1
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Liu YC, Tsai FJ, Chen CJ. A rapid, multiplexed kinase activity assay using 8-plex iTRAQ labeling, SPE, and MALDI-TOF/TOF MS. Analyst 2020; 145:992-1000. [PMID: 31829320 DOI: 10.1039/c9an01810g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesized peptide substrates have been used for in vitro phosphorylation using purified kinases or cell lysates. For screening assays, a direct readout and comparison among different experimental conditions without using an internal standard would be preferred. In this study, we developed a rapid, quantitative measurement method of multikinase activity based on MALDI-TOF/TOF MS. We combined 8-plex iTRAQ-labeled peptide substrates, solid phase extraction (SPE), and a phosphorylated peptide purification plate to rapidly determine multikinase activity in cell lysates. To enable our platform to be applicable in insulin stimulation and cancer drug inhibition, a list of peptide substrates was designed. By labeling peptide substrates with 8-plex iTRAQ reagents, protein kinase activity in 8 samples could be directly compared using the mass tags on their fragmented ion spectra. The protein amount and incubation time for multikinase activity assays were optimized, and the effect of insulin stimulation and an inhibitory drug on the cellular protein kinase activity was evaluated.
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Affiliation(s)
- Yu-Ching Liu
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 40402, Taiwan.
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2
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Maiti S, Hassan A, Mitra P. Boosting phosphorylation site prediction with sequence feature-based machine learning. Proteins 2019; 88:284-291. [PMID: 31412138 DOI: 10.1002/prot.25801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/13/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation is one of the essential posttranslation modifications playing a vital role in the regulation of many fundamental cellular processes. We propose a LightGBM-based computational approach that uses evolutionary, geometric, sequence environment, and amino acid-specific features to decipher phosphate binding sites from a protein sequence. Our method, while compared with other existing methods on 2429 protein sequences taken from standard Phospho.ELM (P.ELM) benchmark data set featuring 11 organisms reports a higher F1 score = 0.504 (harmonic mean of the precision and recall) and ROC AUC = 0.836 (area under the curve of the receiver operating characteristics). The computation time of our proposed approach is much less than that of the recently developed deep learning-based framework. Structural analysis on selected protein sequences informs that our prediction is the superset of the phosphorylation sites, as mentioned in P.ELM data set. The foundation of our scheme is manual feature engineering and a decision tree-based classification. Hence, it is intuitive, and one can interpret the final tree as a set of rules resulting in a deeper understanding of the relationships between biophysical features and phosphorylation sites. Our innovative problem transformation method permits more control over precision and recall as is demonstrated by the fact that if we incorporate output probability of the existing deep learning framework as an additional feature, then our prediction improves (F1 score = 0.546; ROC AUC = 0.849). The implementation of our method can be accessed at http://cse.iitkgp.ac.in/~pralay/resources/PPSBoost/ and is mirrored at https://cosmos.iitkgp.ac.in/PPSBoost.
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Affiliation(s)
- Shyantani Maiti
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Atif Hassan
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
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3
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Vriz O, Pirisi M, Habib E, Galzerano D, Fadel B, Antonini-Canterin F, Veldtman G, Bossone E. Age related structural and functional changes in left ventricular performance in healthy subjects: a 2D echocardiographic study. Int J Cardiovasc Imaging 2019; 35:2037-2047. [PMID: 31297672 DOI: 10.1007/s10554-019-01665-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/03/2019] [Indexed: 12/19/2022]
Abstract
Left ventricular (LV) adaptation to aging is currently poorly understood. We aimed to characterize age related changes in LV structure and function by studying a large group of healthy subjects across a wide age range. Prospectively enrolled healthy volunteers (n = 778, 327 females; age 18 to 100 years, mean age 49.8 ± 18.1 years), were divided into 4 age groups: 18 to 34 years (n = 165); 35 to 49 years (n = 242), 50 to 79 years (n = 334) and ≥ 80 years (n = 40). All subjects underwent clinical examination, as well as comprehensive transthoracic echocardiogram [TTE]. Body mass index, systolic blood pressure (BP), and left atrial volume (p < 0.0001) increased with age while diastolic BP (p < 0.0001) decreased over time. LV mass/body surface area (BSA) and relative wall thickness increased with age (p < 0.0001) coincident with worsening parameters of diastolic function (E/A and E/Em, p < 0.0001). The ejection fraction and Sm did not change significantly. Stroke volume, ejection time index, flow rate and stroke work significantly increased with age (p < 0.01). The arterial elastance (Ea), a measure of ventricular afterload, and ventricular elastance (Ees), an index of LV systolic stiffness did not change with age nor did their ratio (Ees/Ea) the latter being an expression of ventricular-arterial coupling. Age, gender and LVM were the main independent variables associated with LV systolic function. In conclusion, LV adaptation to aging in a healthy cohort is characterized by concentric LV remodeling, increased contractility and preserved ventricular-arterial coupling.
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Affiliation(s)
- Olga Vriz
- Heart Centre Department, King Faisal Specialist Hospital & Research Center, Riyadh, Kingdom of Saudi Arabia. .,Cardiology and Emergency San Antonio Hospital, San Daniele del Friuli, Italy.
| | - Mario Pirisi
- Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Eiad Habib
- Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | - Domenico Galzerano
- Heart Centre Department, King Faisal Specialist Hospital & Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Bahaa Fadel
- Heart Centre Department, King Faisal Specialist Hospital & Research Center, Riyadh, Kingdom of Saudi Arabia
| | | | - Gruschen Veldtman
- Heart Centre Department, King Faisal Specialist Hospital & Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Eduardo Bossone
- U.O.C Riabilitazione Cardiovascolare, A Cardarelli, Naples, Italy
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4
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Peppelenbosch MP, Frijns N, Fuhler G. Systems medicine approaches for peptide array-based protein kinase profiling: progress and prospects. Expert Rev Proteomics 2016; 13:571-8. [PMID: 27241729 DOI: 10.1080/14789450.2016.1187564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Pharmacological manipulation of signalling pathways is becoming an increasingly important avenue for the rational clinical management of disease but is hampered by a lack of technologies that allow the generation of comprehensive descriptions of cellular signalling. AREAS COVERED Herein, the authors discuss the potential of peptide array-based kinome profiling for evaluating cellular signalling in the context of drug discovery. Expert commentary: Genomic and proteomic approaches have been of significant value to our elucidation of the molecular mechanisms that govern physiology. However, an equally, if not more important goal, is to define those proteins that participate in signalling pathways that ultimately control cell fate, especially kinases. Traditional genetic and biochemical approaches can certainly provide answers here, but for technical and practical reasons, are typically pursued one gene or pathway at a time. A more comprehensive approach is one in which peptide arrays of kinase-specific substrates are incubated with cell lysates and (33)P-ATP generating comprehensive descriptions, or where arrays are interrogated with phosphospecific antibodies. Both approaches allow analysis of cellular signalling without a priori assumptions to possibly influenced pathways.
