Summary of Study ST000054
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 PR000051. The data can be accessed directly via it's Project DOI: 10.21228/M8MS3J This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST000054 |
| Study Title | Metabolic Microenvironments in Normal Breast and Breast Cancer (MS analysis) |
| Study Type | Metabolomic analysis of normal breast tissue |
| Study Summary | The purpose of this study was to understand the metabolomic changes in a breast tissue microenvironment at various stages of cancer development and progression (i.e. normal breast, DCIS, and invasive cancer). The goal of this metabolomics pilot and feasibility study was to apply a broad spectrum GC-MS metabolomics method to determine whether changes in normal tissue of women with cancer correlate with progression and or the subtype of the disease. |
| Institute | University of North Carolina |
| Department | Systems and Translational 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 | 2014-04-30 |
| Num Groups | 8 |
| Total Subjects | 192 |
| Study Comments | sample preparation and analysis randomized with data collection over multiple days |
| Publications | 1. Brauer HA, Makowski L, Hoadley KA, Casbas-Hernandez P, Lang LJ, Roman-Perez E, D’Arcy M, Freemerman AJ, Perou CM, Troester MA: Impact of tumor microenvironment and epithelial phenotypes on metabolism in breast cancer. Clin Cancer Res 2012;19:571-585. 2. J Budczies, C Denkert, B Muller, S Brockmoller, F Klauschen, B Gyorffy, M Dietel, C Richter-Ehrenstein, U Marten, R Salek, J Griffin, M Hilvo, M Oresic, G Wohlgemuth, O Fiehn: Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue – a GC-TOFMS based metabolomics study. BMC Genomics 2012; 13:334. |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Uploaded File Size | 8.4 G |
| Analysis Type Detail | GC-MS |
| Release Date | 2018-08-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000051 |
| Project DOI: | doi: 10.21228/M8MS3J |
| Project Title: | Metabolic Microenvironments in Normal Breast and Breast Cancer |
| Project Type: | Broad Spectrum |
| Project Summary: | Breast cancers evolve and acquire adaptive changes while in active communication with the surrounding host normal tissue. It is important to understand the genomic and metabolomic changes in breast microenvironment at various stages of cancer development and progression (i.e., normal breast, DCIS, benign disease and invasive cancer). Since intrinsic breast cancer subtypes are very distinct from each other in terms of clinical features as well as the genomic profiling, these subtypes may also have distinct metabolic microenvironment signatures. |
| Institute: | University of North Carolina at Chapel Hill |
| Department: | Epidemiology |
| Laboratory: | Troester Laboratory |
| Last Name: | Troester |
| First Name: | Melissa |
| Address: | University of North Carolina at Chapel Hill Chapel Hill, NC 27599 |
| Email: | troester@unc.edu |
| Phone: | 919-966-7408 |
Subject:
| Subject ID: | SU000073 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | female |
| Species Group: | Human |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | treatment |
|---|---|---|
| SA002629 | 1402110jcsa35_1 | Basal | pool aliquot:no |
