PXD002556 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Comparative proteome analysis across non-small cell lung cancer cell lines |
Description | Non-small cell lung cancer (NSCLC) cell lines are widely used model systems to study molecular aspects of lung cancer. Comparative and in-depth proteome expression data across many NSCLC cell lines has not been generated yet, but would be of utility for the investigation of candidate targets and markers in oncogenesis. We employed a SILAC reference approach to perform replicate proteome quantifications across 23 distinct NSCLC cell lines. On average, close to 4000 distinct proteins were identified and quantified per cell line. These included many known targets and diagnostic markers, indicating that our proteome expression data represents a useful resource for NSCLC pre-clinical research. To assess proteome diversity within the NSCLC cell line panel, we performed hierarchical clustering and principal component analysis of proteome expression data. Our results indicate that general proteome diversity among NSCLC cell lines supersedes potential effects common to K-Ras or epidermal growth factor receptor (EGFR) oncoprotein expression. However, we observed partial segregation of EGFR or KRAS mutant cell lines for certain principal components, which reflected biological differences according to gene ontology enrichment analyses. Moreover, statistical analysis revealed several proteins that were significantly overexpressed in KRAS or EGFR mutant cell lines. Biological significance Despite enormous progress in molecular characterization and targeted therapy NSCLC represents a major cause for cancer-related deaths. While pre-clinical models such as NSCLC cell lines have been studied on the genomic and transcriptional level, proteome composition is poorly characterized. We conducted quantitative profiling across 23 NSCLC cell lines and studied global proteome diversity in relation to the presence of oncogenic KRAS or EGFR mutations. Notably, in-depth bioinformatics analysis pointed to prominent biological processes as well as up-regulated proteins in KRAS and EGFR mutant cells, highlighting the utility of cancer cell proteomics to identify target or biomarker candidates in the context of specific oncogenic mechanisms. |
HostingRepository | PRIDE |
AnnounceDate | 2015-09-14 |
AnnouncementXML | Submission_2015-09-14_03:13:56.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Kathrin Grundner-Culemann |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-07-20 01:08:32 | ID requested | |
⏵ 1 | 2015-09-14 03:13:57 | announced | |
Publication List
Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, Comparative proteome analysis across non-small cell lung cancer cell lines. J Proteomics, 130():1-10(2016) [pubmed] |
Keyword List
curator keyword: Biomedical |
submitter keyword: Proteome profiling, non-small cell lung cancer, SILAC, PCA, K-Ras, EGFR |
Contact List
Henrik Daub |
contact affiliation | 1: Evotec (München) GmbH, Am Klopferspitz 19a, 82151 Martinsried, Germany 2: Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany |
contact email | henrik.daub@evotec.com |
lab head | |
Kathrin Grundner-Culemann |
contact affiliation | Evotec (München) GmbH |
contact email | kathrin.grundner-culemann@evotec.com |
dataset submitter | |
Full Dataset Link List
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/2015/09/PXD002556 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002556
- Label: PRIDE project
- Name: Comparative proteome analysis across non-small cell lung cancer cell lines