title: Comparative proteome analysis across non-small cell lung cancer cell lines.
abstract: 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.
authors.affiliation: Evotec (München) GmbH, Am Klopferspitz 19a, 82151 Martinsried, Germany; Cell Signaling Group, Department of Molecular Biology, Am Klopferspitz 19a, 82151 Martinsried, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Grundner-Culemann
authors.affiliation: Evotec (München) GmbH, Am Klopferspitz 19a, 82151 Martinsried, Germany.
authors.forename: J Nikolaj
authors.initials: JN
authors.lastname: Dybowski
authors.affiliation: Evotec (München) GmbH, Am Klopferspitz 19a, 82151 Martinsried, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Klammer
authors.affiliation: Evotec (München) GmbH, Am Klopferspitz 19a, 82151 Martinsried, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Tebbe
authors.affiliation: Evotec (München) GmbH, Am Klopferspitz 19a, 82151 Martinsried, Germany; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Schaab
authors.affiliation: Evotec (München) GmbH, Am Klopferspitz 19a, 82151 Martinsried, Germany; Cell Signaling Group, Department of Molecular Biology, Am Klopferspitz 19a, 82151 Martinsried, Germany. Electronic address: henrik.daub@evotec.com.
authors.forename: Henrik
authors.initials: H
authors.lastname: Daub
mesh_terms: D002289:Carcinoma, Non-Small-Cell Lung / Q000378:metabolism*; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D019295:Computational Biology; D066246:ErbB Receptors / Q000235:genetics; D011905:Genes, ras / Q000235:genetics; D006801:Humans; D008175:Lung Neoplasms / Q000378:metabolism*; D013058:Mass Spectrometry; D025341:Principal Component Analysis; D025941:Protein Interaction Mapping; D020543:Proteome; D040901:Proteomics / Q000379:methods*
chemical_list: D020543:Proteome; C512478:EGFR protein, human; D066246:ErbB Receptors
keywords: EGFR; K-Ras; Non-small cell lung cancer; PCA; Proteome profiling; SILAC