Summary of Study ST000438
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 PR000338. The data can be accessed directly via it's Project DOI: 10.21228/M8X01N This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000438 |
| Study Title | Characterizing commonalities and differences between the breast and prostate cancer metabotypes in African-American cohorts (part I) |
| Study Type | Identify Breast Cancer Progression and Prostate Cancer correlative Metabolite Markers |
| Study Summary | Thus, we aimed to 1) understand mechanisms related to the onset and progression of BCa, 2) identify precursors and targets for prevention and therapy for each stage, grade and subtype which may contribute to the disparate impact of BCa in African American women, and 3) Identify common and different BCa metabolite markers versus PCa markers. |
| Institute | University of North Carolina |
| Department | NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC) |
| 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 | 2 |
| Total Subjects | 48 |
| Num Females | 48 |
| Raw Data Available | Yes |
| Analysis Type Detail | NMR |
| Release Date | 2016-09-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000338 |
| Project DOI: | doi: 10.21228/M8X01N |
| Project Title: | Characterizing commonalities and differences between the breast and prostate cancer metabotypes in African-American cohorts |
| Project Type: | Identify Breast Cancer Progression and Prostate Cancer correlative Metabolite Markers |
| Project Summary: | Many attempts have been made to identify critical events responsible for the development and progression of breast cancer (BCa). In spite of this, the mechanisms underlying notably tumor invasion and BCa dissemination remain largely unclear. The pathological features of BCa follow a sequential progression from the transformation of a normal cell to benign proliferation, hyperplasia, atypical ductal hyperplasia (ADH), ductal carcinoma in-situ (DCIS) to invasive ductal carcinoma (IDC) and metastatic diseases. It has been reported that the disease phenotype is distinguishable in ADH and progresses along distinct pathways for each subtype. The genetic signature for disease heterogeneity across subtypes is greater than the heterogeneity of progression from DCIS to IDC within a subtype, suggesting that the disease subtypes have distinct progression pathways. Even so, genetics does not fully explain etiology nor progression. Additionally, a large population based study reported an increased risk of male BCa after prostate cancer (PCa). The two cancers share similarities with a wide heterogeneity of both phenotype and biology. A unique feature of PCa and BCa is that at least in the initial stages, they are hormone-dependent and have remarkable underlying biological similarities. Our recent study and others showed an increased level of common metabolites in BCa and PCa. Thus, understanding the metabolic profiles of breast and prostate cancer would pave the way for new biomarkers to improve diagnosis and treatment strategies. |
| Institute: | Howard University |
| Department: | Department of Microbiology and Cancer Center |
| Last Name: | Kanaan |
| First Name: | Yasmine |
| Address: | 1840 Seventh Street, NW Suite 309, Washington, DC 20001 |
| Email: | ymkanaan@Howard.edu |
| Phone: | 202 806 9540 |
Subject:
| Subject ID: | SU000459 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
| Human Race: | African American |
| Human Ethnicity: | African American |
| Species Group: | Human |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA022035 | S_104 | BC |
| SA022036 | S_90 | BC |
| SA022037 | S_110 | BC |
| SA022038 | S_95 | BC |
| SA022039 | S_99 | BC |
| SA022040 | S_79 | BC |
| SA022041 | S_98 | BC |
| SA022042 | S_100 | BC |
| SA022043 | S_81 | BC |
