Summary of Study ST003637
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 PR002249. The data can be accessed directly via it's Project DOI: 10.21228/M8XC02 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003637 |
| Study Title | lomitapide effects on lipidomics |
| Study Summary | To understand the effects of lomitapide treatment on lipid metabolism in PDAC cells, CLSA-25 MiaPaCa2 cells were treated with 1 uM lomitapide; the lipids were extracted, and targeted metabolomics screening were carried out to determine the effects of lomitapide treatment. |
| Institute | Pennsylvania State University |
| Last Name | Yang |
| First Name | Shengyu |
| Address | 500 University Drive |
| sxy99@psu.edu | |
| Phone | 7175311721 |
| Submit Date | 2024-11-06 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002249 |
| Project DOI: | doi: 10.21228/M8XC02 |
| Project Title: | Adaptation to cystine limitation stress confers a targetable lipid metabolism vulnerability in pancreatic ductal adenocarcinoma (PDAC). |
| Project Summary: | Cystine/cysteine is critical for antioxidant response and sulfur metabolism in cancer cells and is one of the most depleted amino acids in the PDAC microenvironment. The effects of cystine limitation stress (CLS) on PDAC progression are poorly understood. Here we report that adaptation to CLS (CLSA) promotes PDAC cell proliferation and tumor growth through translational upregulation of the oxidative pentose phosphate pathway (OxPPP). OxPPP activates the de novo synthesis of nucleotides and fatty acids to support tumor growth. On the other hand, CLSA-mediated lipidomic reprogramming depends on triacylglycerides synthesis to mitigate lipotoxicity. Through drug screening, we identified lomitapide as an inhibitor of CLSA PDAC tumor growth and a potent sensitizer of FOLFIRINOX chemotherapy. Mechanistically, lomitapide inhibits triacylglycerides synthesis to interfere with CLSA and chemotherapy-induced lipidomic reprograming. Taken together, CLSA-mediated metabolic and lipidomics reprograming promotes PDAC tumor growth and lomitapide could be used to target the dysregulated lipid metabolism in PDAC. |
| Institute: | Pennsylvania State University |
| Last Name: | Yang |
| First Name: | Shengyu |
| Address: | 500 University Drive |
| Email: | sxy99@psu.edu |
| Phone: | 7175311721 |
Subject:
| Subject ID: | SU003767 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA394015 | clsa_lom-1 | 1uM lomitapide treated |
| SA394016 | clsa_lom-2 | 1uM lomitapide treated |
| SA394017 | clsa_lom-3 | 1uM lomitapide treated |
| SA394018 | clsa-1 | vehicle treatment |
| SA394019 | clsa-2 | vehicle treatment |
| SA394020 | clsa-3 | vehicle treatment |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO003760 |
| Collection Summary: | 1x107 cells were harvested using a cell scrapper. The cell pellets were resuspended in 100 µL dH2O containing proteinase inhibitors. 50 µL cell suspensions were used for lipid extraction while the remaining samples were used for protein assay. |
| Sample Type: | pancreatic cancer cells |
Treatment:
| Treatment ID: | TR003776 |
| Treatment Summary: | Cells were treated with vehicle control or 1 µM lomitapide for 24 hours before being harvested for lipidomics analysis. |
Sample Preparation:
| Sampleprep ID: | SP003774 |
| Sampleprep Summary: | 1x107 cells were harvested using a cell scrapper. The cell pellets were resuspended in 100 µL dH2O containing proteinase inhibitors. 50 µL cell suspensions were used for lipid extraction while the remaining samples were used for protein assay. |
Combined analysis:
| Analysis ID | AN005973 | AN005974 |
|---|---|---|
| Chromatography ID | CH004537 | CH004537 |
| MS ID | MS005686 | MS005687 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Ultra Performance Liquid Chromatography (UPLC) (Nexera LC-40) | Ultra Performance Liquid Chromatography (UPLC) (Nexera LC-40) |
