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 |
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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 |
