Summary of Study ST000454

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000351. The data can be accessed directly via it's Project DOI: 10.21228/M8PC8X This work is supported by NIH grant, U2C- DK119886.


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Study IDST000454
Study TitleUtilizing Metabolomics to Understand Novel Anti-Desmoid Tumor Drugs (part I)
Study SummaryThis pilot study will use broad spectrum metabolomics to study the tumorigenesis process of fibroblasts to desmoids by investigating paired desmoid and fibroblast cell lines, in addition to unaffected fibroblast cells. Additionally, this pilot study will explore the effects of two of the active drugs identified on the desmoid and fibroblast cells.
RTI International
Last NameMercier
First NameKelly
Address3040 E. Cornwallis Road
Submit Date2016-08-31
Raw Data AvailableYes
Raw Data File Type(s)1r
Analysis Type DetailNMR
Release Date2018-02-07
Release Version1
Kelly Mercier Kelly Mercier application/zip

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Project ID:PR000351
Project DOI:doi: 10.21228/M8PC8X
Project Title:Utilizing Metabolomics to Understand Novel Anti-Desmoid Tumor Drugs
Project Summary:Desmoid tumors (DT) are locally invasive soft tissue growths with no directed therapies currently. While two genes (β-catenin and adenomatous polyposis coli) have been found in patients who develop desmoids, it is unclear how these mutations and other downstream mechanisms lead to desmoid tumorigenesis. Extensive research has been explored in the molecular biology of desmoids; however, the use of metabolomics to understand the how the low molecular weight complements of cells, tissues, and biological fluids are perturbed by this highly localized disease. Additionally, the Desmoid Collaboration for a Cure has identified 45 active drugs against primary cell lines. It is unclear how these therapies perturb the metabolome, outside the Wnt and notch pathways.
Institute:RTI International
Last Name:Mercier
First Name:Kelly
Address:3040 E. Cornwallis Road


Subject ID:SU000475
Subject Type:Human Cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human


