PXD007919 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-10-09 02:31:09 | ID requested | |
⏵ 1 | 2019-05-28 00:26:06 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biomedical |
submitter keyword: Lung Cancer, Emphysema, Proteomics, Transcriptomics, Translatomics, Data Integration, JIVE, COPD, RNA |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD007919
- Label: PRIDE project
- Name: Matched Lung Tumor And Emphysematous Matrix Proteomics, Transcriptomics, and Translatomics