PXD007919

PXD007919 is an original dataset announced via ProteomeXchange.

Title	Matched Lung Tumor And Emphysematous Matrix Proteomics, Transcriptomics, and Translatomics
Description	Chronic obstructive pulmonary disease (COPD) is a known risk factor for developing lung cancer suggesting that the COPD stroma contains factors supporting tumorigenesis. Since cancer initiation is complex we used a multi-omic approach to identify gene expression patterns that distinguish COPD stroma in patients with or without lung cancer. Our overall objective is the identification of gene expression pathways and levels of regulation in lung stroma of patients with COPD that harbor lung cancer. We obtained lung tissue from patients with COPD and lung cancer (tumor and adjacent non-malignant tissue) and those with COPD without lung cancer for proteomic and mRNA (cytoplasmic and polyribosomal) profiling. We used the joint and individual variation explained (JIVE) method to integrate and analysis across the three datasets. JIVE identified eight latent patterns that robustly distinguished and separated the three groups of tissue samples. Predictive variables that associated with the tumor, compared to adjacent stroma, were mainly represented in the transcriptomic data, whereas, predictive variables associated with adjacent tissue compared to controls was represented at the translatomic level. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed extracellular matrix (ECM) and PI3K-Akt signaling pathways as important signals in the pre-malignant stroma. COPD stroma adjacent to lung cancer is unique and differs from non-malignant COPD tissue and is distinguished by the extracellular matrix and PI3K-Akt signaling pathways.
HostingRepository	PRIDE
AnnounceDate	2019-05-28
AnnouncementXML	Submission_2019-05-28_00:26:04.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brian Sandri
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iTRAQ8plex-116 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-09 02:31:09	ID requested
⏵ 1	2019-05-28 00:26:06	announced

Sandri BJ, Kaplan A, Hodgson SW, Peterson M, Avdulov S, Higgins L, Markowski T, Yang P, Limper AH, Griffin TJ, Bitterman P, Lock EF, Wendt CH, Multi-omic molecular profiling of lung cancer in COPD. Eur Respir J, 52(1):(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: Lung Cancer, Emphysema, Proteomics, Transcriptomics, Translatomics, Data Integration, JIVE, COPD, RNA

Chris Wendt
contact affiliation	Pulmonary, Critical Care, and Sleep Medicine Veterans Affairs Medical Center, Minneapolis, MN Pulmonary, Critical Care, and Sleep Medicine University of Minnesota, Minneapolis, MN
contact email	wendt005@umn.edu
lab head
Brian Sandri
contact affiliation	University of Minnesota
contact email	sand0449@umn.edu
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/2019/05/PXD007919

PRIDE project URI

• PRIDE
  1. PXD007919
     1. Label: PRIDE project
     2. Name: Matched Lung Tumor And Emphysematous Matrix Proteomics, Transcriptomics, and Translatomics