| SA002630 | 140217ajcsa17_1 | Basal | pool aliquot:no |
| SA002631 | 140214ajcsa10_1 | Basal | pool aliquot:no |
| SA002632 | 140217ajcsa46_1 | Basal | pool aliquot:no |
| SA002633 | 140219ajcsa08_1 | Basal | pool aliquot:no |
| SA002634 | 140219ajcsa38_1 | Basal | pool aliquot:no |
| SA002635 | 1402110jcsa37_1 | Basal | pool aliquot:no |
| SA002636 | 140217ajcsa16_1 | Basal | pool aliquot:no |
| SA002637 | 140214ajcsa40_1 | Basal | pool aliquot:no |
| SA002638 | 140214ajcsa08_1 | Basal | pool aliquot:no |
| SA002639 | 140214ajcsa44_1 | Basal | pool aliquot:no |
| SA002640 | 140217ajcsa09_1 | Basal | pool aliquot:no |
| SA002641 | 1402110jcsa42_1 | Basal | pool aliquot:no |
| SA002642 | 1402110jcsa19_1 | Basal | pool aliquot:no |
| SA002643 | 140214ajcsa28_1 | Basal | pool aliquot:no |
| SA002644 | 140219ajcsa19_1 | Basal | pool aliquot:no |
| SA002645 | 140219ajcsa24_1 | Basal | pool aliquot:no |
| SA002646 | 1402110jcsa12_1 | Basal | pool aliquot:no |
| SA002647 | 140219ajcsa22_1 | Basal | pool aliquot:no |
| SA002648 | 140219ajcsa28_1 | Basal | pool aliquot:no |
| SA002649 | 140219ajcsa36_1 | Basal | pool aliquot:no |
| SA002650 | 140217ajcsa36_1 | Basal | pool aliquot:yes |
| SA002651 | 1402110jcsa44_1 | Basal | pool aliquot:yes |
| SA002652 | 140214ajcsa35_1 | Basal | pool aliquot:yes |
| SA002653 | 140219ajcsa26_1 | Basal | pool aliquot:yes |
| SA002654 | 140219ajcsa45_1 | DCIS | pool aliquot:no |
| SA002655 | 140214ajcsa45_1 | DCIS | pool aliquot:no |
| SA002656 | 140214ajcsa17_1 | DCIS | pool aliquot:no |
| SA002657 | 140217ajcsa10_1 | DCIS | pool aliquot:no |
| SA002658 | 1402110jcsa07_1 | DCIS | pool aliquot:no |
| SA002659 | 140217ajcsa11_1 | DCIS | pool aliquot:no |
| SA002660 | 140219ajcsa32_1 | DCIS | pool aliquot:no |
| SA002661 | 140219ajcsa51_1 | DCIS | pool aliquot:no |
| SA002662 | 140214ajcsa39_1 | DCIS | pool aliquot:no |
| SA002663 | 140219ajcsa17_1 | DCIS | pool aliquot:no |
| SA002664 | 140219ajcsa54_1 | DCIS | pool aliquot:no |
| SA002665 | 140214ajcsa43_1 | DCIS | pool aliquot:no |
| SA002666 | 140219ajcsa50_1 | DCIS | pool aliquot:no |
| SA002667 | 140217ajcsa45_1 | DCIS | pool aliquot:no |
| SA002668 | 140217ajcsa12_1 | DCIS | pool aliquot:no |
| SA002669 | 140219ajcsa14_1 | DCIS | pool aliquot:no |
| SA002670 | 140214ajcsa22_1 | DCIS | pool aliquot:no |
| SA002671 | 1402110jcsa32_1 | DCIS | pool aliquot:no |
| SA002672 | 140217ajcsa26_1 | DCIS | pool aliquot:no |
| SA002673 | 140214ajcsa16_1 | DCIS | pool aliquot:no |
| SA002674 | 1402110jcsa17_1 | DCIS | pool aliquot:no |
| SA002675 | 140214ajcsa33_1 | DCIS | pool aliquot:no |
| SA002676 | 140214ajcsa31_1 | DCIS | pool aliquot:no |
| SA002677 | 140219ajcsa29_1 | DCIS | pool aliquot:no |
| SA002678 | 140219ajcsa40_1 | DCIS | pool aliquot:no |
| SA002679 | 140214ajcsa36_1 | DCIS | pool aliquot:yes |
| SA002680 | 140217ajcsa19_1 | DCIS | pool aliquot:yes |
| SA002681 | 1402110jcsa23_1 | DCIS | pool aliquot:yes |
| SA002682 | 140219ajcsa10_1 | DCIS | pool aliquot:yes |
| SA002683 | 140214ajcsa23_1 | HER2 | pool aliquot:no |
| SA002684 | 140217ajcsa21_1 | HER2 | pool aliquot:no |
| SA002685 | 140219ajcsa21_1 | HER2 | pool aliquot:no |
| SA002686 | 140219ajcsa31_1 | HER2 | pool aliquot:no |
