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Defining Kinase Activity for Personalized Cancer Treatment: Development of Next Generation Multiplex Mass-Spectrometry based Kinome Profiling

Project nummer 
Deelnemende kennisinstellingen 

Dr. T.M. Luider
Erasmus MC
Postbus 2040

Type project 
13 augustus 2012
31 oktober 2017
Under normal conditions, cell growth and differentiation are tightly controlled by signaling pathways. These molecular pathways are essential cellular communication routes, transmitting signals from the outside world and coordinating cell actions. Especially a specific class of enzymes called kinases plays a critical role in cell signaling, with more than 518 individual kinases known in humans.
In cancer, signaling pathways and kinase activity are almost invariably altered, resulting in uncontrolled cell growth. Developing specific drugs (inhibitors) targeting signaling pathways is a major focus of the pharmaceutical industry to combat cancer. Kinase inhibitors are increasingly available in the clinic (e.g. Imatinib, also known as Gleevec) and many more are under (clinical) development. However, in different tumor types and patients, different signaling pathways and kinases can be affected.
It is apparent that most tumors can escape from the inhibition of any single kinase, and treatment with one kinase inhibitor is often not effective. It is therefore critical to be able to identify which kinases are aberrant in individual patients and tumors. This will allow to determine the most optimal treatment with (combinations of) kinase inhibitors, will provide more insight into the molecular mechanisms underlying tumor formation, and can reveal new targets for treatment. Currently, a fast, reliable and sensitive method for determining activity of the full set of human kinases in clinical samples is not available.
We will develop a novel method for determining kinase activity (kinome profiling) in clinical samples based on mass spectrometry (MS). This highly sensitive and specific technology will provide a full view of kinase activity in (clinical) samples in a single experiment. We will generate novel highly specific peptides integrated in a multiplex MS-based assay that allows for simultaneous measurement of full kinase activity in one experiment. Thereby, a snap-shot of the kinase activity in (clinical) samples can be generated. This has major potential as tool for scientific research, target discovery and as clinical diagnostic tool to select the most optimal treatment with kinase inhibitors.
Proof-of-Principle for the new kinome profiling technology will be provided using glioblastoma patient samples. This tumor is the most aggressive type of brain cancer for which improved treatment options are urgently needed. Treatment with one kinase inhibitor is typically ineffective since multiple pathways are affected. Glioblastoma was chosen as first indication because aberrant kinase activity affecting multiple pathways has been demonstrated, and well-characterized samples including clinical data are already available. If successful, the technology can easily be transferred to other types of cancer.
Kinome profiling is considered an important step towards understanding the complex cell response and will be of great value to select the most optimal treatment for cancer patients. Although several methods for kinome profiling are available, there is no technique that can accurately and rapidly profile the full kinome in one single assay, providing highly sensitive and specific results for diagnostic applications. We aim to develop a novel  kinome profiling method based on MS, providing a reliable snap-shot of kinase activity in clinical samples. Importantly, novel highly specific peptides will be generated to reliably determine activity of individual kinases and pathways across the kinome.
The MS-based readout requires low sample volumes, generates highly reliable results and is not hampered by technical issues common to other technologies (e.g. steric hindrance on microarray chips). Importantly, MS is increasingly used in clinical setting and the new technology can be provided as kinome profiling kit, allowing its use in any well-equipped laboratory (see utilization). The Proof-of-Principle experiments will reveal aberrant kinase pathways in a well-characterized set of glioblastoma samples, providing valuable scientific data on signaling pathways in glioblastoma and demonstrating the value of the new technology for selecting most optimal treatment. Importantly, MS-based kinome profiling can be used for other types of cancer without major technical adaptations.