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Affiliation(s)
| | | | - Gwenny Fuhler
- c Erasmus MC , Erasmus MC Cancer Institute , Rotterdam , Zuid-Holland, CA , Netherlands
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5
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Scholma J, Fuhler GM, Joore J, Hulsman M, Schivo S, List AF, Reinders MJT, Peppelenbosch MP, Post JN. Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots. Sci Rep 2016; 6:26695. [PMID: 27225531 PMCID: PMC4881024 DOI: 10.1038/srep26695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/06/2016] [Indexed: 12/16/2022] Open
Abstract
Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of “housekeeping” kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling.
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Affiliation(s)
- Jetse Scholma
- Department of Developmental BioEngineering, MIRA institute for biomedical technology and technical medicine, University of Twente, P.O. Box 217, NL-7500 AE Enschede, The Netherlands
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology. Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwal 230, NL-3015 CE Rotterdam, The Netherlands
| | - Jos Joore
- Pepscope BV, Dantelaan 83, 3533 VB Utrecht, The Netherlands
| | - Marc Hulsman
- Department of Clinical Genetics, VU University Medical Center, 1007 MB Amsterdam, The Netherlands.,Delft Bioinformatics Lab. Delft University of Technology, Mekelweg 4, NL-2628 CD Delft, The Netherlands
| | - Stefano Schivo
- Department of Formal Methods and Tools, CTIT institute, University of Twente, P.O. Box 217, NL-7500 AE Enschede, The Netherlands
| | - Alan F List
- Department of Malignant Hematology, Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Marcel J T Reinders
- Delft Bioinformatics Lab. Delft University of Technology, Mekelweg 4, NL-2628 CD Delft, The Netherlands
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology. Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwal 230, NL-3015 CE Rotterdam, The Netherlands
| | - Janine N Post
- Department of Developmental BioEngineering, MIRA institute for biomedical technology and technical medicine, University of Twente, P.O. Box 217, NL-7500 AE Enschede, The Netherlands
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6
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RF-Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3281590. [PMID: 27066500 PMCID: PMC4811047 DOI: 10.1155/2016/3281590] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/13/2016] [Accepted: 01/31/2016] [Indexed: 01/17/2023]
Abstract
Protein phosphorylation is one of the most widespread regulatory mechanisms in eukaryotes. Over the past decade, phosphorylation site prediction has emerged as an important problem in the field of bioinformatics. Here, we report a new method, termed Random Forest-based Phosphosite predictor 2.0 (RF-Phos 2.0), to predict phosphorylation sites given only the primary amino acid sequence of a protein as input. RF-Phos 2.0, which uses random forest with sequence and structural features, is able to identify putative sites of phosphorylation across many protein families. In side-by-side comparisons based on 10-fold cross validation and an independent dataset, RF-Phos 2.0 compares favorably to other popular mammalian phosphosite prediction methods, such as PhosphoSVM, GPS2.1, and Musite.
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7
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Resjö S, Ali A, Meijer HJG, Seidl MF, Snel B, Sandin M, Levander F, Govers F, Andreasson E. Quantitative Label-Free Phosphoproteomics of Six Different Life Stages of the Late Blight Pathogen Phytophthora infestans Reveals Abundant Phosphorylation of Members of the CRN Effector Family. J Proteome Res 2014; 13:1848-59. [DOI: 10.1021/pr4009095] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Svante Resjö
- Department
of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden
| | - Ashfaq Ali
- Department
of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden
| | - Harold J. G. Meijer
- Laboratory
of Phytopathology, Wageningen University, 6700 EE Wageningen, The Netherlands
| | - Michael F. Seidl
- Laboratory
of Phytopathology, Wageningen University, 6700 EE Wageningen, The Netherlands
- Theoretical
Biology and Bioinformatics, Department of Biology, Utrecht University, 3508
TC Utrecht, The Netherlands
- Centre
for BioSystems
Genomics, 6700 AB Wageningen, The Netherlands
| | - Berend Snel
- Theoretical
Biology and Bioinformatics, Department of Biology, Utrecht University, 3508
TC Utrecht, The Netherlands
- Centre
for BioSystems
Genomics, 6700 AB Wageningen, The Netherlands
| | - Marianne Sandin
- Department
of Immunotechnology, Lund University, S-223 81 Lund, Sweden
| | - Fredrik Levander
- Department
of Immunotechnology, Lund University, S-223 81 Lund, Sweden
| | - Francine Govers
- Laboratory
of Phytopathology, Wageningen University, 6700 EE Wageningen, The Netherlands
- Centre
for BioSystems
Genomics, 6700 AB Wageningen, The Netherlands
| | - Erik Andreasson
- Department
of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden
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8
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Trost B, Kindrachuk J, Scruten E, Griebel P, Kusalik A, Napper S. Kinotypes: stable species- and individual-specific profiles of cellular kinase activity. BMC Genomics 2013; 14:854. [PMID: 24314169 PMCID: PMC3924188 DOI: 10.1186/1471-2164-14-854] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/29/2013] [Indexed: 12/31/2022] Open
Abstract
Background Recently, questions have been raised regarding the ability of animal models to recapitulate human disease at the molecular level. It has also been demonstrated that cellular kinases, individually or as a collective unit (the kinome), play critical roles in regulating complex biology. Despite the intimate relationship between kinases and health, little is known about the variability, consistency and stability of kinome profiles across species and individuals. Results As a preliminary investigation of the existence of species- and individual-specific kinotypes (kinome signatures), peptide arrays were employed for the analysis of peripheral blood mononuclear cells collected weekly from human and porcine subjects (n = 6) over a one month period. The data revealed strong evidence for species-specific signalling profiles. Both humans and pigs also exhibited evidence for individual-specific kinome profiles that were independent of natural changes in blood cell populations. Conclusions Species-specific kinotypes could have applications in disease research by facilitating the selection of appropriate animal models or by revealing a baseline kinomic signature to which treatment-induced profiles could be compared. Similarly, individual-specific kinotypes could have implications in personalized medicine, where the identification of molecular patterns or signatures within the kinome may depend on both the levels of kinome diversity and temporal stability across individuals.
