Summary of Study ST000442
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 PR000341. The data can be accessed directly via it's Project DOI: 10.21228/M8989V This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000442 |
| Study Title | Metabolomics Analysis of Triple Negative Breast Cancer (BCa) Cell Lines |
| Study Type | Metabolomics comparison of different breast cancer cell lines |
| Study Summary | We 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. |
| Institute | University of North Carolina |
| Department | Discovery Sciences |
| Laboratory | Sumner Lab |
| Last Name | Sumner |
| First Name | Susan |
| Address | Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081 |
| susan_sumner @unc.edu | |
| Phone | 704-250-5066 |
| Submit Date | 2016-08-02 |
| Num Groups | 4 |
| Total Subjects | 24 |
| Study Comments | 4 breast cancer cell lines, treated with paclitaxel compared to controls (3 replicates/line/condition) |
| Publications | J. Proteome Res., Article ASAP, DOI: 10.1021/acs.jproteome.6b00430 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | 1r |
| Analysis Type Detail | NMR |
| Release Date | 2016-12-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| 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 |
| Email: | dstewart@rti.org |
| Phone: | 919-541-7204 |
| Funding Source: | Internal IR&D (RTI International) and RCMRC |
| Publications: | J. Proteome Res., Article ASAP |
Subject:
| 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 |
Factors:
Subject type: Cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA022538 | TB231CDM48R2N | Media alone |
| SA022539 | LB474CDM48R1N | Media alone |
| SA022540 | TB231CDM48R3N | Media alone |
| SA022541 | TB468CDM48R2N | Media alone |
| SA022542 | TB468CDM48R3N | Media alone |
| SA022543 | LBMCFCDM48R3N | Media alone |
| SA022544 | TB468CDM48R1N | Media alone |
| SA022545 | TB231CDM48R1N | Media alone |
| SA022546 | LB474CDM48R3N | Media alone |
| SA022547 | LBMCFCDM48R2N | Media alone |
| SA022548 | LBMCFCDM48R1N | Media alone |
| SA022549 | LB474CDM48R2N | Media alone |
| SA022550 | LB474TDM48R1N | Taxol |
| SA022551 | TB468TDM48R1N | Taxol |
| SA022552 | TB468TDM48R2N | Taxol |
| SA022553 | LB474TDM48R2N | Taxol |
| SA022554 | TB468TDM48R3N | Taxol |
| SA022555 | TB231TDM48R2N | Taxol |
| SA022556 | LBMCFTDM48R3N | Taxol |
| SA022557 | LBMCFTDM48R2N | Taxol |
| SA022558 | LB474TDM48R3N | Taxol |
| SA022559 | TB231TDM48R1N | Taxol |
| SA022560 | LBMCFTDM48R1N | Taxol |
| SA022561 | TB231TDM48R3N | Taxol |
| Showing results 1 to 24 of 24 |
Collection:
| 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:
| 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:
| 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:
| 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 |
| Apodization: | Lorentzian |
| 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) |
