Summary of Study ST003758

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 PR002341. The data can be accessed directly via it's Project DOI: 10.21228/M81N8S This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST003758
Study TitleUntargeted lipidomics of gemcitabine-resistant cells
Study SummaryIn this work we developed gemcitabine (GEMC) resistant (GEMR) PDAC cell lines from Panc1 and MiaPaCa2 cells. This dataset contains results and raw data for untargeted lipidomics of Panc1 cells, including control (CON), and GEMR cells alongside internal quality controls (iQC) and blank samples for background subtraction (as described under sample prep). Untargeted lipidomics enabled the quantification of more than 400 distinct molecular lipid species within Panc1 & MiaPaCa2 control (CON) & GEMR cells from 12 different classes of lipid, with 79 molecular species being differentially abundant between MiaPaCa2 control and GEMR cells following unpaired t test. Data were analysed using MS-DIAL 4.9.
Institute
Victor Chang Cardiac Research Institute
Last NameHancock
First NameSarah
AddressLowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
Emails.hancock@victorchang.edu.au
Phone+61414537526
Submit Date2025-02-19
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-03-21
Release Version1
Sarah Hancock Sarah Hancock
https://dx.doi.org/10.21228/M81N8S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002341
Project DOI:doi: 10.21228/M81N8S
Project Title:Untargeted lipidomics of gemcitabine-resistant PDAC cells
Project Summary:Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with few treatment options and poor survivability. In this work we sought to characterise metabolic adaptations to gemcitabine (GEMC)-based chemotherapy exposure to discover new therapeutic targets for improving treatment efficacy. We show that GEMC resistance (GEMR) upregulates de novo lipogenesis in Panc1 and MiaPaCa2 cells.
Institute:Victor Chang Cardiac Research Institute
Last Name:Hancock
First Name:Sarah
Address:Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
Email:s.hancock@victorchang.edu.au
Phone:+61414537526

Subject:

Subject ID:SU003891
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 Sample source group group
SA409065Blank_cells_neg_20211210204022- Blank Blank
SA409066Blank_cells_neg- Blank Blank
SA409067Blank_cells_pos_20211210152840- Blank Blank
SA409068Blank_cells_pos- Blank Blank
SA409069iQC_cells_neg_20211210211133- pool iQC
SA409070iQC_cells_pos- pool iQC
SA409071iQC_cells_pos_20211210155952- pool iQC
SA409072iQC_cells_neg- pool iQC
SA409073MiaPaCa2_CON_3_posPancreas MiaPaCa2 cells CON
SA409074MiaPaCa2_CON_3_negPancreas MiaPaCa2 cells CON
SA409075MiaPaCa2_CON_2_posPancreas MiaPaCa2 cells CON
SA409076MiaPaCa2_CON_1_posPancreas MiaPaCa2 cells CON
SA409077MiaPaCa2_CON_1_negPancreas MiaPaCa2 cells CON
SA409078MiaPaCa2_CON_2_negPancreas MiaPaCa2 cells CON
SA409079MiaPaCa2_GEMR_1_negPancreas MiaPaCa2 cells GEMR
SA409080MiaPaCa2_GEMR_1_posPancreas MiaPaCa2 cells GEMR
SA409081MiaPaCa2_GEMR_2_negPancreas MiaPaCa2 cells GEMR
SA409082MiaPaCa2_GEMR_2_posPancreas MiaPaCa2 cells GEMR
SA409083MiaPaCa2_GEMR_3_negPancreas MiaPaCa2 cells GEMR
SA409084MiaPaCa2_GEMR_3_posPancreas MiaPaCa2 cells GEMR
Showing results 1 to 20 of 20

Collection:

Collection ID:CO003884
Collection Summary:Samples were obtained from established immortalised adherent human pancreatic ductal adenocarcinoma cells (MiaPaCa2). Cells were cultured in high glucose DMEM containing 4.5 g/L glucose and 4 mM glutamine and were supplemented with 10% FCS. Cells were cultured under 5% CO2 at 37ºC and routinely passaged every 2-3 days (when ~80-90% confluent). Cell lines were regularly screened for mycoplasma infection.
Sample Type:Pancreas

Treatment:

Treatment ID:TR003900
Treatment Summary:MiaPaCa2 GEMR cells were produced by serial treatment with escalating doses of gemcitabine for approximately 12 weeks. The final concentration of GEMC for MiaPaCa2 cells was 64 nM, resulting in a half-maximal inhibitory concentration of 92.2 nM (approximately 3x increase over control (CON) cells, 30.6 nM)

Sample Preparation:

Sampleprep ID:SP003897
Sampleprep Summary:Lipids were extracted from cells grown to 80-90% confluency in 6 well plates using a modified methyl tert-butyl ether (MTBE) method. Adherent cells were washed with ice-cold PBS and scraped into methanol containing 0.01% butylated hydroxytoluene and 100 pmol each of internal standards (phosphatidylcholine 19:0/19:0, phosphatidylethanolamine 17:0/17:0, phosphatidylserine 17:0/17:0, lysophosphatidylcholine 17:0, lysophosphatidylethanolamine 14:0, phosphatidylglycerol 17:0/17:0, phosphatidic acid 17:0/17:0, ceramide d18:1/17:0, dihydrosphingomyelin 12:0, cholesteryl ester 22:1, diacylglycerol 17:0/17:0, D5-triacylglycerol 16:0/16:0/16:0 and cardiolipin 14:0/14:0/14:0/14:0). An empty well was also scraped for use in background subtraction. To this, MTBE was added at a ratio of 3:1 v/v, and extracts were rotated overnight at 4°C. Following overnight rotation, 1 part of ice-cold 150 mM ammonium acetate was added, samples were vortexed vigorously and centrifuged at 2000 x g for 5 min. The upper organic phase containing lipids was transferred into a 1.5 mL autosampler vial and dried under N2 at 37ºC Dried lipids were reconstituted in chloroform:methanol:water (60:30:4.5 v/v/v), transferred to a sleeved vial, and stored at -20°C until analysis. The aqueous phase containing the protein pellet was dried under N2 and digested with 1M NaOH overnight at 4ºC. Digested protein was diluted 1:2 v/v with water and protein concentration was determined using a Pierce BCA assay kit (ThermoFisher Scientific)

Chromatography:

Chromatography ID:CH004685
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 μm)
Column Temperature:60°C
Flow Gradient:0.1-1.5 min 68% A (32% B), 1.4-4 min 55% A (45% B), 4-5 min 48% A (52% B), 5-8 min 42% A (58% B), 8-11 min 34% A (66% B), 11-14 min 30% A (70% B), 14-18 min 25% A (75% B), 18-21 min 3% A (97% B), 21-25 min 3% A (97% B), 25.1-30 min 68% A (32% B).
Flow Rate:0.26 mL/min
Solvent A:60% Acetonitrile/40% Water; 10 mM Ammonium Formate; 0.1% Formic acid
Solvent B:10% Acetonitrile/90% Isopropanol; 10 mM Ammonium Formate; 0.1% Formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006170
Analysis Type:MS
Chromatography ID:CH004685
Num Factors:4
Num Metabolites:289
Rt Units:Minutes
Units:nmol/mg protein
  
Analysis ID:AN006171
Analysis Type:MS
Chromatography ID:CH004685
Num Factors:4
Num Metabolites:198
Rt Units:Minutes
Units:nmol/mg protein
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