Summary of Study ST000439
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 | ST000439 |
| Study Title | Characterizing commonalities and differences between the breast and prostate cancer metabotypes in African-American cohorts |
| 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 | 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 | 4 |
| Total Subjects | 66 |
| Num Males | 33 |
| Num Females | 33 |
| 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: | SU000460 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| 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 | Gender | Group |
|---|---|---|---|
| SA022083 | S_40 | F | BC |
| SA022084 | S_41 | F | BC |
| SA022085 | S_42 | F | BC |
| SA022086 | S_39 | F | BC |
| SA022087 | S_38 | F | BC |
| SA022088 | S_36 | F | BC |
| SA022089 | S_37 | F | BC |
| SA022090 | S_43 | F | BC |
| SA022091 | S_45 | F | BC |
| SA022092 | S_49 | F | BC |
| SA022093 | S_50 | F | BC |
| SA022094 | S_51 | F | BC |
| SA022095 | S_48 | F | BC |
| SA022096 | S_47 | F | BC |
| SA022097 | S_35 | F | BC |
| SA022098 | S_46 | F | BC |
| SA022099 | S_44 | F | BC |
| SA022100 | S_34 | F | BC |
| SA022101 | S_10 | F | WC |
| SA022102 | S_9 | F | WC |
| SA022103 | S_12 | F | WC |
| SA022104 | S_13 | F | WC |
| SA022105 | S_15 | F | WC |
| SA022106 | S_14 | F | WC |
| SA022107 | S_8 | F | WC |
| SA022108 | S_7 | F | WC |
| SA022109 | S_3 | F | WC |
| SA022110 | S_2 | F | WC |
| SA022111 | S_4 | F | WC |
| SA022112 | S_5 | F | WC |
| SA022113 | S_6 | F | WC |
| SA022114 | S_1 | F | WC |
| SA022115 | S_11 | F | WC |
| SA022116 | S_26 | M | MC |
| SA022117 | S_27 | M | MC |
| SA022118 | S_28 | M | MC |
| SA022119 | S_25 | M | MC |
| SA022120 | S_24 | M | MC |
| SA022121 | S_21 | M | MC |
| SA022122 | S_19 | M | MC |
| SA022123 | S_23 | M | MC |
| SA022124 | S_29 | M | MC |
| SA022125 | S_22 | M | MC |
| SA022126 | S_16 | M | MC |
| SA022127 | S_17 | M | MC |
| SA022128 | S_20 | M | MC |
| SA022129 | S_33 | M | MC |
| SA022130 | S_18 | M | MC |
| SA022131 | S_30 | M | MC |
| SA022132 | S_31 | M | MC |
| SA022133 | S_32 | M | MC |
| SA022134 | S_63 | M | PC |
| SA022135 | S_61 | M | PC |
| SA022136 | S_62 | M | PC |
| SA022137 | S_65 | M | PC |
| SA022138 | S_60 | M | PC |
| SA022139 | S_66 | M | PC |
| SA022140 | S_64 | M | PC |
| SA022141 | S_56 | M | PC |
| SA022142 | S_53 | M | PC |
| SA022143 | S_52 | M | PC |
| SA022144 | S_54 | M | PC |
| SA022145 | S_55 | M | PC |
| SA022146 | S_58 | M | PC |
| SA022147 | S_57 | M | PC |
| SA022148 | S_59 | M | PC |
| Showing results 1 to 66 of 66 |
Collection:
| Collection ID: | CO000454 |
| Collection Summary: | Blood samples were collected from each subject using 10 ml blood BD Vacutainer tubes containing coagulants (EDTA). Tubes were centrifuged at 1850 x g for 10 min at room temperature and the upper layer serum in 1 ml aliquots was transferred to cryo-preservative tubes and preserved in –80 C freezer. |
| Sample Type: | Blood |
Treatment:
| Treatment ID: | TR000474 |
| Treatment Summary: | No treatments. |
Sample Preparation:
| Sampleprep ID: | SP000467 |
| 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 66 study samples were thawed on ice for sample preparation. A 300 uL aliquot of plasma was transferred to new labeled tubes for each study sample. Analytical quality control (QC) phenotypic pooled samples were generated by transferring a 80µL aliquot of each sample from each respective phenotypic group (Control-women, BCa-women, Control-men and PCa-men) into different 1.5 mL tubes. Phenotypic pooled samples were vortexed and 300 uL aliquots were transferred into 3 tubes/group. A total study pool was generated by transferring 250 uL of plasma from each Phenotypic pooled sample into a new 1.5 mL tube. The Total Pool sample was vortexed and 300 uL aliquots were transferred into 3 Total Pool-labeled tubes. For extraction, 900 uL of MeOH was added to all tubes, they were vortexed for 2 min on a multi-tube vortexer and centrifuged at 16,000 rcf for 5 min. A 1000 µl aliquot of the supernatant was transferred into pre-labeled 2.0mL LoBind Eppendorf tubes, and samples were lyophilized to complete dryness overnight. Samples were reconstituted with 700 uL of NMR Master Mix solution containing Chenomx ISTD: DSS-d6 and Phosphate Buffer at 7.4 pH. The tubes were vortexed for 2 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: | AN000690 |
| Analysis Type: | NMR |
| Num Factors: | 4 |
NMR:
| NMR ID: | NM000075 |
| Analysis ID: | AN000690 |
| 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 |
