Summary of Study ST003341

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 PR002077. The data can be accessed directly via it's Project DOI: 10.21228/M84R60 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.

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Study IDST003341
Study TitleUntargeted Lipidomic Profiling of Canine Cancer Cell Lines
Study SummaryCell sensitivity to ferroptosis is closely associated with cellular lipid composition and unsaturation. To further characterize the 31 canine cell lines tested for ferroptosis sensitivity, we collected untargeted lipidomic data for each line in duplicate. Omics characterizations of cancer cell lines and integration with viability data in efforts such as the Cancer Cell Line Encyclopedia (CCLE) and the Cancer Dependency Map (www.depmap.org) have yielded powerful resources to explore causal and predictive biomarkers of response to genetic and small molecule perturbations. Our data facilitate a similar approach for the canine lines included in this study. Lipidomics data covered over 750 individual species falling into 18 main lipid classes. Total concentrations varied widely between individual cell lines, as did relative lipid composition. Likewise, the fraction of cellular polyunsaturated fatty acids (PUFAs), previously reported as a contributor to ferroptosis sensitivity, varied from 20% to almost 70%. Thus, the panel of tested canine cell lines represented a wide spectrum of cellular lipid composition.
Institute
Kojin Therapeutics, Inc.
Last NameWawer
First NameMathias
Address451 D St., Suite 502, Boston, MA 02210
Emailmwawer@kojintx.com
Phone617-952-0636
Submit Date2024-07-12
Total Subjects31
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-09-12
Release Version1
Mathias Wawer Mathias Wawer
https://dx.doi.org/10.21228/M84R60
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002077
Project DOI:doi: 10.21228/M84R60
Project Title:Validation of ferroptosis in canine cancer cells to enable comparative oncology and translational medicine
Project Summary:Ferroptosis is a cell death mechanism that has attracted significant attention as a potential basis for the development of new cancer therapies. Validation of ferroptosis biology in species commonly used in translation and pre-clinical development is a necessary foundation for enabling the advancement of such ferroptosis modulating drugs. Here, we demonstrate that canine cancer cells exhibit sensitivity to a wide range of ferroptosis-inducing perturbations in a manner indistinguishable from human cancer cells, and recapitulate characteristic patterns of ferroptotic response across tumor types seen in the human setting. We further performed lipidomic profiling of all canine cancer cell lines to enable the discovery of lipid biomarkers for ferroptosis sensitivity. The foundation provided herein establishes the dog as a relevant efficacy and toxicology model for ferroptosis and creates new opportunities to leverage the canine comparative oncology paradigm to accelerate the development of ferroptosis-inducing drugs for human cancer patients.
Institute:Kojin Therapeutics, Inc.
Last Name:Wawer
First Name:Mathias
Address:451 D St., Suite 502, Boston, MA 02210
Email:mwawer@kojintx.com
Phone:617-952-0636
Publications:https://www.biorxiv.org/content/10.1101/2024.04.28.591561v1

Subject:

Subject ID:SU003462
Subject Type:Cultured cells
Subject Species:Canis lupus familiaris
Taxonomy ID:9615
Species Group:Mammals

Factors:

Subject type: Cultured cells; Subject species: Canis lupus familiaris (Factor headings shown in green)

mb_sample_id local_sample_id Cell_Line
SA364571461771
SA364572451771
SA3645736017CM98
SA3645745917CM98
SA36457531Abram
SA36457632Abram
SA36457723Angus
SA36457824Angus
SA36457929Bliley
SA36458030Bliley
SA36458111C2
SA36458212C2
SA36459548Cindy-HSA
SA36459647Cindy-HSA
SA36458317CLL1390
SA36458418CLL1390
SA36458528CML10C2
SA36458627CML10C2
SA36458743CML6M
SA36458844CML6M
SA36458921CMT12
SA36459022CMT12
SA36459161CMT27
SA36459262CMT27
SA36459338CTAC
SA36459437CTAC
SA36459750D17
SA36459849D17
SA3646018Den-HSA
SA3646027Den-HSA
SA36459956DH82
SA36460055DH82
SA36460333Gracie
SA36460434Gracie
SA36460515HMPOS
SA36460616HMPOS
SA3646073Jones
SA3646084Jones
SA36460939Kinsey
SA36461040Kinsey
SA36461119McKinley
SA36461220McKinley
SA36461325Moresco
SA36461426Moresco
SA3646156Nike
SA3646165Nike
SA36461736OS24
SA36461835OS24
SA3646199OSA8
SA36462010OSA8
SA36462142PARKS
SA36462241PARKS
SA36462357SB
SA36462458SB
SA3646252STSA
SA3646261STSA
SA36462714Tyler1
SA36462813Tyler1
SA36462953Tyler2
SA36463054Tyler2
SA36463151Yamane
SA36463252Yamane
Showing results 1 to 62 of 62

Collection:

