Summary of Study ST001265
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 PR000850. The data can be accessed directly via it's Project DOI: 10.21228/M8T98G This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001265 |
| Study Title | Comparative metabolomics of MCF-7 breast cancer cells using different extraction solvents assessed by mass spectroscopy |
| Study Type | Analysing metabolomics using GC Mass Spectroscopy |
| Study Summary | Metabolic profiling of cancer cells can play a vital role in revealing the molecular bases of cancer development and progression. In this study, gas chromatography coupled with mass spectrometry (GC-MS) was employed for the determination of signatures found in ER+/ PR+ breast cancer cells derived from MCF-7 using different extraction solvents including: A, formic acid in water; B, ammonium hydroxide in water; C, ethyl acetate; D, methanol: water (1:1, v/v); and E, acetonitrile: water (1:1, v/v). The greatest extraction rate and diversity of metabolites occurs with extraction solvents A and E. Extraction solvent D showed moderate extraction efficiency, whereas extraction solvent B and C showed inferior metabolite diversity. Metabolite set enrichment analysis results showed energy production pathways to be key in MCF-7 cell lines. This study showed that mass spectrometry could identify key metabolites associated with cancers. The highest enriched pathways were related to energy production as well as Warburg effect pathways, which may shed light on how energy metabolism has been hijacked to encourage tumour progression and eventually metastasis in breast cancer. |
| Institute | Sharjah Institute for Medical Research |
| Department | Clinical Science |
| Last Name | Hamoudi |
| First Name | Rifat |
| Address | College of Medicine, University of Sharjah |
| rhamoudi@sharjah.ac.ae | |
| Phone | 567154756 |
| Submit Date | 2019-07-08 |
| Total Subjects | Five different extractions |
| Study Comments | MCF-7 cell line |
| Raw Data Available | Yes |
| Raw Data File Type(s) | gqd |
| Analysis Type Detail | GC-MS |
| Release Date | 2019-10-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Sample Preparation:
| Sampleprep ID: | SP001341 |
| Sampleprep Summary: | A total of 5 triplicated MCF-7 cell culture samples were provided in Eppendorf vials dissolved in PBS, and stored at 4 °C for preservation purposes. Samples were centrifuged at 13000 rpm for 10 minutes at -4 °C. Supernatant was discarded, and cell pellets, each containing 3 million cells, were subjected to metabolomics analysis. In order to evaluate the influence of the solvents on the extraction rate, samples were divided in five different extraction groups: A, 0.2 % formic acid in water; B, 0.2 % ammonium hydroxide in water; C, ethyl acetate; D, methanol/water (1:1, v/v); and E, acetonitrile/water (1:1, v/v). Briefly, 300 µL of the extraction solvent was added to 3 million cell pellets, then vortexed for 2 minutes. All samples have been stored in ice for 1 hour, during which samples have been vortexed every 15 minutes. After this, cell insoluble matrix was centrifuged (13000 rpm, 10 minutes, -4 °C). Supernatant was collected then dried using EZ-2 Plus (GeneVac, Ipswich, UK) at 37 ± 1 °C. To detect all amino acids and metabolites, all samples were derivatized with methoxyamine hydrochloride and MSTFA + 1% TMCS prior to injection to GC-MS. |
| Processing Storage Conditions: | Described in summary |
| Extraction Method: | Direct extraction |
| Extract Enrichment: | described in Summary |
| Extract Storage: | Described in summary |
| Sample Derivatization: | methoxyamine hydrochloride and MSTFA + 1% TMCS |
