Summary of Study ST003717
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 | ST003717 |
| Study Title | Lipidomics analysis of mouse pancreatic cancer cells cultured RPMI, TIFM, or TIFM + arginine under lipid deprivation |
| Study Type | Lipidomics |
| Study Summary | KrasG12D mutant mouse pancreatic ductal adenocarcinoma cell lines (mPDAC1) were cultured in lipid replete or lipid deplete medium and analyzed for lipidomic changes. Cell lines were cultured in RPMI-1640, TIFM (https://elifesciences.org/articles/81289), or TIFM + arginine (1.149 mM). To do this, cells in each of the three mediums were deprived of lipids for 24 hours and their lipidomes were analyzed for changes. We find that mPDAC1 cells cultured in arginine-deprived conditions (TIFM) were unable to maintain their pools of monounsaturated and saturated fatty acids, whereas cells cultured in RPMI or in TIFM + arginine were able to maintain monounsaturated and saturated fatty acid pools upon lipid deprivation. |
| Institute | University of Chicago |
| Department | Ben May Department for 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 |
| Num Groups | 10 |
| Study Comments | Lipidomics analysis performed at Van Andel Institute (Grand Rapids, MI). Thanks to Dr. Ryan Sheldon and the Mass Spec Core for running and processing these samples. |
| 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: | SU003849 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | Mouse cell lines derived from Kras G12D; tp53(-/-); Pdx-1-Cre mice. |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Media | Treatment |
|---|---|---|---|---|
| SA406689 | S48_RPMI-NoArg-NoLipids_3 | Mouse PDAC cell line | RPMI | Lipid deplete |
| SA406690 | S46_RPMI-NoArg-NoLipids_1 | Mouse PDAC cell line | RPMI | Lipid deplete |
| SA406691 | S47_RPMI-NoArg-NoLipids_2 | Mouse PDAC cell line | RPMI | Lipid deplete |
| SA406692 | S44_RPMI-NoArg-Lipids_2 | Mouse PDAC cell line | RPMI | Lipid replete |
| SA406693 | S43_RPMI-NoArg-Lipids_1 | Mouse PDAC cell line | RPMI | Lipid replete |
| SA406694 | S45_RPMI-NoArg-Lipids_3 | Mouse PDAC cell line | RPMI | Lipid replete |
| SA406695 | S53_TIFM-Arg-NoLipids_2 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Lipid deplete |
| SA406696 | S54_TIFM-Arg-NoLipids_3 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Lipid deplete |
| SA406697 | S52_TIFM-Arg-NoLipids_1 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Lipid deplete |
| SA406698 | S49_TIFM-Arg-Lipids_1 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Lipid replete |
| SA406699 | S50_TIFM-Arg-Lipids_2 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Lipid replete |
| SA406700 | S51_TIFM-Arg-Lipids_3 | Mouse PDAC cell line | TIFM + arg (1.149 mM) | Lipid replete |
| SA406701 | S40_TIFM-NoArg-NoLipids_1 | Mouse PDAC cell line | TIFM | Lipid deplete |
| SA406702 | S41_TIFM-NoArg-NoLipids_2 | Mouse PDAC cell line | TIFM | Lipid deplete |
| SA406703 | S42_TIFM-NoArg-NoLipids_3 | Mouse PDAC cell line | TIFM | Lipid deplete |
| SA406704 | S37_TIFM-NoArg-Lipids_1 | Mouse PDAC cell line | TIFM | Lipid replete |
| SA406705 | S38_TIFM-NoArg-Lipids_2 | Mouse PDAC cell line | TIFM | Lipid replete |
| SA406706 | S39_TIFM-NoArg-Lipids_3 | Mouse PDAC cell line | TIFM | Lipid replete |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO003842 |
| Collection Summary: | Plated pancreatic cancer cells were washed once with ice cold saline and then scraped and collected in 800 uL cold MeOH and 600 uL 0.88% KCl. Cells were then transferred to glass tubes and lipids extracted by adding 1600 uL ice cold dichloromethane and shaking for 15 minutes. Tubes were then centrifuged at 4000xg for 10 minutes and dichloromethane layer was removed and dried under nitrogen gas to generate lipid pellet for lipidomics analysis. |
| Sample Type: | Pancreatic cancer epithelial cells |
Treatment:
| Treatment ID: | TR003858 |
| Treatment Summary: | Mouse pancreatic cancer cells were plated at 621,000 cells in 15 cm dishes. Cells were washed once with PBS and treated with media (TIFM, RPMI, or TIFM + arg) with FBS that was lipid replete or lipid depleted for 24 hours. After 24 hour treatment cells were extracted for lipidomics analysis. |
Sample Preparation:
| Sampleprep ID: | SP003855 |
| 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 | AN006098 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| 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: | CH004629 |
| Instrument Name: | Thermo Vanquish |
| 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: | MS005805 |
| Analysis ID: | AN006098 |
| Instrument Name: | Thermo Orbitrap ID-X Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | 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 |