Collection ID:CO003455
Collection Summary:All cell lines were obtained through the Flint Animal Cancer Center (FACC) and were part of the published FACC tumor cell line panel. [1] Cell lines were maintained in RPMI 1640 culture medium containing 10% fetal bovine serum (FBS), penicillin (100 units/mL), streptomycin (100 μg/mL) and incubated at 37 °C in a humidified atmosphere of 5% CO2:95% air. Cell medium was removed by vacuum aspiration and cells were washed with 4 mL cold PBS (no Mg2+/Ca2+). After vacuum aspiration of PBS, 0.25% Trypsin-EDTA (Gibco™25200056) was added and incubated for 5 minutes at 37°C. Cells were resuspended in media (RPMI 1640) to stop the digestion and transferred to 15 ml conical tubes. Cell pellets were collected by centrifuging at 3500 rpm for 10 min (4°C). Cells were then washed twice by resuspending them in cold PBS and repeating centrifugation. Before the final centrifugation, cells were counted and aliquoted to 1,000,000 cells per tube. Cell pellets were stored at -80°C before lipid extraction and LC-MS analysis. [1] Fowles, J. S., Dailey, D. D., Gustafson, D. L., Thamm, D. H. & Duval, D. L. The Flint Animal Cancer Center (FACC) Canine Tumour Cell Line Panel: a resource for veterinary drug discovery, comparative oncology and translational medicine. Vet. Comp. Oncol. 15, 481–492 (2017).
Sample Type:Cultured cells
Tissue Cell Quantity Taken:1,000,000

Treatment:

Treatment ID:TR003471
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP003469
Sampleprep Summary:After thawing, cells were mixed with PBS to make a suspension of 1 million cells in 200 μL, utilizing vortexing and sonication. A methyl-tert-butyl ether (MTBE)-based liquid-liquid extraction protocol was used. The cell suspensions were transferred to 8 mL screw-cap glass tubes containing 1.2 mL methanol, 10 μL internal standard mix (see Sampleprep Protocol Comments) and 4 mL MTBE. Samples were vortexed, sonicated for 15 min, and incubated on a tabletop shaker at 500 rpm at room temperature for 1 h. After incubation, phase separation was induced by adding 0.75 mL water to each sample before vortexing and centrifuging at 2000 x g for 20 min. The upper organic phase of each sample was carefully removed using a Pasteur pipette and transferred into a clean glass tube. The remaining aqueous phase was re-extracted with 2 mL of the upper phase of a mixture MTBE/methanol/water 10:3:2.5 (v/v/v). After vortexing and centrifuging, the organic phase was collected and combined with the initial organic phase. The extracted lipids were dried overnight in a SpeedVac vacuum concentrator. The dried lipid extracts were reconstituted in 200 μL n-butanol/methanol 1:1 (v/v) and transferred into autosampler vials for analysis by LC-MS/MS.
Sampleprep Protocol Filename:standards.xlsx
Sampleprep Protocol Comments:Internal Standard Cayman Item # Concentration in Mix (µg/mL) Polarity Used to Normalize TG(16:0-d9/16:0/16:0) 30181 10 Positive TG, pos-ion features not specified below and unidentified features DG(16:0-d9/16:0/0:0) 28781 5 Positive DG SM(d18:1/16:0-d9) 30141 10 Positive SM Cer(d18:1-d7/16:0) 22787 5 Positive Cer CE(16:0-d9) 30134 100 Positive CE CAR(17:0-d3) 35459 5 Positive CAR PE(16:0-d9/16:0) 30597 5 Negative PE, neg-ion features not specified below and unidentified features FA(16:0-d9) 30557 40 Negative FA PI(16:0-d9/16:0) 31102 10 Negative PI PS(16:0-d9/16:0) 30706 10 Negative PS PC(16:0-d9/16:0) 30581 10 Negative PC LPC(16:0-d9/0:0) 30580 10 Negative LPC

Chromatography:

Chromatography ID:CH004159
Chromatography Summary:Solvent A: Acetonitrile/water/formic acid 60:40:0.1 (v/v/v), 10 mM ammonium formate; Solvent B: Acetonitrile/isopropanol/formic acid 10:90:0.1 (v/v/v), 10 mM ammonium formate
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Thermo Accucore C30 (150 x 2.1mm,2.6um)
Column Temperature:40
Flow Gradient:(minute, % Pump B): (0,30),(5,43),(5.1,50),(14,70),(14.1,70),(21,99),(28,99),(28.1,30),(33,30)
Flow Rate:300 uL/min
Solvent A:60% Acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:10% Acetonitrile/90% isopropanol; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN005475
Analysis Type:MS
Analysis Protocol File:Internal_Standard.pdf
Chromatography ID:CH004159
Num Factors:31
Num Metabolites:318
Rt Units:Minutes
Units:area ratio (analyte peak area / internal class standard peak area)
  
Analysis ID:AN005476
Analysis Type:MS
Analysis Protocol File:Internal_Standard.pdf
Chromatography ID:CH004159
Num Factors:31
Num Metabolites:441
Rt Units:Minutes
Units:area ratio (analyte peak area / internal class standard peak area)
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