Summary of Study ST001920

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 PR001211. The data can be accessed directly via it's Project DOI: 10.21228/M85Q6Z 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 IDST001920
Study TitleMetabolic and lipidomic characterization of radioresistant MDA-MB-231 human breast cancer cells to investigate potential therapeutic targets
Study SummaryTo provide preliminary insights into metabolic and lipidomic characteristics in radioresistant triple-negative breast cancer (TNBC) cells and suggest potential therapeutic targets, we performed a comprehensive metabolic and lipidomic profiling of radioresistant MDA-MB-231 (MDA-MB-231/RR) TNBC cells and their parental cells using gas chromatography-mass spectrometry and nano electrospray ionization-mass spectrometry, followed by multivariate statistical analysis. Buthionine sulfoximine (BSO) and radiation were co-treated to radioresistant TNBC cells. The level of glutathione (GSH) was significantly increased, and the levels of GSH synthesis-related metabolites, such as cysteine, glycine, and glutamine were also increased in MDA-MB-231/RR cells. In contrast, the level of lactic acid was significantly reduced. In addition, reactive oxygen species (ROS) level was decreased in MDA-MB-231/RR cells. In the lipidomic profiles of MDA-MB-231/RR cells, the levels of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were significantly increased, whereas those of most of the phosphatidylinositol species were significantly decreased. BSO sensitized MDA-MB-231/RR cells to radiotherapy, which resulted in decreased GSH level and increased ROS level and apoptosis. Radioresistant TNBC cells showed distinct metabolic and lipidomic characteristics compared to their parental cells. We suggested activated GSH, PC, and PE biosynthesis pathways as potential targets for treating radioresistant TNBC cells. Particularly, enhanced radiosensitivity was achieved by inhibition of GSH biosynthesis in MDA-MB-231/RR cells.
Institute
ChungAng University
DepartmentCollege of Pharmacy
LaboratoryNatural product biotechnology and Metabolomics
Last NameLee
First NameHwanhui
AddressCollege of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
Emailhwanhui56@gmail.com
Phone+8228205605
Submit Date2021-09-22
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo), d
Analysis Type DetailGC-MS/MS(Dir. inf.)
Release Date2021-10-02
Release Version1
Hwanhui Lee Hwanhui Lee
https://dx.doi.org/10.21228/M85Q6Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001211
Project DOI:doi: 10.21228/M85Q6Z
Project Title:Comprehensive metabolic and lipidomic profiling of radioresistant MDA-MB-231 human breast cancer cells
Project Type:Untargeted MS
Project Summary:Metabolic and lipidomic characteristics of radioresistant MDA-MB-231 human breast cancer cells were revealed using GC-MS and nanoESI-MS analyses.
Institute:ChungAng University
Department:College of Pharmacy
Laboratory:Natural product biotechnology and Metabolomics
Last Name:Lee
First Name:Hwanhui
Address:College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
Email:hwanhui56@gmail.com
Phone:+82-2-820-5605

Subject:

Subject ID:SU001998
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 Factors
SA177871MDAMB231_4_2Factors;Control
SA177872MDAMB231_4_1Factors;Control
SA177873MDAMB231_4_3Factors;Control
SA177874MDAMB231_5_3Factors;Control
SA177875MDAMB231_1_1Factors;Control
SA177876MDAMB231_3_3Factors;Control
SA177877MDAMB231_5_2Factors;Control
SA177878MDAMB231_5_1Factors;Control
SA177879MDAMB231_1_3Factors;Control
SA177880MDAMB231_3_2Factors;Control
SA177881MDAMB231_1_2Factors;Control
SA177882MDAMB231_2_1Factors;Control
SA177883MDAMB231_2_2Factors;Control
SA177884MDAMB231_3_1Factors;Control
SA177885MDAMB231_2_3Factors;Control
SA177886QC_2Factors;Quality control
SA177887QC_1Factors;Quality control
SA177888QC_3Factors;Quality control
SA177889QC_5Factors;Quality control
SA177890QC_4Factors;Quality control
SA177891QC_6Factors;Quality control
SA177892MDAMB231RR_5_1Factors;radioresistant cells
SA177893MDAMB231RR_5_2Factors;radioresistant cells
SA177894MDAMB231RR_4_3Factors;radioresistant cells
SA177895MDAMB231RR_5_3Factors;radioresistant cells
SA177896MDAMB231RR_2_1Factors;radioresistant cells
SA177897MDAMB231RR_2_2Factors;radioresistant cells
SA177898MDAMB231RR_1_3Factors;radioresistant cells
SA177899MDAMB231RR_1_2Factors;radioresistant cells
SA177900MDAMB231RR_1_1Factors;radioresistant cells
SA177901MDAMB231RR_2_3Factors;radioresistant cells
SA177902MDAMB231RR_3_1Factors;radioresistant cells
SA177903MDAMB231RR_4_1Factors;radioresistant cells
SA177904MDAMB231RR_3_3Factors;radioresistant cells
SA177905MDAMB231RR_3_2Factors;radioresistant cells
SA177906MDAMB231RR_4_2Factors;radioresistant cells
Showing results 1 to 36 of 36

Collection:

