Summary of Study ST000010

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 PR000009. The data can be accessed directly via it's Project DOI: 10.21228/M80591 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000010
Study TitleLung Cancer Cells 4
Study TypeMS analysis (Untargeted)
Study SummaryIn cancer cells, the process of epithelial–mesenchymal transition (EMT) confers migratory and invasive capacity, resistance to apoptosis, drug resistance, evasion of host immune surveillance and tumor stem cell traits. Cells undergoing EMT may represent tumor cells with metastatic potential. Characterizing the EMT secretome may identify biomarkers to monitor EMT in tumor progression and provide a prognostic signature to predict patient survival. Utilizing a transforming growth factor-β-induced cell culture model of EMT, we quantitatively profiled differentially secreted proteins, by GeLC-tandem mass spectrometry. Integrating with the corresponding transcriptome, we derived an EMT-associated secretory phenotype (EASP) comprising of proteins that were differentially upregulated both at protein and mRNA levels. Four independent primary tumor-derived gene expression data sets of lung cancers were used for survival analysis by the random survival forests (RSF) method. Analysis of 97-gene EASP expression in human lung adenocarcinoma tumors revealed strong positive correlations with lymph node metastasis, advanced tumor stage and histological grade. RSF analysis built on a training set (n = 442), including age, sex and stage as variables, stratified three independent lung cancer data sets into low-, medium- and high-risk groups with significant differences in overall survival. We further refined EASP to a 20 gene signature (rEASP) based on variable importance scores from RSF analysis. Similar to EASP, rEASP predicted survival of both adenocarcinoma and squamous carcinoma patients. More importantly, it predicted survival in the early-stage cancers. These results demonstrate that integrative analysis of the critical biological process of EMT provides mechanism-based and clinically relevant biomarkers with significant prognostic value. Research is published, core data not used but project description is relevant: http://www.jimmunol.org/content/194/12/5789.long
Institute
University of Michigan
LaboratoryKeshamouni Lab (MCTP)
Last NameKeshamouni
First NameVenkat
Emailvkeshamo@umich.edu
Submit Date2013-04-03
Num Groups13
Total Subjects39
Raw Data AvailableNo
Analysis Type DetailLC-MS
Release Date2013-05-03
Release Version1
Venkat Keshamouni Venkat Keshamouni
https://dx.doi.org/10.21228/M80591
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000009
Project DOI:doi: 10.21228/M80591
Project Title:Metabolomics of EMT
Project Type:MS analysis
Project Summary:Lung Cancer Cells 4
Institute:University of Michigan
Laboratory:Keshamouni Lab (MCTP)
Last Name:Keshamouni
First Name:Venkat
Email:vkeshamo@umich.edu

Subject:

Subject ID:SU000012
Subject Type:Human cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id FCS Hours REFED TGF
SA000564S00010482FCS 72 NO_REFED NO_TGF
SA000565S00010483FCS 72 NO_REFED NO_TGF
SA000566S00010484FCS 72 NO_REFED NO_TGF
SA000567S00010485FCS 72 NO_REFED TGF
SA000568S00010486FCS 72 NO_REFED TGF
SA000569S00010487FCS 72 NO_REFED TGF
SA000531S00010449NO_FCS 0 NO_REFED NO_TGF
SA000532S00010450NO_FCS 0 NO_REFED NO_TGF
SA000533S00010451NO_FCS 0 NO_REFED NO_TGF
SA000534S00010458NO_FCS 12 NO_REFED NO_TGF
SA000535S00010459NO_FCS 12 NO_REFED NO_TGF
SA000536S00010460NO_FCS 12 NO_REFED NO_TGF
SA000537S00010461NO_FCS 12 NO_REFED TGF
SA000538S00010462NO_FCS 12 NO_REFED TGF
SA000539S00010463NO_FCS 12 NO_REFED TGF
SA000540S00010464NO_FCS 24 NO_REFED NO_TGF
SA000541S00010465NO_FCS 24 NO_REFED NO_TGF
SA000542S00010466NO_FCS 24 NO_REFED NO_TGF
SA000543S00010467NO_FCS 24 NO_REFED TGF
SA000544S00010468NO_FCS 24 NO_REFED TGF
SA000545S00010469NO_FCS 24 NO_REFED TGF
SA000546S00010452NO_FCS 2 NO_REFED NO_TGF
SA000547S00010453NO_FCS 2 NO_REFED NO_TGF
SA000548S00010454NO_FCS 2 NO_REFED NO_TGF
SA000549S00010455NO_FCS 2 NO_REFED TGF
SA000550S00010456NO_FCS 2 NO_REFED TGF
SA000551S00010457NO_FCS 2 NO_REFED TGF
SA000552S00010470NO_FCS 72 NO_REFED NO_TGF
SA000554S00010471NO_FCS 72 NO_REFED NO_TGF
SA000556S00010472NO_FCS 72 NO_REFED NO_TGF
SA000558S00010473NO_FCS 72 NO_REFED TGF
SA000560S00010474NO_FCS 72 NO_REFED TGF
SA000562S00010475NO_FCS 72 NO_REFED TGF
SA000553S00010476NO_FCS 72 REFED_48 NO_TGF
SA000555S00010477NO_FCS 72 REFED_48 NO_TGF
SA000557S00010478NO_FCS 72 REFED_48 NO_TGF
SA000559S00010479NO_FCS 72 REFED_48 TGF
SA000561S00010480NO_FCS 72 REFED_48 TGF
SA000563S00010481NO_FCS 72 REFED_48 TGF
Showing results 1 to 39 of 39

Collection:

Collection ID:CO000010
Collection Summary:-
Sample Type:Lung

Treatment:

Treatment ID:TR000018

Sample Preparation:

Sampleprep ID:SP000020
Sampleprep Summary:-

Combined analysis:

Analysis ID AN000025 AN000026
Analysis type MS MS
Chromatography type
Chromatography system
Column
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH000010

MS:

MS ID:MS000024
Analysis ID:AN000025
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000025
Analysis ID:AN000026
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
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