Subject type: Human Cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Growth_type
SA023007C_14_r2Das. Normal
SA023008C_14_r3Das. Normal
SA023009C_2_r2Das. Normal
SA023010C_2_r3Das. Normal
SA023011C_14_r1Das. Normal
SA023012C_2_r1Das. Normal
SA023013C_16_r2Das. Tumor
SA023014C_4_r3Das. Tumor
SA023015C_4_r2Das. Tumor
SA023016C_4_r1Das. Tumor
SA023017C_16_r1Das. Tumor
SA023018C_16_r3Das. Tumor
SA023019C_18_r1Das. Unaffected
SA023020C_18_r4Das. Unaffected
SA023021C_18_r6Das. Unaffected
SA022992C_1_r5DMSO Normal
SA022993C_13_r1DMSO Normal
SA022994C_1_r6DMSO Normal
SA022995C_13_r3DMSO Normal
SA022996C_13_r2DMSO Normal
SA022997C_1_r4DMSO Normal
SA022998C_15_r1DMSO Tumor
SA022999C_15_r3DMSO Tumor
SA023000C_3_r1DMSO Tumor
SA023001C_15_r2DMSO Tumor
SA023002C_3_r3DMSO Tumor
SA023003C_3_r2DMSO Tumor
SA023004C_17_r6DMSO Unaffected
SA023005C_17_r4DMSO Unaffected
SA023006C_17_r5DMSO Unaffected
SA023022C_11_r2FAK Inh. 14 Normal
SA023023C_5_r3FAK Inh. 14 Normal
SA023024C_11_r1FAK Inh. 14 Normal
SA023025C_5_r2FAK Inh. 14 Normal
SA023026C_11_r3FAK Inh. 14 Normal
SA023027C_5_r1FAK Inh. 14 Normal
SA023028C_6_r6FAK Inh. 14 Tumor
SA023029C_9_r2FAK Inh. 14 Tumor
SA023030C_6_r4FAK Inh. 14 Tumor
SA023031C_6_r5FAK Inh. 14 Tumor
SA023032C_9_r1FAK Inh. 14 Tumor
SA023033C_9_r3FAK Inh. 14 Tumor
SA023034C_19_r4FAK Inh. 14 Unaffected
SA023035C_19_r5FAK Inh. 14 Unaffected
SA023036C_19_r6FAK Inh. 14 Unaffected
SA023037C_12_r6H2O Normal
SA023038C_12_r5H2O Normal
SA023039C_12_r4H2O Normal
SA023040C_7_r1H2O Normal
SA023041C_7_r3H2O Normal
SA023042C_7_r2H2O Normal
SA023043C_10_r2H2O Tumor
SA023044C_10_r1H2O Tumor
SA023045C_10_r3H2O Tumor
SA023046C_8_r1H2O Tumor
SA023047C_8_r2H2O Tumor
SA023048C_8_r3H2O Tumor
SA023049C_20_r4H2O Unaffected
SA023050C_20_r6H2O Unaffected
SA023051C_20_r5H2O Unaffected
SA023052CP_3_r2Total Pool Total Pool
SA023053CP_3_r3Total Pool Total Pool
SA023054CP_1_r2Total Pool Total Pool
SA023055CP_3_r1Total Pool Total Pool
SA023056CP_2_r6Total Pool Total Pool
SA023057CP_2_r4Total Pool Total Pool
SA023058CP_2_r5Total Pool Total Pool
SA023059CP_1_r3Total Pool Total Pool
SA023060CP_1_r1Total Pool Total Pool
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Collection ID:CO000469
Collection Summary:An aliquot of the media following treatment was collected, and the remainder of the media was aspirated. The cells were washed with PBS twice, and quenched with 8mL ice-cold isotonic 0.9% (w/v) saline for 2 minutes. Total cellular content was then extracted with 1.7mL ice-cold acetonitrile/water (50:50, v/v) solution. Cell extracts were collected using a cell scraper and quickly transferred to MagNA Lyser Green Beads tubes (Roche, Indianapolis, USA) and stored in -80°C. Media was added to empty plates and incubated together with the cells for the duration of the experiment served as a blank.
Sample Type:Fibroblasts


Treatment ID:TR000489
Treatment Summary:Monolayer cell cultures of desmoid tumors and normal fibroblasts from desmoid patients and an unaffected fibroblast cell line were grown in DMEM supplemented with 5% fetal bovine serum and maintained at 37°C in 5% CO2. Cells were divided when confluent and experiments were performed between the third and sixth passages. Approximately 10 x 106 cells were treated with 1.0uM Dasatinib (Selleck, Houston, USA) dissolved in DMSO, or 0.5uM FAK Inhibitor 14 (Cayman Chemicals Company, Michigan, USA) dissolved in water. Cells were incubated in fresh media containing the inhibitors, or vehicle, for 24 hours.

Sample Preparation:

Sampleprep ID:SP000482
Sampleprep Summary:Cells were homogenized on the MagNA Lyzer, with two 30-sec cycles at 2000 rpm, resting in a -20 °C chilling block for 1 min in between pulses, and centrifuged samples at 16,000 rcf for 4 min. The cell lysate was transferred to a new 2 mL Lo-Bind Eppendorf tubes, with the final cell count approximately 10x10^6 cells for each sample. Of the twenty cell lysate samples, six samples had sufficient volume for study samples and to be included in an analytical quality control (QC) total pool. Aliquots from these cell lysate samples were combined, divided into three total pool aliquots, and processed identically to the cell lysate study samples. All study and pool samples were lyophilized to dryness and reconstituted in a 0.2M phosphate buffer, pH 7.4, in D2O with 10% Chenomx ISTD.


Analysis ID:AN000711
Analysis Type:NMR
Num Factors:13


NMR ID:NM000078
Analysis ID:AN000711
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Spectrometer Frequency:700 MHz