| SA002687 | 140219ajcsa18_1 | HER2 | pool aliquot:no |
| SA002688 | 140217ajcsa33_1 | HER2 | pool aliquot:no |
| SA002689 | 140217ajcsa15_1 | HER2 | pool aliquot:no |
| SA002690 | 140217ajcsa28_1 | HER2 | pool aliquot:no |
| SA002691 | 140217ajcsa14_1 | HER2 | pool aliquot:no |
| SA002692 | 140214ajcsa42_1 | HER2 | pool aliquot:no |
| SA002693 | 140214ajcsa12_1 | HER2 | pool aliquot:no |
| SA002694 | 1402110jcsa36_1 | HER2 | pool aliquot:no |
| SA002695 | 1402110jcsa45_1 | HER2 | pool aliquot:no |
| SA002696 | 1402110jcsa46_1 | HER2 | pool aliquot:no |
| SA002697 | 1402110jcsa43_1 | HER2 | pool aliquot:no |
| SA002698 | 1402110jcsa28_1 | HER2 | pool aliquot:no |
| SA002699 | 140214ajcsa21_1 | HER2 | pool aliquot:yes |
| SA002700 | 140219ajcsa16_1 | HER2 | pool aliquot:yes |
| SA002701 | 1402110jcsa47_1 | HER2 | pool aliquot:yes |
| SA002702 | 140217ajcsa30_1 | HER2 | pool aliquot:yes |
| SA002703 | 140217ajcsa37_1 | LumA | pool aliquot:no |
| SA002704 | 140217ajcsa47_1 | LumA | pool aliquot:no |
| SA002705 | 1402110jcsa10_1 | LumA | pool aliquot:no |
| SA002706 | 140219ajcsa42_1 | LumA | pool aliquot:no |
| SA002707 | 1402110jcsa26_1 | LumA | pool aliquot:no |
| SA002708 | 140217ajcsa07_1 | LumA | pool aliquot:no |
| SA002709 | 140217ajcsa18_1 | LumA | pool aliquot:no |
| SA002710 | 1402110jcsa14_1 | LumA | pool aliquot:no |
| SA002711 | 140217ajcsa29_1 | LumA | pool aliquot:no |
| SA002712 | 1402110jcsa29_1 | LumA | pool aliquot:no |
| SA002713 | 140217ajcsa24_1 | LumA | pool aliquot:no |
| SA002714 | 1402110jcsa33_1 | LumA | pool aliquot:no |
| SA002715 | 140214ajcsa47_1 | LumA | pool aliquot:no |
| SA002716 | 140217ajcsa43_1 | LumA | pool aliquot:no |
| SA002717 | 140219ajcsa23_1 | LumA | pool aliquot:no |
| SA002718 | 1402110jcsa39_1 | LumA | pool aliquot:no |
| SA002719 | 140219ajcsa43_1 | LumA | pool aliquot:no |
| SA002720 | 140214ajcsa11_1 | LumA | pool aliquot:no |
| SA002721 | 1402110jcsa25_1 | LumA | pool aliquot:no |
| SA002722 | 1402110jcsa21_1 | LumA | pool aliquot:no |
| SA002723 | 140219ajcsa12_1 | LumA | pool aliquot:no |
| SA002724 | 1402110jcsa18_1 | LumA | pool aliquot:no |
| SA002725 | 140219ajcsa55_1 | LumA | pool aliquot:no |
| SA002726 | 140217ajcsa42_1 | LumA | pool aliquot:yes |
| SA002727 | 140214ajcsa15_1 | LumA | pool aliquot:yes |
| SA002728 | 140219ajcsa30_1 | LumA | pool aliquot:yes |
Collection:
| Collection ID: | CO000056 |
| Collection Summary: | Cancer-adjacent, normal breast tissue was collected |
| Collection Protocol ID: | UNC-CH IRB #09-1436 |
| Collection Protocol Filename: | Normal_Breast_Study |
| Collection Protocol Comments: | Breast tissue samples were collected from patients in the UNC hospital system under the Normal Breast Study (IRB #09-1436). Normal breast tissue from patients with reduction mammoplasty, DCIS and invasive breast cancer were analyzed in this study. Tissue samples 2-4 cm away from the tumor were collected and stored at -80°C after surgery. Samples were cut on dry ice to yield a metabolomics sample comprising 50-120 mg tissue. The tissue was placed in a tissue homogenization tube with ceramic beads and stored at -80°C. The samples were delivered to the RTI RCMRC and stored at -80°C. |
| Sample Type: | tissue |