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Affiliation(s)
| | | | | | | | | | - Scott Napper
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada.
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9
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Trost B, Kusalik A. Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights. Bioinformatics 2013; 29:686-94. [PMID: 23341503 DOI: 10.1093/bioinformatics/btt031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
MOTIVATION Phosphorylation is the most important post-translational modification in eukaryotes. Although many computational phosphorylation site prediction tools exist for mammals, and a few were created specifically for Arabidopsis thaliana, none are currently available for other plants. RESULTS In this article, we propose a novel random forest-based method called PHOSFER (PHOsphorylation Site FindER) for applying phosphorylation data from other organisms to enhance the accuracy of predictions in a target organism. As a test case, PHOSFER is applied to phosphorylation sites in soybean, and we show that it more accurately predicts soybean sites than both the existing Arabidopsis-specific predictors, and a simpler machine-learning scheme that uses only known phosphorylation sites and non-phosphorylation sites from soybean. In addition to soybean, PHOSFER will be extended to other organisms in the near future.
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Affiliation(s)
- Brett Trost
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada.
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10
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Peppelenbosch MP. Kinome profiling. SCIENTIFICA 2012; 2012:306798. [PMID: 24278683 PMCID: PMC3820527 DOI: 10.6064/2012/306798] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 07/12/2012] [Indexed: 06/02/2023]
Abstract
The use of arrays in genomics has led to a fast and reliable way to screen the transcriptome of an organism. It can be automated and analysis tools have become available and hence the technique has become widely used within the past few years. Signal-transduction routes rely mainly on the phosphorylation status of already available proteins; therefore kinases are central players in signal-transduction routes. The array technology can now also be used for the analysis of the kinome. To enable array analysis, consensus peptides for kinases are spot on a solid support. After incubation with cell lysates and in the presence of radioactive ATP, radioactive peptides can be visualized and the kinases that are active in the cells can be determined. The present paper reviews comprehensively the different kinome array platforms available and results obtained hitherto using such platforms. It will appear that this technology does not disappoint its high expectations and is especially powerful because of its species independence. Nevertheless, improvements are still possible and I shall also sketch future possible directions.
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Affiliation(s)
- Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, L-459, P.O. Box 2040, NL-3000 CA Rotterdam, The Netherlands
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11
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Sikkema AH, den Dunnen WFA, Diks SH, Peppelenbosch MP, de Bont ESJM. Optimizing targeted cancer therapy: towards clinical application of systems biology approaches. Crit Rev Oncol Hematol 2012; 82:171-86. [PMID: 21641230 DOI: 10.1016/j.critrevonc.2011.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 04/28/2011] [Accepted: 05/04/2011] [Indexed: 12/13/2022] Open
Abstract
In cancer, genetic and epigenetic alterations ultimately culminate in discordant activation of signal transduction pathways driving the malignant process. Pharmacological or biological inhibition of such pathways holds significant promise with respect to devising rational therapy for cancer. Thus, technical concepts pursuing robust characterization of kinase activity in tissue samples from cancer patients have been subject of investigation. In the present review we provide a comprehensive overview of these techniques and discuss their advantages and disadvantages for systems biology approaches to identify kinase targets in oncological disease. Recent advances in the development and application of array-based peptide-substrate kinase activity screens show great promise in overcoming the discrepancy between the evaluation of aberrant cell signaling in specific malignancies or even individual patients and the currently available ensemble of highly specific targeted treatment strategies. These developments have the potential to result in a more effective selection of kinase inhibitors and thus optimize mechanism-based patient-specific therapeutic strategies. Given the results from current research on the tumor kinome, generating network views on aberrant tumor cell signaling is critical to meet this challenge.
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Affiliation(s)
- Arend H Sikkema
- Beatrix Children's Hospital, Department of Pediatric Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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12
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Kozlov IA, Thomsen ER, Munchel SE, Villegas P, Capek P, Gower AJ, Pond SJK, Chudin E, Chee MS. A highly scalable peptide-based assay system for proteomics. PLoS One 2012; 7:e37441. [PMID: 22701568 PMCID: PMC3373263 DOI: 10.1371/journal.pone.0037441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022] Open
Abstract
We report a scalable and cost-effective technology for generating and screening high-complexity customizable peptide sets. The peptides are made as peptide-cDNA fusions by in vitro transcription/translation from pools of DNA templates generated by microarray-based synthesis. This approach enables large custom sets of peptides to be designed in silico, manufactured cost-effectively in parallel, and assayed efficiently in a multiplexed fashion. The utility of our peptide-cDNA fusion pools was demonstrated in two activity-based assays designed to discover protease and kinase substrates. In the protease assay, cleaved peptide substrates were separated from uncleaved and identified by digital sequencing of their cognate cDNAs. We screened the 3,011 amino acid HCV proteome for susceptibility to cleavage by the HCV NS3/4A protease and identified all 3 known trans cleavage sites with high specificity. In the kinase assay, peptide substrates phosphorylated by tyrosine kinases were captured and identified by sequencing of their cDNAs. We screened a pool of 3,243 peptides against Abl kinase and showed that phosphorylation events detected were specific and consistent with the known substrate preferences of Abl kinase. Our approach is scalable and adaptable to other protein-based assays.
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Affiliation(s)
- Igor A Kozlov
- Prognosys Biosciences Inc., La Jolla, California, United States of America.
