Summary of Study ST000442

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000341. The data can be accessed directly via it's Project DOI: 10.21228/M8989V This work is supported by NIH grant, U2C- DK119886.


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Study IDST000442
Study TitleMetabolomics Analysis of Triple Negative Breast Cancer (BCa) Cell Lines
Study TypeMetabolomics comparison of different breast cancer cell lines
Study SummaryWe used untargeted metabolomic profiling to distinguish this form of BCa from estrogen receptor positive (ER+) subtypes (+/- HER2/neu) and determine that may explain why a commonly used chemotherapeutic, paclitaxel, is generally ineffective at eliciting long-term cytotoxic and/or cytostatic responses in cell line models of TNBC. This metabolomics study used broad spectrum 1H NMR to compare Luminal A (BT474, MCF-7) and triple-negative (MDA-MB-231, MDA-MB-468) BCa cell lines, to determine differences in the two subtypes as well as distinguish therapeutic treatment responses for identifying new targets for drug discovery.
University of North Carolina
DepartmentDiscovery Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Submit Date2016-08-02
Num Groups4
Total Subjects24
Study Comments4 breast cancer cell lines, treated with paclitaxel compared to controls (3 replicates/line/condition)
PublicationsJ. Proteome Res., Article ASAP, DOI: 10.1021/acs.jproteome.6b00430
Raw Data AvailableYes
Raw Data File Type(s)1r
Analysis Type DetailNMR
Release Date2016-12-22
Release Version1
Susan Sumner Susan Sumner application/zip

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Project ID:PR000341
Project DOI:doi: 10.21228/M8989V
Project Title:Metabolomics Analysis of Triple Negative Breast Cancer Cell Lines
Project Type:Metabolomics Analysis
Project Summary:To date there are no clinically approved targeted therapies for triple negative breast cancer (TNBC). In addition to the absence of estrogen, progesterone, and HER2/neu receptors, TNBCs possess characteristics that make them some of the most aggressive forms of breast cancer (BCa). In terms of epidemiology, breast cancers with the triple negative profile present at a higher prevalence in premenopausal women under the age of 40, usually with a BMI greater than 30, and have higher incidences of mutations in BRCA1 or BRCA2 genes. Additionally, several studies have shown a higher prevalence in African American women, demonstrating a health disparity. In spite of this knowledge and the fact that most people respond to initial chemotherapeutic treatment, lasting treatment modalities used for the cure and maintenance of other BCa subtypes generally fail to significantly increase disease-free survival or diminish the rates of recurrence within the first five years after initial detection of TNBC. Our ultimate goal is to identify novel biomarkers which may be leveraged for initiating prevention strategies in high risk populations, earlier detection, or targeted treatment of this disease.
Institute:RTI International
Department:Discovery Sciences
Laboratory:STS/NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC)
Last Name:Delisha
First Name:Stewart
Address:3040, East Cornwallis Road, Research Triangle Park, NC 27709
Funding Source:Internal IR&D (RTI International) and RCMRC
Publications:J. Proteome Res., Article ASAP


Subject ID:SU000463
Subject Type:Cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Biosource Or Supplier:American Type Culture Collection
Cell Strain Details:Breast Cancer Cell lines (BT474, MCF-7, MDA-MB-231, MDA-MB-468)
Cell Primary Immortalized:Immortalized
Species Group:Human


Subject type: Cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA022538TB231CDM48R2NMedia alone
SA022539LB474CDM48R1NMedia alone
SA022540TB231CDM48R3NMedia alone
SA022541TB468CDM48R2NMedia alone
SA022542TB468CDM48R3NMedia alone
SA022543LBMCFCDM48R3NMedia alone
SA022544TB468CDM48R1NMedia alone
SA022545TB231CDM48R1NMedia alone
SA022546LB474CDM48R3NMedia alone
SA022547LBMCFCDM48R2NMedia alone
SA022548LBMCFCDM48R1NMedia alone
SA022549LB474CDM48R2NMedia alone
Showing results 1 to 24 of 24