| Column | Thermo Accucore™C30 (100 x 2.1 mm, 2.6 μm) | Thermo Accucore™C30 (100 x 2.1 mm, 2.6 μm) |
| MS Type | ESI | ESI |
| MS instrument type | QTRAP | QTRAP |
| MS instrument name | ABI Sciex 6500+ QTrap | ABI Sciex 6500+ QTrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | pmol/mg protein | pmol/mg protein |
Chromatography:
| Chromatography ID: | CH004537 |
| Instrument Name: | Ultra Performance Liquid Chromatography (UPLC) (Nexera LC-40) |
| Column Name: | Thermo Accucore™C30 (100 x 2.1 mm, 2.6 μm) |
| Column Temperature: | 45℃ |
| Flow Gradient: | Gradient program: 80:20(V/V) at 0 min, 70:30(V/V) at 2 min, 40:60(V/V) at 4 min , 15:85(V/V) at 9 min, 10:90(V/V) at 14 min, 5:95(V/V) at 15.5 min, 5:95(V/V) at 17.3 min, 80:20(V/V) at 17.5 min, 80:20(V/V) at 20 min; |
| Flow Rate: | 0.35 mL/min; |
| Solvent A: | 60% Acetonitrile/40% Water; 0.1% formic acid, 10 mmol/L ammonium formate |
| Solvent B: | 10% Acetonitrile/90% Isopropyl alcohol; 0.1% formic acid, 10 mmol/L ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005686 |
| Analysis ID: | AN005973 |
| Instrument Name: | ABI Sciex 6500+ QTrap |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | Chromatography-mass spectrometry acquisition conditions 1x107 cells were harvested using a cell scrapper. The cell pellets were resuspended in 100 ul dH2O containing proteinase inhibitors. 50 ul cell suspensions were used for lipid extraction while the remainding samples were used for protein assay. The data acquisition instruments consisted of Ultra Performance Liquid Chromatography (UPLC) (NexeraLC-40, Shimadzu) equipped with Thermo Accucore™C30 (2.6 μm, 2.1 mm×100 mm i.d.) column and tandem mass spectrometry (MS/MS) (Triple Quad 6500+, AB/SCIEX). Liquid phase conditions: Mobile phase: A phase was acetonitrile /water (60/40, V/V) (0.1% formic acid added, 10 mmol/Lammonium formate); B phase was acetonitrile / Isopropyl alcohol (10/90, V/V) (0.1% formic acid added, 10 mmol/L ammonium formate); Gradient program: 80:20(V/V) at 0 min, 70:30(V/V) at 2 min, 40:60(V/V) at 4 min , 15:85(V/V) at 9 min, 10:90(V/V) at 14 min, 5:95(V/V) at 15.5 min, 5:95(V/V) at 17.3 min, 80:20(V/V) at 17.5 min, 80:20(V/V) at 20 min; Flow rate: 0.35 ml/min; Column temperature: 45∘C; Injection volume: 2 μL. Mass spectrometry conditions: LIT and triple quadrupole (QQQ) scans were acquired on a triple quadrupole-linear ion trap mass spectrometer (QTRAP), QTRAP® 6500+ LC-MS/MS System, equipped with an ESI Turbo Ion-Spray interface,operating in positive and negative ion mode and controlled by Analyst 1.6.3 software (Sciex). The ESI source operation parameters were as following: ion source, turbo spray; source temperature 500 ∘C; ion spray voltage (IS) 5500 V(Positive),-4500 V(Neagtive); Ion source gas 1 (GS1), gas 2 (GS2), curtain gas (CUR) were set at 45, 55, and 35 psi, respectively. Instrument tuning and mass calibration were performed with 10 and 100 μmol/L polypropylene glycol solutions in QQQ and LIT modes, respectively. QQQ scans were acquired as MRM experiments with collision gas (nitrogen) set to 5 psi. DP and CE for individual MRM transitions was done with further DP and CE optimization. A specific set of MRM transitions were monitored for each period according to the lipids eluted within this period. Principles of lipid qualification and quantification With Metware Bio in-house database MWDB, lipids were annotated based on its retention time and ion-pair information from MRM mode. In MRM mode, the first quadrupole screens the precursor ions for target substance and excluded ions of other molecular weights. After ionization induced by the impact chamber, the precursor ions were fragmented, and a characteristic fragment ion was selected through the third quadrupole to exclude the interference of other non-target ions. By selecting a particular fragment, quantification is more accurate and reproducible. Data pre-processing Analyst 1.6.3 was used to process mass spectrum data. The following figure shows the total ions current (TIC) and MRM lipid detection multi-peak diagram (XIC) of the mixed QC samples. The X-axis shows the Retention time (RT) from lipid detection, and the Y-axis shows the ion flow intensity from ion detection (intensity unit: CPS, count per second). |