| Collection Method: | tissue collected during surgery |
| Collection Location: | breast microenvironment |
| Collection Frequency: | one time collection |
| Volumeoramount Collected: | 50 - 120mg |
| Storage Conditions: | -80 C |
| Tissue Cell Identification: | breast |
| Tissue Cell Quantity Taken: | 50mg |
Treatment:
| Treatment ID: | TR000074 |
| Treatment Summary: | Stages of breast cancer progression and different subtypes compared to a non-malignant control |
| Treatment Protocol Comments: | DCIS, Luminal A, Luminal B, HER2, Basal, Reduction, Total Pool1 (equal mix of DCIS, HER2, LumA, LumB, Reduction, and Basal pool samples),Total Pool2 (unequal mix of DCIS, HER2, LumA, LumB, Reduction, and Basal pool samples) |
Sample Preparation:
| Sampleprep ID: | SP000069 |
| Sampleprep Summary: | Breast tissue samples were homogenized in 3:3:2 (acetonitrile:isopropanol:water) at a concentration of 100 mg/mL. Samples dried and extracted into 50% acetonitrile. Sample dried and aliquot taken for NMR. Sample returned and extract processed for GC/MS analysis. Samples were derivatized using 2 step derivatization method (methoximation with methoxy amine followed by TMS derivatization with MSTFA). |
| Sampleprep Protocol Filename: | RTI_MT_Breast_Tissue_Procedures_GC-TOF-MS.docx |
| Processing Method: | Homogenization and Solvent Removal with SpeedVac |
| Processing Storage Conditions: | 4°C |
| Extraction Method: | 3:3:2 (acetonitrile:isopropanol:water) and then 50% Acetonitrile |
| Extract Concentration Dilution: | dried on SpeedVac |
| Extract Storage: | -80°C |
| Sample Resuspension: | resuspended in D2O + Chenomix ISTD solution |
| Sample Derivatization: | Methoximation with methoxy amine at 40 mg/ml in pyridine followed by TMS derivatization with MSTFA |
| Sample Spiking: | FAMES (C8-C30) added to MSTFA as retention time markers |
Combined analysis:
| Analysis ID | AN000092 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus 4D GC |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC x GC-TOF |
| MS instrument name | Leco Pegasus 4D GCxGC TOF |
| Ion Mode | POSITIVE |
| Units | Peak height |
Chromatography:
| Chromatography ID: | CH000060 |
| Chromatography Summary: | GC/MS analysis is based on Oliver Fiehn methods |
| Instrument Name: | Leco Pegasus 4D GC |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Column Pressure: | 10.4 psi |
| Column Temperature: | 50C(0.5 min)-330C(@20C/min)-330C(5 min) |
| Flow Gradient: | constant flow |
| Flow Rate: | 1.0 mL/min |
| Injection Temperature: | 250C |
| Retention Index: | FAMEs markers (C8-C30) |
| Retention Time: | FAMEs markers (C8-C30) |
| Analytical Time: | 20 minutes |
| Oven Temperature: | 50C(0.5 min)-330C(@20C/min)-330C(5 min) |
| Transferline Temperature: | 280C |
| Sample Syringe Size: | 10 L |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000069 |
| Analysis ID: | AN000092 |
| Instrument Name: | Leco Pegasus 4D GCxGC TOF |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 280C (transfer line) |
| Helium Flow: | 1.0 ml/min |
| Ion Source Temperature: | 250C |
| Ionization Energy: | 70 eV |
| Source Temperature: | 250C |
| Dataformat: | netcdf |
| Resolution Setting: | 1200 |
| Scan Range Moverz: | 50-800 |
| Scanning: | 20 spectra/sec |