Collection ID:CO000457
Collection Summary:Cell samples were scraped off the dish in 4 mL of 50:50 acetonitrile:water and collected into 15 mL tubes prior to homogenization and extraction.
Sample Type:cells
Storage Conditions:-80°C


Treatment ID:TR000477
Treatment Summary:Briefly, mycoplasma tested and certified BCa cell lines will be purchased from American Type Culture Collection (ATCC) and maintained under the manufacturer’s recommended conditions. Cells were grown for 48 h in the presence or absence of chemotherapeutic agent paclitaxel (10 nM).

Sample Preparation:

Sampleprep ID:SP000470
Sampleprep Summary:Added 1 mL of an ice-cold chloroform to the tubes and 10 ceramic beads. Tubes were vortexed for 30 seconds on a multi-tube vortexer at 5000 rpm three times to homogenize and centrifuged samples at 4 °C in a swinging bucket centrifuge for 60 min at 3,700 rpm. Majority of aqueous (top) layer was carefully transferred to 5 mL cryotubes. Majority of lipid (bottom) layer was carefully transferred to 7 mL glass vials. Remaining protein layer and residual aqueous & lipid layers were transferred into a 2 mL Lo-Bind tubes. Original tubes were rinsed with 600 µL of 2:1 chloroform:methanol solution and transferred to the 2 mL tubes. Centrifuged tubes at 15,000 rpm at 4 °C for 20 min and transferred remaining aqueous & lipid fractions into respective tubes. For each study sample, an 800 µL aliquot of the aqueous fractions was transferred to labeled 2.0 mL Lo-Bind tubes. Analytical pooled QC samples were generated by transferring an additional 75 µL aliquot from all study samples into a 10 mL tube. The total pooled sample was vortexed and 800 µL aliquots were transferred to 2.0 mL tubes labeled Pool. All tubes were frozen for 1 hr and lyophilized to dryness overnight. Samples were reconstituted by adding 700 µL of 90:10 D2O:Chenomx ISTD master mix to each, vortexed for 2 mins and centrifuged at 16,000 rcf for 4 min. A 600 µL aliquot of the supernatant was transferred into 5 mm NMR tubes (Bruker-Biospin, Switzerland), and kept on ice until data acquisition.
Processing Method:lyophilization
Extraction Method:Acetonitrile:water and chloroform
Sample Resuspension:NMR master mix
Cell Type:breast cancer


Analysis ID:AN000693
Laboratory Name:David H. Murdock Research Institute.
Analysis Type:NMR
Acquisition Date:7/29/14 and 8/13/14
Software Version:TopSpin 3.2
Operator Name:Jason Winnike
Detector Type:NMR
Num Factors:2


NMR ID:NM000077
Analysis ID:AN000693
Instrument Name:Bruker Avance III 600 MHz
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Field Frequency Lock:Deuterium
Standard Concentration:0.5 mM DSS
Spectrometer Frequency:600 MHz
NMR Probe:5 mm ATMA Cryoprobe
NMR Solvent:D2O
NMR Tube Size:5 mm
Shimming Method:Topshim
Pulse Sequence:noesyprid
Water Suppression:yes
Pulse Width:9.28 us
Power Level:39.811 W
Receiver Gain:50.8
Offset Frequency:2817.50 Hz
Presaturation Power Level:0.000025119 W
Chemical Shift Ref Cpd:DSS
Temperature:298.1 K
Number Of Scans:256
Dummy Scans:4
Acquisition Time:2.482 s
Relaxation Delay:2 s
Spectral Width:11.0011 ppm, 6602.113 Hz
Num Data Points Acquired:32768
Real Data Points:16384
Line Broadening:0.5 Hz
Zero Filling:yes
Baseline Correction Method:Polynomial
Chemical Shift Ref Std:DSS
Binned Increment:0.04
Binned Data Excluded Range:water (4.66 - 4.86 ppm); imidazole (7.15-7.26 ppm)