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Kinome Profiling in Pediatric Brain Tumors as a New Approach for Target Discovery

Departments of ¹ Pediatric Oncology, ² Cell Biology, ³ Pathology and Medical Biology, and ⁴ Neurosurgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands and ⁵ PamGene International B.V., Hertogenbosch, The Netherlands

Requests for reprints: Eveline S.J.M. de Bont, Department of Pediatric Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands. Phone: 31-50-3614146; Fax: 31-50-3611671; E-mail: e.de.bont{at}bkk.umcg.nl.

Key Words: pediatric brain tumors • PamChip • Src • kinome profiling • target discovery

Progression in pediatric brain tumor growth is thought to be the net result of signaling through various protein kinase-mediated networks driving cell proliferation. Defining new targets for treatment of human malignancies, without a priori knowledge on aberrant cell signaling activity, remains exceedingly complicated. Here, we introduce kinome profiling using flow-through peptide microarrays as a new concept for target discovery. Comprehensive tyrosine kinase activity profiles were identified in 29 pediatric brain tumors using the PamChip kinome profiling system. Previously reported activity of epidermal growth factor receptor, c-Met, and vascular endothelial growth factor receptor in pediatric brain tumors could be appreciated in our array results. Peptides corresponding with phosphorylation consensus sequences for Src family kinases showed remarkably high levels of phosphorylation compared with normal tissue types. Src activity was confirmed applying Phos-Tag SDS-PAGE. Furthermore, the Src family kinase inhibitors PP1 and dasatinib induced substantial tumor cell death in nine pediatric brain tumor cell lines but not in control cell lines. Thus, this study describes a new high-throughput technique to generate clinically relevant tyrosine kinase activity profiles as has been shown here for pediatric brain tumors. In the era of a rapidly increasing number of small-molecule inhibitors, this approach will enable us to rapidly identify new potential targets in a broad range of human malignancies. [Cancer Res 2009;69(14):5987–95]