Abstract
Identification of predictive biomarkers for targeted therapies requires information on drug exposure at the target site as well as its effect on the signaling context of a tumor. To obtain more insight in the clinical mechanism of action of protein kinase inhibitors (PKIs), we studied tumor drug concentrations of protein kinase inhibitors (PKIs) and their effect on the tyrosine-(pTyr)-phosphoproteome in patients with advanced cancer. Tumor biopsies were obtained from 31 patients with advanced cancer before and after 2 weeks of treatment with sorafenib (SOR), erlotinib (ERL), dasatinib (DAS), vemurafenib (VEM), sunitinib (SUN) or everolimus (EVE). Tumor concentrations were determined by LC-MS/MS. pTyr-phosphoproteomics was performed by pTyr-immunoprecipitation followed by LC-MS/MS. Median tumor concentrations were 2–10 µM for SOR, ERL, DAS, SUN, EVE and >1 mM for VEM. These were 2–178 × higher than median plasma concentrations. Unsupervised hierarchical clustering of pTyr-phosphopeptide intensities revealed patient-specific clustering of pre- and on-treatment profiles. Drug-specific alterations of peptide phosphorylation was demonstrated by marginal overlap of robustly up- and downregulated phosphopeptides. These findings demonstrate that tumor drug concentrations are higher than anticipated and result in drug specific alterations of the phosphoproteome. Further development of phosphoproteomics-based personalized medicine is warranted.
Highlights
With the identification of driver DNA alterations and molecular subtypes that predict benefit from protein kinase inhibitors (PKIs), great strides towards realization of personalized or precision medicine have been made [1].Focus in precision medicine has shifted from identification of single genomic events to a more comprehensive assessment of tumor biology through integration of genomic, transcriptomic and proteomic data [2,3,4]
Since plasma concentrations do not predict tumor concentrations accurately, our results question the relevance of therapeutic drug monitoring tumor concentrations accurately, our results question the relevance of therapeutic drug monitoring (TDM) using plasma to optimize clinical activity of PKIs [30]. These results reveal that (TDM) using plasma to optimize clinical activity of PKIs [30]. These results reveal that tumor drug concentrations well exceed concentrations required for inhibition of the assumed drug tumor drug concentrations well exceed concentrations required for inhibition of the assumed drug specific kinase targets [27,28]
In this large-scale Mass spectrometry (MS)-based phosphoproteomic analysis of pre- and on treatment tumor needle biopsies obtained in a clinical trial, we studied to what extent these high tumor drug concentrations
Summary
With the identification of driver DNA alterations and molecular subtypes that predict benefit from PKIs, great strides towards realization of personalized or precision medicine have been made [1].Focus in precision medicine has shifted from identification of single genomic events to a more comprehensive assessment of tumor biology through integration of genomic, transcriptomic and proteomic data [2,3,4]. With regard to PKIs, pre- and on-treatment tumor biopsies may provide the opportunity to analyze drug concentration as well as inhibition of (off-) target kinases in target tissue. Identification of predictive biomarkers for PKI treatment will require an approach that can take these factors into consideration. Mass spectrometry (MS)-based phosphoproteomics has more recently emerged as an approach of molecular tumor profiling to obtain insight in aberrantly activated signaling pathways and potential drug targets. This is achieved through global analysis of phosphorylated proteins that form the basis for cellular signaling activities and protein-protein interaction [9]. Phosphotyrosine-(pTyr)-phospho-proteomics provides an opportunity for the identification of patient subgroups likely to benefit from tyrosine kinase inhibitors [10]
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