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.

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Study IDST000438
Study TitleCharacterizing commonalities and differences between the breast and prostate cancer metabotypes in African-American cohorts (part I)
Study TypeIdentify Breast Cancer Progression and Prostate Cancer correlative Metabolite Markers
Study SummaryThus, 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
DepartmentNIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC)
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2016-08-02
Num Groups2
Total Subjects48
Num Females48
Raw Data AvailableYes
Analysis Type DetailNMR
Release Date2016-09-23
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8X01N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA022035S_104BC
SA022036S_90BC
SA022037S_110BC
SA022038S_95BC
SA022039S_99BC
SA022040S_79BC
SA022041S_98BC
SA022042S_100BC
SA022043S_81BC
SA022044S_82BC
SA022045S_97BC
SA022046S_113BC
SA022047S_92BC
SA022048S_106BC
SA022049S_107BC
SA022050S_83BC
SA022051S_111BC
SA022052S_89BC
SA022053S_102BC
SA022054S_87BC
SA022055S_114BC
SA022056S_112BC
SA022057S_77BC
SA022058S_101BC
SA022059S_96BC
SA022060S_85BC
SA022061S_109BC
SA022062S_88BC
SA022063S_93BC
SA022064S_105BC
SA022065S_103BC
SA022066S_115BC
SA022067S_84BC
SA022068S_94BC
SA022069S_78BC
SA022070S_80BC
SA022071S_91BC
SA022072S_108BC
SA022073S_70WC
SA022074S_72WC
SA022075S_75WC
SA022076S_71WC
SA022077S_76WC
SA022078S_73WC
SA022079S_68WC
SA022080S_74WC
SA022081S_67WC
SA022082S_69WC
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
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