Collection ID:CO001991
Collection Summary:The cells were seeded at a density of 1 × 10^6 cells/mL in a culture flask. The cells which had grown to 80-90% confluence, were harvested by treatment with trypsin- ethylenediaminetetraacetic acid and centrifuged. To remove the residual medium, the cell pellet was washed with 1× phosphate buffered saline twice. The cells were freeze-dried and stored at −70 °C until further analysis.
Sample Type:Breast cancer cells
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR002010
Treatment Summary:Cells at 70–80% confluency were subjected to irradiation using a ^60CO Theratron-780 teletherapy unit at a dose rate of 1.52 Gy per minute. The cells were subjected to 25 cycles of 2 Gy irradiation over 5 weeks, and the surviving cells were designated as MDA-MB-231/RR cells.
Cell Media:DMEM supplemented with 10% FBS and 1% penicillin-streptomycin
Cell Envir Cond:A humidified incubator at 37 °C (95% air and 5% CO2)

Sample Preparation:

Sampleprep ID:SP002004
Sampleprep Summary:Extraction of metabolites and intact lipid species was performed using a modified Folch procedur. Briefly, 1 mL of ice-cold chloroform containing 0.1% BHT and 0.5 mL of ice-cold methanol containing 0.1% BHT were added to the freeze-dried cells and vortexed. The mixture were sonicated for 30 min at 4 °C and incubated for 40 min on ice with shaking. Ice-cold water containing 0.1% BHT (0.38 mL) was added to the mixture for phase separation, and then centrifuged. The upper (methanol) and lower (chloroform) phases were dried under nitrogen gas and used GC-MS and nanoESI-MS analyses, respectively. To conduct metabolic profiling using GC-MS, derivatization reaction was conducted by adding 30 μL of 20,000 μg/mL methoxylamine hydrochloride in pyridine, 10 μL of myristic-d27 acid (300 μg/mL as an internal standard), and 50 μL of BSTFA containing 1% TMCS into dried (methanol phase) sample and incubated for 60 min at 65 °C. After derivatization, 15 μL of each sample was pooled for quality control (QC) and analyzed in sextuplicate. To conduct metabolic profiling using nanoESI-MS, dried (chloroform phase) sample was resuspended with 130 μL of buffer solution (7.5 mM ammonium acetate in methanol-chloroform (9:1, v/v)) and 10 μL of each resuspended sample was pooled for QC and analyzed in sextuplicate.
Processing Storage Conditions:Described in summary
Extraction Method:A modified Folch method
Extract Storage:-80℃
Sample Resuspension:Described in summary
Sample Derivatization:Described in summary

Combined analysis:

Analysis ID AN003119 AN003120 AN003121
Analysis type MS MS MS
Chromatography type GC None (Direct infusion) None (Direct infusion)
Chromatography system Agilent 7890A automated nanoinfusion/nanospray source automated nanoinfusion/nanospray source
Column Agilent DB5-MS (30m x 0.25mm, 0.25um) None None
MS Type EI ESI ESI
MS instrument type Triple axis detector Ion trap Ion trap
MS instrument name Agilent 5975C Thermo LTQ XL Thermo LTQ XL
Ion Mode POSITIVE POSITIVE NEGATIVE
Units relative intensity/µg proteins relative intensity/µg proteins relative intensity/µg proteins

Chromatography:

Chromatography ID:CH002304
Instrument Name:Agilent 7890A
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Internal Standard:myristic-d27 acid (300 μg/mL as an internal standard
Chromatography Type:GC
  
Chromatography ID:CH002305
Instrument Name:automated nanoinfusion/nanospray source
Column Name:None
Chromatography Type:None (Direct infusion)
  
Chromatography ID:CH002306
Instrument Name:automated nanoinfusion/nanospray source
Column Name:None
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002900
Analysis ID:AN003119
Instrument Name:Agilent 5975C
Instrument Type:Triple axis detector
MS Type:EI
MS Comments:The initial oven temperature was set at 70 °C and then increased to 190°C (5 °C/min), 240 °C (6 °C/min), and 280 °C (5 °C/min). Data was processed using Expressionist® MSX software (version 2013.0.39, Genedata, Basel, Switzerland).
Ion Mode:POSITIVE
  
MS ID:MS002901
Analysis ID:AN003120
Instrument Name:Thermo LTQ XL
Instrument Type:Ion trap
MS Type:ESI
MS Comments:The raw data files (*.raw) were transformed to *.mzXML using the ProteoWizard MSConvert. Data was processed using Expressionist® MSX software (version 2013.0.39, Genedata, Basel, Switzerland).
Ion Mode:POSITIVE
Capillary Temperature:200 °C
Capillary Voltage:20 V
Gas Pressure:0.4 psi
Ion Spray Voltage:1.4 kV
  
MS ID:MS002902
Analysis ID:AN003121
Instrument Name:Thermo LTQ XL
Instrument Type:Ion trap
MS Type:ESI
MS Comments:The raw data files (*.raw) were transformed to *.mzXML using the ProteoWizard MSConvert. Data was processed using Expressionist® MSX software (version 2013.0.39, Genedata, Basel, Switzerland).
Ion Mode:NEGATIVE
Capillary Temperature:200 °C
Capillary Voltage:−2 V
Gas Pressure:0.6 psi
Ion Spray Voltage:1.7 kV
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