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13
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Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
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14
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Nakagami H, Sugiyama N, Ishihama Y, Shirasu K. Shotguns in the front line: phosphoproteomics in plants. PLANT & CELL PHYSIOLOGY 2012; 53:118-24. [PMID: 22039104 DOI: 10.1093/pcp/pcr148] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The emergence of 'shotgun proteomics' has paved the way for high-throughput proteome analysis, by which thousands of proteins can be identified simultaneously from complex samples. Although the shotgun approach has the potential to monitor many different post-translational modifications, further technological development is needed to enrich each post-translational 'modificome'. Large-scale in vivo phosphorylation site mapping, so-called shotgun phosphoproteomics, has become feasible in various organisms, including plants, owing to recent technological breakthroughs. Shotgun phosphoproteomics is not a mature technology, but progress has been rapid. In this review, we highlight the scope and limitations of current methods, and some key technological issues in this field.
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15
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Trost B, Kusalik A. Computational prediction of eukaryotic phosphorylation sites. Bioinformatics 2011; 27:2927-35. [DOI: 10.1093/bioinformatics/btr525] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Snir E, Joore J, Timmerman P, Yitzchaik S. Monitoring selectivity in kinase-promoted phosphorylation of densely packed peptide monolayers using label-free electrochemical detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:11212-11221. [PMID: 21774536 DOI: 10.1021/la202247m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper describes remarkably high sensitivities in the label-free detection of kinase-promoted phosphorylation for 14 different peptide substrates on electrode-immobilized monolayers (gold or nitride) using serine/threonine kinases PKA, PKC, and CaMK2. Peptide substrates were preselected using (33)P-labeling in a microarray of 1024 substrates. The three most active peptides (A1-A3, C1-C3, and M1-M3) were investigated using electrochemical impedance spectroscopy (EIS) and ion-sensitive field effect transistors (ISFETs). Some of the peptide substrates, for example, the PKC-specific substrate PPRRSSIRNAH (C1), showed a remarkably high sensitivity in the EIS-based sensor measurements. Our studies revealed that this high sensitivity is primarily due to the monolayer's packing density. Nanoscopic studies demonstrated a distinct disordering of the C1-monolayer upon phosphorylation, while phosphatase-promoted dephosphorylation regenerated the highly ordered peptide monolayer. As a matter of fact, the initial surface packing of the peptide monolayer mainly determined the level of sensitivity, whereas electrostatic repulsion of the redox-active species was found to be much less important.
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Affiliation(s)
- Elza Snir
- Institute of Chemistry and The Nanoscience and Nanotechnology Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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17
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Hazen AL, Diks SH, Wahle JA, Fuhler GM, Peppelenbosch MP, Kerr WG. Major remodelling of the murine stem cell kinome following differentiation in the hematopoietic compartment. J Proteome Res 2011; 10:3542-50. [PMID: 21648952 DOI: 10.1021/pr2001594] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The changes in signal transduction associated with the acquisition of specific cell fates remain poorly understood. We performed massive parallel assessment of kinase signatures of the radiations of the hematopoietic system, including long-term repopulating hematopoietic stem cells (LT-HSC), short-term repopulating HSC (ST-HSC), immature natural killer (iNK) cells, NK cells, B cells, T cells, and myeloid cells. The LT-HSC kinome is characterized by noncanonical Wnt, Ca(2+) and classical protein kinase C (PKC)-driven signaling, which is lost upon the transition to ST-HSC, whose kinome signature prominently features receptor tyrosine kinase (RTK) activation of the Ras/MAPK signaling cassette. Further differentiation to iNK maintains signaling through this cassette but simultaneously leads to activation of a PI3K/PKB/Rac signaling, which becomes the dominant trait in the kinase signature following full differentiation toward NK cells. Differentiation along the myeloid and B cell lineages is accompanied by hyperactivation of both the Ras/MAPK and PI3K/PKB/Rac signaling cassette. T cells, however, deactivate signaling and only display residual G protein-coupled pathways. Thus, differentiation along the hematopoietic lineage is associated with major remodelling of cellular kinase signature.
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Affiliation(s)
- Amy L Hazen
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
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18
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Zambuzzi WF, Coelho PG, Alves GG, Granjeiro JM. Intracellular signal transduction as a factor in the development of "smart" biomaterials for bone tissue engineering. Biotechnol Bioeng 2011; 108:1246-50. [PMID: 21351075 DOI: 10.1002/bit.23117] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 01/21/2011] [Accepted: 02/16/2011] [Indexed: 11/11/2022]
Abstract
Signal transduction involves studying the intracellular mechanisms that govern cellular responses to external stimuli such as hormones, cytokines, and also cell adhesion to biomaterials surfaces. Several events have been shown to be responsible for cellular adhesion and adaptation onto different surfaces. For instance, cytoskeletal rearrangements during cell adhesion require the recruitment of specific protein tyrosine kinases into focal adhesion structures that promote transient focal adhesion kinase and Src phosphorylations, initially modulating cell behavior. In addition, the phosphorylation of tyrosine (Y) residues have been generally accepted as a critical regulator of a wide range of cell-related processes, including cell proliferation, migration, differentiation, survival signalling, and energy metabolism. The understanding of the signaling involved on the mechanisms of osteoblast adhesion, proliferation, and differentiation on implant surfaces is fundamental for the successful design of novel "smart" materials, potentially decreasing the repair time, thereby allowing for faster patient rehabilitation.
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Affiliation(s)
- Willian F Zambuzzi
- Fluminense Federal University, Cell Therapy Center, Avenida Marquês de Paraná, 303, Niterói, BR 24030-215, Brazil.