| SA022044 | S_82 | BC |
| SA022045 | S_97 | BC |
| SA022046 | S_113 | BC |
| SA022047 | S_92 | BC |
| SA022048 | S_106 | BC |
| SA022049 | S_107 | BC |
| SA022050 | S_83 | BC |
| SA022051 | S_111 | BC |
| SA022052 | S_89 | BC |
| SA022053 | S_102 | BC |
| SA022054 | S_87 | BC |
| SA022055 | S_114 | BC |
| SA022056 | S_112 | BC |
| SA022057 | S_77 | BC |
| SA022058 | S_101 | BC |
| SA022059 | S_96 | BC |
| SA022060 | S_85 | BC |
| SA022061 | S_109 | BC |
| SA022062 | S_88 | BC |
| SA022063 | S_93 | BC |
| SA022064 | S_105 | BC |
| SA022065 | S_103 | BC |
| SA022066 | S_115 | BC |
| SA022067 | S_84 | BC |
| SA022068 | S_94 | BC |
| SA022069 | S_78 | BC |
| SA022070 | S_80 | BC |
| SA022071 | S_91 | BC |
| SA022072 | S_108 | BC |
| SA022073 | S_70 | WC |
| SA022074 | S_72 | WC |
| SA022075 | S_75 | WC |
| SA022076 | S_71 | WC |
| SA022077 | S_76 | WC |
| SA022078 | S_73 | WC |
| SA022079 | S_68 | WC |
| SA022080 | S_74 | WC |
| SA022081 | S_67 | WC |
| SA022082 | S_69 | WC |
| Showing results 1 to 48 of 48 |
Collection:
| Collection ID: | CO000453 |
| Collection Summary: | The collection was approved and executed in compliance with HU Institutional Review Board (IRB-06-CC-01-A) following HIPPA guidelines and all samples have been de-identified and coded to preserve patients’ confidentiality. |
| Sample Type: | Breast |
Treatment:
| Treatment ID: | TR000473 |
| Treatment Summary: | No treatments. |
Sample Preparation:
| Sampleprep ID: | SP000466 |
| Sampleprep Summary: | Aliquots of each de-identified sample were shipped to the NIH RTI-RCMRC on dry ice and immediately stored at -80 °C after being logged in for metabolomics analysis. A total of 48 study samples were weighed on dry ice to confirm weights and approximately 50 mg of the tissue was transferred to labeled MagNa Lyser bead tubes on ice and ice cold 50:50 acetonitrile:water was added, and samples were homogenized with two 30sec pulses at 3000rpm. Tubes were centrifuged at 16,000 rcf for 10 minutes at room temperature and supernatants were transferred to 1.5mL pre-labeled LoBind Eppendorf tubes. Aliquots of 500uL were then transferred into labeled 2.0mL LoBind Eppendorf tubes. Analytical quality control (QC) whole study pool samples were generated by transferring an additional 125µL aliquot of each study sample into a 10mL cyrovial and vortexed. To generate Total Pooled QC samples 500uL was transferred to 5 labeled 2.0mL LoBind Eppendorf tubes. All samples were lyophilized to complete dryness overnight, then reconstituted with 700uL of NMR Master Mix solution containing Chenomx ISTD: DSS-d6 and Phosphate Buffer at 7.4 pH. The tubes were vortexed for 4 min on a multi-tube vortexer and centrifuged at 16,000 rcf for 5 min. A 600uL aliquot of supernatants were transferred into a pre-labeled 5mm 4 NMR tubes for data acquisition on a 700 MHz spectrometer. |
Analysis:
| Analysis ID: | AN000689 |
| Analysis Type: | NMR |
| Num Factors: | 2 |
NMR:
| NMR ID: | NM000074 |
| Analysis ID: | AN000689 |
| Instrument Name: | Bruker |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 0.5mM |
| Spectrometer Frequency: | 700 MHz |
| NMR Probe: | 5mm ATMA Cryoprobe |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5mm |
| Shimming Method: | Topshim |
| Water Suppression: | yes |
| Receiver Gain: | 4.5 |
| Offset Frequency: | 3299 |
| Chemical Shift Ref Cpd: | DSS |
| Temperature: | 298.1K |
| Number Of Scans: | 128 |
| Dummy Scans: | 4 |
| Acquisition Time: | 3.893s |
| Relaxation Delay: | 2s |
| Spectral Width: | 12.0277ppm |
| Num Data Points Acquired: | 65536 |
| Real Data Points: | 65536 |
| Line Broadening: | 0.5Hz |
| Zero Filling: | yes |
| Apodization: | Lorentzian |
| Baseline Correction Method: | Polynomial |
| Chemical Shift Ref Std: | DSS-d6 |
| Binned Increment: | 0.04ppm |
