Global proteome analysis of the NCI-60 cell line panel.
The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 panel covering, in total, 10,350 proteins (including 375 protein kinases) and including a core cancer proteome of 5,578 proteins that were consistently quantified across all tissue types. Bioinformatic analysis revealed strong cell line clusters according to tissue type and disclosed hundreds of differentially regulated proteins representing potential biomarkers for numerous tumor properties. Integration with public transcriptome data showed considerable similarity between mRNA and protein expression. Modeling of proteome and drug-response profiles for 108 FDA-approved drugs identified known and potential protein markers for drug sensitivity and resistance. To enable community access to this unique resource, we incorporated it into a public database for comparative and integrative analysis (http://wzw.tum.de/proteomics/nci60).
Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany. amin@tum.de.
Amin Moghaddas
AM
Gholami
Hannes
H
Hahne
Zhixiang
Z
Wu
Florian Johann
FJ
Auer
Chen
C
Meng
Mathias
M
Wilhelm
Bernhard
B
Kuster
D045744:Cell Line, Tumor; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D009369:Neoplasms / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000032:analysis* / Q000235:genetics / Q000378:metabolism
D009363:Neoplasm Proteins; D020543:Proteome