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19
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Hoogendijk AJ, Diks SH, Peppelenbosch MP, Van Der Poll T, Wieland CW. Kinase activity profiling of gram-negative pneumonia. Mol Med 2011; 17:741-7. [PMID: 21424109 DOI: 10.2119/molmed.2011.00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 03/09/2011] [Indexed: 01/15/2023] Open
Abstract
Pneumonia is a severe disease with high morbidity and mortality. A major causative pathogen is the Gram-negative bacterium Klebsiella (K.) pneumoniae. Kinases play an integral role in the transduction of intracellular signaling cascades and regulate a diverse array of biological processes essential to immune cells. The current study explored signal transduction events during murine Gram-negative pneumonia using a systems biology approach. Kinase activity arrays enable the analysis of 1,024 consensus sequences of protein kinase substrates. Using a kinase activity array on whole lung lysates, cellular kinase activities were determined in a mouse model of K. pneumoniae pneumonia. Notable kinase activities also were validated with phospho-specific Western blots. On the basis of the profiling data, mitogen-activated protein kinase (MAPK) signaling via p42 mitogen-activated protein kinase (p42) and p38 mitogen-activated protein kinase (p38) and transforming growth factor β (TGFβ) activity were reduced during infection, whereas v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) (SRC) activity generally was enhanced. AKT signaling was represented in both metabolic and inflammatory (mitogen-activated protein kinase kinase 2 [MKK], apoptosis signal-regulating kinase/mitogen-activated protein kinase kinase kinase 5 [ASK] and v-raf murine sarcoma viral oncogene homolog B1 [b-RAF]) context. This study reaffirms the importance of classic inflammation pathways, such as MAPK and TGFβ signaling and reveals less known involvement of glycogen synthase kinase 3β (GSK-3β), AKT and SRC signaling cassettes in pneumonia.
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20
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Ritsema T, van Zanten M, Leon-Reyes A, Voesenek LACJ, Millenaar FF, Pieterse CMJ, Peeters AJM. Kinome profiling reveals an interaction between jasmonate, salicylate and light control of hyponastic petiole growth in Arabidopsis thaliana. PLoS One 2010; 5:e14255. [PMID: 21170386 PMCID: PMC2999534 DOI: 10.1371/journal.pone.0014255] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 11/17/2010] [Indexed: 12/13/2022] Open
Abstract
Plants defend themselves against infection by biotic attackers by producing distinct phytohormones. Especially jasmonic acid (JA) and salicylic acid (SA) are well known defense-inducing hormones. Here, the effects of MeJA and SA on the Arabidopsis thaliana kinome were monitored using PepChip arrays containing kinase substrate peptides to analyze posttranslational interactions in MeJA and SA signaling pathways and to test if kinome profiling can provide leads to predict posttranslational events in plant signaling. MeJA and SA mediate differential phosphorylation of substrates for many kinase families. Also some plant specific substrates were differentially phosphorylated, including peptides derived from Phytochrome A, and Photosystem II D protein. This indicates that MeJA and SA mediate cross-talk between defense signaling and light responses. We tested the predicted effects of MeJA and SA using light-mediated upward leaf movement (differential petiole growth also called hyponastic growth). We found that MeJA, infestation by the JA-inducing insect herbivore Pieris rapae, and SA suppressed low light-induced hyponastic growth. MeJA and SA acted in a synergistic fashion via two (partially) divergent signaling routes. This work demonstrates that kinome profiling using PepChip arrays can be a valuable complementary ∼omics tool to give directions towards predicting behavior of organisms after a given stimulus and can be used to obtain leads for physiological relevant phenomena in planta.
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Affiliation(s)
- Tita Ritsema
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
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21
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Ter Elst A, Diks SH, Kampen KR, Hoogerbrugge PM, Ruijtenbeek R, Boender PJ, Sikkema AH, Scherpen FJG, Kamps WA, Peppelenbosch MP, de Bont ESJM. Identification of new possible targets for leukemia treatment by kinase activity profiling. Leuk Lymphoma 2010; 52:122-30. [PMID: 21133721 DOI: 10.3109/10428194.2010.535181] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To date, the biology of acute leukemia has been unclear, and defining new therapeutic targets without prior knowledge remains complicated. The use of high-throughput techniques would enable us to learn more about the biology of the disease, and make it possible to directly assess a broader range of therapeutic targets. In this study we have identified comprehensive tyrosine kinase activity profiles in leukemia samples using the PamChip® kinase activity profiling system. Strikingly, 31% (44/120) of the detected peptides were active in all three groups of leukemia samples. The recently reported activity of platelet-derived growth factor receptor (PDGFR) and neurotrophic tyrosine kinase receptors (NTRK1 and NTRK2) in leukemia could be appreciated in our array results. In addition, high levels of peptide phosphorylation were demonstrated for peptides related to macrophage stimulating 1 receptor (MST1R). A provisional signal transduction scheme of the common active peptides was constructed and used to specifically select an inhibitor for leukemic blast cell survival assays. As expected, a dose-dependent decrease in leukemic blast cell survival was achieved for all leukemia samples. Our data demonstrate that kinase activity profiling in leukemic samples is feasible and provides novel insights into the pathogenesis of leukemia. This approach can be used for the rapid discovery of potential drug targets.
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Affiliation(s)
- Arja Ter Elst
- Department of Pediatric Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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22
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Fraser JA, Vojtesek B, Hupp TR. A novel p53 phosphorylation site within the MDM2 ubiquitination signal: I. phosphorylation at SER269 in vivo is linked to inactivation of p53 function. J Biol Chem 2010; 285:37762-72. [PMID: 20851891 DOI: 10.1074/jbc.m110.143099] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
p53 is a thermodynamically unstable protein containing a conformationally flexible multiprotein docking site within the DNA-binding domain. A combinatorial peptide chip used to identify the novel kinase consensus site RXSΦ(K/D) led to the discovery of a homologous phosphorylation site in the S10 β-strand of p53 at Ser(269). Overlapping peptide libraries confirmed that Ser(269) was a phosphoacceptor site in vitro, and immunochemical approaches evaluated whether p53 is phosphorylated in vivo at Ser(269). Mutation or phosphorylation of p53 at Ser(269) attenuates binding of the p53-specific monoclonal antibody DO-12, identifying an assay for measuring Ser(269) phosphorylation of p53 in vivo. The mAb DO-12 epitope of p53 is masked via phosphorylation in a range of human tumor cells with WT p53 status, as defined by increased mAb DO-12 binding to endogenous p53 after phosphatase treatment. Phospho-Ser(269)-specific monoclonal antibodies were generated and used to demonstrate that p53 phosphorylation is induced at Ser(269) after irradiation with kinetics similar to those of p53 protein induction. Phosphomimetic mutation at Ser(269) inactivated the transcription activation function and clonogenic suppressor activity of p53. These data suggest that the dynamic equilibrium between native and unfolded states of WT p53 can be modulated by phosphorylation of the conformationally flexible multiprotein binding site in the p53 DNA-binding domain.