| Ion Mode: | POSITIVE |
| MS ID: | MS005687 |
| Analysis ID: | AN005974 |
| Instrument Name: | ABI Sciex 6500+ QTrap |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | Chromatography-mass spectrometry acquisition conditions 1x107 cells were harvested using a cell scrapper. The cell pellets were resuspended in 100 ul dH2O containing proteinase inhibitors. 50 ul cell suspensions were used for lipid extraction while the remainding samples were used for protein assay. The data acquisition instruments consisted of Ultra Performance Liquid Chromatography (UPLC) (NexeraLC-40, Shimadzu) equipped with Thermo Accucore™C30 (2.6 μm, 2.1 mm×100 mm i.d.) column and tandem mass spectrometry (MS/MS) (Triple Quad 6500+, AB/SCIEX). Liquid phase conditions: Mobile phase: A phase was acetonitrile /water (60/40, V/V) (0.1% formic acid added, 10 mmol/Lammonium formate); B phase was acetonitrile / Isopropyl alcohol (10/90, V/V) (0.1% formic acid added, 10 mmol/L ammonium formate); Gradient program: 80:20(V/V) at 0 min, 70:30(V/V) at 2 min, 40:60(V/V) at 4 min , 15:85(V/V) at 9 min, 10:90(V/V) at 14 min, 5:95(V/V) at 15.5 min, 5:95(V/V) at 17.3 min, 80:20(V/V) at 17.5 min, 80:20(V/V) at 20 min; Flow rate: 0.35 ml/min; Column temperature: 45∘C; Injection volume: 2 μL. Mass spectrometry conditions: LIT and triple quadrupole (QQQ) scans were acquired on a triple quadrupole-linear ion trap mass spectrometer (QTRAP), QTRAP® 6500+ LC-MS/MS System, equipped with an ESI Turbo Ion-Spray interface,operating in positive and negative ion mode and controlled by Analyst 1.6.3 software (Sciex). The ESI source operation parameters were as following: ion source, turbo spray; source temperature 500 ∘C; ion spray voltage (IS) 5500 V(Positive),-4500 V(Neagtive); Ion source gas 1 (GS1), gas 2 (GS2), curtain gas (CUR) were set at 45, 55, and 35 psi, respectively. Instrument tuning and mass calibration were performed with 10 and 100 μmol/L polypropylene glycol solutions in QQQ and LIT modes, respectively. QQQ scans were acquired as MRM experiments with collision gas (nitrogen) set to 5 psi. DP and CE for individual MRM transitions was done with further DP and CE optimization. A specific set of MRM transitions were monitored for each period according to the lipids eluted within this period. Principles of lipid qualification and quantification With Metware Bio in-house database MWDB, lipids were annotated based on its retention time and ion-pair information from MRM mode. In MRM mode, the first quadrupole screens the precursor ions for target substance and excluded ions of other molecular weights. After ionization induced by the impact chamber, the precursor ions were fragmented, and a characteristic fragment ion was selected through the third quadrupole to exclude the interference of other non-target ions. By selecting a particular fragment, quantification is more accurate and reproducible. Data pre-processing Analyst 1.6.3 was used to process mass spectrum data. The following figure shows the total ions current (TIC) and MRM lipid detection multi-peak diagram (XIC) of the mixed QC samples. The X-axis shows the Retention time (RT) from lipid detection, and the Y-axis shows the ion flow intensity from ion detection (intensity unit: CPS, count per second). |
| Ion Mode: | NEGATIVE |
