acid free BSA |
| SA406639 | S14_TIFM-Arg-BSA_2 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Fatty acid free BSA |
| SA406640 | S15_TIFM-Arg-BSA_3 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Fatty acid free BSA |
| SA406641 | S04_TIFM-NoArg-ESA_1 | Mouse PDAC cell line | TIFM | 50 uM ESA |
| SA406642 | S05_TIFM-NoArg-ESA_2 | Mouse PDAC cell line | TIFM | 50 uM ESA |
| SA406643 | S06_TIFM-NoArg-ESA_3 | Mouse PDAC cell line | TIFM | 50 uM ESA |
| SA406644 | S01_TIFM-NoArg-BSA_1 | Mouse PDAC cell line | TIFM | Fatty acid free BSA |
| SA406645 | S02_TIFM-NoArg-BSA_2 | Mouse PDAC cell line | TIFM | Fatty acid free BSA |
| SA406646 | S03_TIFM-NoArg-BSA_3 | Mouse PDAC cell line | TIFM | Fatty acid free BSA |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO003839 |
| Collection Summary: | Mouse PDAC cells (mPDAC1) were plated at 620,000 cells on 10 cm dishes. Cells were treated with 50 uM alpha-eleostearic acid (a-ESA) or an equivalent volume of fatty acid free BSA as a vehicle control. After 24 hours of growth, cells were washed once with saline and then scraped with 400 uL ice cold MeOH and 300 uL 0.88% KCl. Cells were then transferred into glass tubes and mixed with 800 uL dichloromethane. Extracts were shaken for 15 minutes then centrifuged at 4000xg for 10 minutes. Dichloromethane layer was dried under nitrogen gas and pellets were saved for lipidomics analysis. |
| Sample Type: | Pancreatic cancer epithelial cells |
Treatment:
| Treatment ID: | TR003855 |
| Treatment Summary: | Cells were treated with alpha-eleostearic acid (a-ESA) at 50 uM for 24 hours, or with fatty acid free BSA as a vehicle control. |
Sample Preparation:
| Sampleprep ID: | SP003852 |
| Sampleprep Summary: | All samples, blanks, and QC sample pools were resuspended in 50µL of LC/MS grade acetonitrile (A955, Fisher) and LC/MS grade isopropanol (A461, Fisher) 50:50 (v/v), pulse vortexed, and sonicated for 5 min in a room temperature water bath prior to LC-MS/MS analysis. |
Combined analysis:
| Analysis ID | AN006095 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish dual pump |
| Column | Thermo Accucore C30 (150 x 2.1mm, 2.6um) with Accucore guard cartridge (10 x 2.1mm, 2.6um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X Tribrid |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH004626 |
| Chromatography Summary: | All samples, blanks, and QC sample pools were resuspended in 50µL of LC/MS grade acetonitrile (A955, Fisher) and LC/MS grade isopropanol (A461, Fisher) 50:50 (v/v), pulse vortexed, and sonicated for 5 min in a room temperature water bath prior to LC-MS/MS analysis. Samples were analyzed with a Vanquish dual pump liquid chromatography system coupled to an Orbitrap ID-X (Thermo Fisher Scientific) using a H-ESI source in both positive and negative mode. All samples were injected at 2 μL and lipids were separated with a reversed-phase chromatography using an Accucore C30 column (2.6 μm, 2.1mm × 150mm, 27826-152130, Thermo) combined with an Accucore guard cartridge (2.6 μm, 2.1 mm × 10 mm, 27826-012105, Thermo). Mobile phase A consisted of 60% LC/MS grade acetonitrile (A955, Fisher). Mobile phase B consisted of 90% LC/MS grade isopropanol (A461, Fisher) and 8% LC/MS grade acetonitrile. Both mobile phases contained 10mM ammonium formate (70221, Sigma) and 0.1% LC/MS grade formic acid (A11710X1-AMP, Fisher). Column temperature was kept at 50 °C, flow rate was held at 0.4 mL/min, and the chromatography gradient was as follows: 0-1 min held at 25% B,1-3 min from 25% B to 40% B, 3-19 min from 40% B to 75% B, 19-20.5 min from 75% B to 90% B, 20.5-28 min from 90% B to 95% B, 28-28.1 min from 95% B to 100% B, and 28.1-30 min held at 100% B. A 30 minute re-equilibration went as follows: 0-10 min held at 100% B and 0.2 mL/min, 10-15 min from 100% B to 50% B and held at 0.2 mL/min, 15-20 min held at 50% B and 0.2 mL/min, 20-25 min from 50% B to 25% B and held at 0.2 mL/min, 25-26 min held at 25% B and ramped from 0.2 mL/min to 0.4 mL/min, and 26-30 min held at 25% B and 0.4 mL/min. |
| Instrument Name: | Thermo Vanquish dual pump |
| Column Name: | Thermo Accucore C30 (150 x 2.1mm, 2.6um) with Accucore guard cartridge (10 x 2.1mm, 2.6um) |
| Column Temperature: | 50 |
| Flow Gradient: | 0-1 min held at 25% B,1-3 min from 25% B to 40% B, 3-19 min from 40% B to 75% B, 19-20.5 min from 75% B to 90% B, 20.5-28 min from 90% B to 95% B, 28-28.1 min from 95% B to 100% B, and 28.1-30 min held at 100% B. A 30 minute re-equilibration went as follows: 0-10 min held at 100% B and 0.2 mL/min, 10-15 min from 100% B to 50% B and held at 0.2 mL/min, 15-20 min held at 50% B and 0.2 mL/min, 20-25 min from 50% B to 25% B and held at 0.2 mL/min, 25-26 min held at 25% B and ramped from 0.2 mL/min to 0.4 mL/min, and 26-30 min held at 25% B and 0.4 mL/min |
| Flow Rate: | 0.2-0.4 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/8% acetonitrile/2% water; 0.1% formic acid; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005802 |
| Analysis ID: | AN006095 |
| Instrument Name: | Thermo Orbitrap ID-X Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Mass spectrometer parameters were: source voltage 3250V for positive mode and -2800V for negative mode, sheath gas 40, aux gas 10, sweep gas 1, ion transfer tube temperature 300°C, and vaporizer temperature 275°C. Full scan data was collected using the orbitrap with scan range of 200-1700 m/z at a resolution of 240,000 for profiling samples and 500,000 for U13C6-Glucose traced samples. Primary fragmentation (MS2) was induced in the orbitrap with assisted HCD collision energies at 15, 30, 45, 75, 110%, CID collision energy was fixed at 35%, and resolution was at 15,000. Secondary fragmentation (MS3) was induced in the ion trap with rapid scan rate and CID collision energy fixed at 35% for 3 scans. Lipid identifications were assigned from ddMS3 files using LipidSearch (v5.0, Thermo), which was then used to generate a transition list for peak picking and integration in Skyline (v23.1). |
| Ion Mode: | POSITIVE |