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Affiliation(s)
- Jennifer A Fraser
- Institute of Genetics and Molecular Medicine, CRUK Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, Scotland, United Kingdom
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23
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Milani R, Ferreira CV, Granjeiro JM, Paredes-Gamero EJ, Silva RA, Justo GZ, Nader HB, Galembeck E, Peppelenbosch MP, Aoyama H, Zambuzzi WF. Phosphoproteome reveals an atlas of protein signaling networks during osteoblast adhesion. J Cell Biochem 2010; 109:957-66. [PMID: 20127719 DOI: 10.1002/jcb.22479] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell adhesion on surfaces is a fundamental process in the emerging biomaterials field and developmental events as well. However, the mechanisms regulating this biological process in osteoblasts are not fully understood. Reversible phosphorylation catalyzed by kinases is probably the most important regulatory mechanism in eukaryotes. Therefore, the goal of this study is to assess osteoblast adhesion through a molecular prism under a peptide array technology, revealing essential signaling proteins governing adhesion-related events. First, we showed that there are main morphological changes on osteoblast shape during adhesion up to 3 h. Second, besides classical proteins activated upon integrin activation, our results showed a novel network involving signaling proteins such as Rap1A, PKA, PKC, and GSK3beta during osteoblast adhesion on polystyrene. Third, these proteins were grouped in different signaling cascades including focal adhesion establishment, cytoskeleton rearrangement, and cell-cycle arrest. We have thus provided evidence that a global phosphorylation screening is able to yield a systems-oriented look at osteoblast adhesion, providing new insights for understanding of bone formation and improvement of cell-substratum interactions. Altogether, these statements are necessary means for further intervention and development of new approaches for the progress of tissue engineering.
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Affiliation(s)
- Renato Milani
- Department of Biochemistry, Institute of Biology, University of Campinas (UNICAMP), 13083-970 Campinas, São Paulo, Brazil
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24
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Ritsema T, Peppelenbosch MP. Kinome profiling of sugar signaling in plants using multiple platforms. PLANT SIGNALING & BEHAVIOR 2009; 4:1169-73. [PMID: 20514238 PMCID: PMC2819448 DOI: 10.4161/psb.4.12.10022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 04/09/2009] [Indexed: 05/08/2023]
Abstract
Although the primary sequence of kinases shows substantial divergence between unrelated eukaryotes, variation in the motifs that are actually phosphorylated by eukaryotic kinases is much smaller. Hence arrays developed for kinome profiling of mammalian cells are useful for kinome profiling of plant tissues as well, facilitating the study of plant signal transduction. We recently employed the Pepscan kinomics chip to reveal the small GTPases in plant sucrose signaling. Here we show that employing a different peptide library (the Pepscan kinase chip) largely similar results are obtained, confirming these earlier data, but such a different library also contributes new insights into the molecular details mediating plant cell responses to a sugar stimulus. Thus when studying plant signal transduction employing peptide arrays, using multiple platforms both increases the confidence of results and provides additional information.
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Affiliation(s)
- Tita Ritsema
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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25
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Ritsema T, Brodmann D, Diks SH, Bos CL, Nagaraj V, Pieterse CM, Boller T, Wiemken A, Peppelenbosch MP. Are small GTPases signal hubs in sugar-mediated induction of fructan biosynthesis? PLoS One 2009; 4:e6605. [PMID: 19672308 PMCID: PMC2720452 DOI: 10.1371/journal.pone.0006605] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 06/20/2009] [Indexed: 11/19/2022] Open
Abstract
External sugar initiates biosynthesis of the reserve carbohydrate fructan, but the molecular processes mediating this response remain obscure. Previously it was shown that a phosphatase and a general kinase inhibitor hamper fructan accumulation. We use various phosphorylation inhibitors both in barley and in Arabidopsis and show that the expression of fructan biosynthetic genes is dependent on PP2A and different kinases such as Tyr-kinases and PI3-kinases. To further characterize the phosphorylation events involved, comprehensive analysis of kinase activities in the cell was performed using a PepChip, an array of >1000 kinase consensus substrate peptide substrates spotted on a chip. Comparison of kinase activities in sugar-stimulated and mock(sorbitol)-treated Arabidopsis demonstrates the altered phosphorylation of many consensus substrates and documents the differences in plant kinase activity upon sucrose feeding. The different phosphorylation profiles obtained are consistent with sugar-mediated alterations in Tyr phosphorylation, cell cycling, and phosphoinositide signaling, and indicate cytoskeletal rearrangements. The results lead us to infer a central role for small GTPases in sugar signaling.
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Affiliation(s)
- Tita Ritsema
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, Basel, Switzerland
- Plant-Microbe interactions, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - David Brodmann
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, Basel, Switzerland
| | - Sander H. Diks
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Carina L. Bos
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Vinay Nagaraj
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, Basel, Switzerland
| | - Corné M.J. Pieterse
- Plant-Microbe interactions, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Thomas Boller
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, Basel, Switzerland
| | - Andres Wiemken
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, Basel, Switzerland
| | - Maikel P. Peppelenbosch
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail:
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26
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Parikh K, Diks SH, Tuynman JHB, Verhaar A, Löwenberg M, Hommes DW, Joore J, Pandey A, Peppelenbosch MP. Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PLoS One 2009; 4:e6440. [PMID: 19649278 PMCID: PMC2713828 DOI: 10.1371/journal.pone.0006440] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 06/22/2009] [Indexed: 01/10/2023] Open
Abstract
Kinases are pivotal regulators of cellular physiology. The human genome contains more than 500 putative kinases, which exert their action via the phosphorylation of specific substrates. The determinants of this specificity are still only partly understood and as a consequence it is difficult to predict kinase substrate preferences from the primary structure, hampering the understanding of kinase function in physiology and prompting the development of technologies that allow easy assessment of kinase substrate consensus sequences. Hence, we decided to explore the usefulness of phosphorylation of peptide arrays comprising of 1176 different peptide substrates with recombinant kinases for determining kinase substrate preferences, based on the contribution of individual amino acids to total array phosphorylation. Employing this technology, we were able to determine the consensus peptide sequences for substrates of both c-Raf and Mitogen Activated Protein Kinase Kinase Kinase 8, two highly homologous kinases with distinct signalling roles in cellular physiology. The results show that although consensus sequences for these two kinases identified through our analysis share important chemical similarities, there is still some sequence specificity that could explain the different biological action of the two enzymes. Thus peptide arrays are a useful instrument for deducing substrate consensus sequences and highly homologous kinases can differ in their requirement for phosphorylation events.
