PXD002622

PXD002622 is an original dataset announced via ProteomeXchange.

Title	A Pilot Proteogenomic Study With Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma
Description	We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_00:48:26.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paul Stewart
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-29 02:15:18	ID requested
1	2015-11-06 02:48:12	announced
2	2017-06-20 05:43:34	announced	Updated project metadata.
⏵ 3	2017-10-24 00:48:27	announced	Updated project metadata.

Stewart PA, Parapatics K, Welsh EA, M, ü, ller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB, A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One, 10(11):e0142162(2015) [pubmed]

curator keyword: Biological

submitter keyword: proteogenomics, non-small cell lung cancer, NSCLC, lung adenocarcinoma, lung squamous cell carcinoma, TMT, MCT1, GLUT1, SLC16A1, SLC2A1

Eric Haura
contact affiliation	Moffitt Cancer Center
contact email	eric.haura@moffitt.org
lab head
Paul Stewart
contact affiliation	Moffitt Cancer Center
contact email	paul.stewart@moffitt.org
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD002622

PRIDE project URI

• PRIDE
  1. PXD002622
     1. Label: PRIDE project
     2. Name: A Pilot Proteogenomic Study With Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma