Submitted on June 23, 2009
Revised on July 29, 2009
Accepted on August 3, 2009
Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics
Cuiping Pan, Jesper V. Olsen, Henrik Daub, and Matthias Mann
Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Martinsried
Corresponding Author: mmann{at}biochem.mpg.de
Aberrant signaling causes many diseases and manipulating signaling pathways with kinase inhibitors has emerged as a promising area of drug research. Most kinase inhibitors target the conserved ATP-binding pocket, therefore specificity is a major concern. Proteomics has previously been used to identify the direct targets of kinase inhibitors upon affinity purification from cellular extracts. Here we introduce a complementary approach to evaluate the effect of kinase inhibitors on the entire cell signaling network. We employ triple labeling SILAC to compare cellular phosphorylation levels for control, EGF growth factor stimulus, and growth factor combined with kinases inhibitor. Of thousands of phosphopeptides, less than ten percent had a response pattern indicative of targets of U0126 and SB202190, two widely used MAPK inhibitors. Interestingly, 83% of the growth factor induced phosphorylation events were affected by either or both inhibitors showing quantitatively that early signaling processes are predominantly transmitted through the MAPK cascade. In contrast to MAPK inhibitors, dasatinib, a clinical drug directed against BCR-ABL, which is the cause of chronic myelogenous leukemia, affected nearly 1000 phosphopeptides. In addition to the proximal effects on Abl and its immediate targets, dasatinib broadly affects the downstream MAPK pathways. Pathway mapping of regulated sites implicated a variety of cellular functions such as chromosome remodeling, RNA splicing and cytoskeletal organization, some of which have been described in the literature before. Our assay is streamlined, generic and could become a useful tool in kinase drug development.