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Affiliation(s)
- Kaushal Parikh
- Department of Cell Biology, Section Immunology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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27
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Sikkema AH, Diks SH, den Dunnen WFA, ter Elst A, Scherpen FJG, Hoving EW, Ruijtenbeek R, Boender PJ, de Wijn R, Kamps WA, Peppelenbosch MP, de Bont ESJM. Kinome profiling in pediatric brain tumors as a new approach for target discovery. Cancer Res 2009; 69:5987-95. [PMID: 19567681 DOI: 10.1158/0008-5472.can-08-3660] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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.
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Affiliation(s)
- Arend H Sikkema
- Department of Pediatric Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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28
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A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry. Proc Natl Acad Sci U S A 2009; 106:11606-11. [PMID: 19564600 DOI: 10.1073/pnas.0905165106] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Most kinases are capable of recognizing and phosphorylating peptides containing short, linear sequence motifs. To measure the activation state of many kinases from the same cell lysate, we created a multiplexed, mass-spectrometry-based in vitro kinase assay. Ninety chemically synthesized peptides derived from well-characterized peptide substrates and in vivo phosphorylation sites with either known or previously unidentified upstream kinases were reacted individually in a plate format with crude cell lysates and ATP. Phosphorylation rates were directly measured based on the addition of 90 same-sequence, site-specific phosphopeptides enriched in stable isotopes to act as ideal quantitative internal standards for analysis by liquid chromatography coupled to tandem mass spectrometry. This approach concurrently measured up to 90 site-specific peptide phosphorylation rates, reporting a diagnostic fingerprint for activated kinase pathways. We applied this unique kinome-activity profiling strategy in a variety of cellular settings, including mitogen stimulation, cell cycle, pharmacological inhibition of pathways, and to a panel of breast cancer cell lines. Finally, we identified the source of activity for a peptide (derived from a PI3K regulatory subunit) from our library. This peptide substrate demonstrated mitotic and tyrosine-specific phosphorylation, which was confirmed to be a novel Src family kinase site in vivo.
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29
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Parikh K, Peppelenbosch MP, Ritsema T. Kinome profiling using peptide arrays in eukaryotic cells. Methods Mol Biol 2009; 527:269-80, x. [PMID: 19241020 DOI: 10.1007/978-1-60327-834-8_20] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the last 10 years array and mass spectrometry technologies have enabled the determination of the transcriptome and proteome of biological and in particular eukaryotic systems. This information will likely be of significant value to our elucidation of the molecular mechanisms that govern eukaryotic physiology. However, an equally, if not more important goal, is to define those proteins that participate in signalling pathways that ultimately control cell fate. Enzymes that phosphorylate tyrosine, serine, and threonine residues on other proteins play a major role in signalling cascades that determine cell-cycle entry, and survival and differentiation fate in the tissues across the eukaryotic kingdoms. Knowing which signalling pathways are being used in these cells is of critical importance. Traditional genetic and biochemical approaches can certainly provide answers here, but for technical and practical reasons there is typically pursued one gene or pathway at a time. Thus, a more comprehensive approach is needed in order to reveal signalling pathways active in nucleated cells. Towards this end, kinome analysis techniques using peptide arrays have begun to be applied with substantial success in a variety of organisms from all major branches of eukaryotic life, generating descriptions of cellular signalling without a priori assumptions as to possibly effected pathways. The general procedure and analysis methods are very similar disregarding whether the primary source of the material is animal, plant, or fungal of nature and will be described in this chapter. These studies will help us better understand what signalling pathways are critical to controlling eukaryotic cell function.
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Affiliation(s)
- Kaushal Parikh
- Department of Cell Biology, University Medical Center Groningen, Groningen, The Netherlands
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30
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Abstract
Enzymes are key molecules in signal transduction pathways. However, only a small fraction of more than 500 predicted human kinases, 250 proteases and 250 phosphatases is characterized so far. Peptide microarray-based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. Additionally, patterns of enzymatic activities could be used to fingerprint the status of cells or organisms. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimization of enzyme substrates. A comprehensive overview regarding enzyme profiling using peptide microarrays is presented with special focus on assay principles.
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Affiliation(s)
- Alexandra Thiele
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
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31
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Extracellular ligation-dependent CD45RB enzymatic activity negatively regulates lipid raft signal transduction. Blood 2008; 113:594-603. [PMID: 18840711 DOI: 10.1182/blood-2008-04-150987] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CD45 is the most prominent membrane protein on lymphocytes. The function and regulation of this protein tyrosine phosphatase remain largely obscure, mainly because of the lack of a known ligand, and it still remains unknown whether such tyrosine phosphatases are subject to extracellular control at all. We report that an anti-CD45RB antibody (Ab) that prevents rejection and induces tolerance activates CD45RB tyrosine phosphatase enzymatic activity in T lymphocytes, allowing us to directly monitor the effects of increased CD45RB activity on signal transduction. Using both kinase substrate peptide arrays as well as conventional biochemistry, we also provide evidence of the various kinases involved in bringing about the inhibitory effect of this Ab on CD3-induced T-cell receptor signaling. Furthermore, we report that activated CD45RB translocates to lipid rafts and interferes with lipid raft localization and activation state of CD45 substrate Lck. Thus, these findings indeed prove that CD45 is subject to extracellular control and also define a novel mechanism by which receptor tyrosine phosphatases control lymphocyte biology and provide further insight into the intracellular signaling pathways effected by anti-CD45RB monoclonal Ab treatment.
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32
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Boekhorst J, van Breukelen B, Heck A, Snel B. Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biol 2008; 9:R144. [PMID: 18828897 PMCID: PMC2760871 DOI: 10.1186/gb-2008-9-10-r144] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 09/03/2008] [Accepted: 10/01/2008] [Indexed: 12/29/2022] Open
Abstract
A comparison of phosphoproteomics datasets of six eukaryotes shows significant overlap between phosphoproteomes. Background Reversible phosphorylation of proteins is involved in a wide range of processes, ranging from signaling cascades to regulation of protein complex assembly. Little is known about the structure and evolution of phosphorylation networks. Recent high-throughput phosphoproteomics studies have resulted in the rapid accumulation of phosphopeptide datasets for many model organisms. Here, we exploit these novel data for the comparative analysis of phosphorylation events between different species of eukaryotes. Results Comparison of phosphoproteomics datasets of six eukaryotes yields an overlap ranging from approximately 700 sites for human and mouse (two large datasets of closely related species) to a single site for fish and yeast (distantly related as well as two of the smallest datasets). Some conserved events appear surprisingly old; those shared by plant and animals suggest conservation over the time scale of a billion years. In spite of the hypothesized incomprehensive nature of phosphoproteomics datasets and differences in experimental procedures, we show that the overlap between phosphoproteomes is greater than expected by chance and indicates increased functional relevance. Despite the dynamic nature of the evolution of phosphorylation, the relative overlap between the different datasets is identical to the phylogeny of the species studied. Conclusion This analysis provides a framework for the generation of biological insights by comparative analysis of high-throughput phosphoproteomics datasets. We expect the rapidly growing body of data from high-throughput mass spectrometry analysis to make comparative phosphoproteomics a powerful tool for elucidating the evolutionary and functional dynamics of reversible phosphorylation.
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Affiliation(s)
- Jos Boekhorst
- Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, The Netherlands.
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33
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Sopko R, Andrews BJ. Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets. MOLECULAR BIOSYSTEMS 2008; 4:920-33. [PMID: 18704230 DOI: 10.1039/b801724g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation is associated with most cell signaling and developmental processes in eukaryotes. Despite the vast extent of the phosphoproteome within the cell, connecting specific kinases with relevant targets remains a significant experimental frontier. The challenge of linking kinases and their substrates reflects the complexity of kinase function. For example, kinases tend to exert their biological effects through supernumerary, redundant phosphorylation, often on multiple protein complex components. Although these types of phosphorylation events are biologically significant, those kinases responsible are often difficult to identify. Recent methods for global analysis of protein phosphorylation promise to substantially accelerate efforts to map the dynamic phosphorylome. Here, we review both conventional methods to identify kinase targets and more comprehensive genomic and proteomic approaches to connect the kinome and phosphorylome.
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Affiliation(s)
- Richelle Sopko
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
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34
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van Baal JWPM, Krishnadath KK. High throughput techniques for characterizing the expression profile of Barrett's esophagus. Dis Esophagus 2008; 21:634-40. [PMID: 18564162 DOI: 10.1111/j.1442-2050.2008.00853.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Barrett's esophagus (BE) is the metaplastic change of the normal lined squamous epithelium of the distal esophagus to a columnar type of epithelium as a result of chronic long-standing gastroesophageal reflux disease. Patients with BE have a significantly increased risk of developing an esophageal adenocarcinoma, with an estimated annual incidence varying from 0.4 to 1.8%. Over the last 3 decades, the incidence of BE and its associated adenocarcinoma has increased in Western countries at a rate that exceeds that of any other malignancy. Despite all the research performed on BE, there is still an inadequate understanding of the biological basis of this mucosal transformation. With the upcoming modern high throughput technologies, important progression has been made in unraveling the expression profiles and gaining more insight in the biology of BE and esophageal adenocarcinoma. Several studies reported genome, transcriptome, proteome, and kinome investigations using high throughput techniques. These studies were conducted to find biomarkers that can be used to detect BE patients with increased risk for malignant progression or to obtain more insight in the mechanism underlying BE development. In the following review, we first discuss the different techniques that are currently available and summarize findings in this field, including several recent publications of our group.
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Affiliation(s)
- J W P M van Baal
- Laboratory of Experimental Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands.
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Sugiyama N, Nakagami H, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y. Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol 2008; 4:193. [PMID: 18463617 PMCID: PMC2424297 DOI: 10.1038/msb.2008.32] [Citation(s) in RCA: 292] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 04/04/2008] [Indexed: 01/17/2023] Open
Abstract
Protein phosphorylation regulates a wide range of cellular processes. Here, we report the proteome-wide mapping of in vivo phosphorylation sites in Arabidopsis by using complementary phosphopeptide enrichment techniques coupled with high-accuracy mass spectrometry. Using unfractionated whole cell lysates of Arabidopsis, we identified 2597 phosphopeptides with 2172 high-confidence, unique phosphorylation sites from 1346 proteins. The distribution of phosphoserine, phosphothreonine, and phosphotyrosine sites was 85.0, 10.7, and 4.3%. Although typical tyrosine-specific protein kinases are absent in Arabidopsis, the proportion of phosphotyrosines among the phospho-residues in Arabidopsis is similar to that in humans, where over 90 tyrosine-specific protein kinases have been identified. In addition, the tyrosine phosphoproteome shows features distinct from those of the serine and threonine phosphoproteomes. Taken together, we highlight the extent and contribution of tyrosine phosphorylation in plants.
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Affiliation(s)
- Naoyuki Sugiyama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
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Tuynman JB, Vermeulen L, Boon EM, Kemper K, Zwinderman AH, Peppelenbosch MP, Richel DJ. Cyclooxygenase-2 inhibition inhibits c-Met kinase activity and Wnt activity in colon cancer. Cancer Res 2008; 68:1213-20. [PMID: 18281498 DOI: 10.1158/0008-5472.can-07-5172] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Activity of receptor tyrosine kinases (RTK) in colorectal cancer (CRC) is associated with enhanced tumor growth and a poorer prognosis. In addition, cyclooxygenase-2 (COX-2) expression contributes to tumor growth and invasion. COX-2 inhibitors exhibit important anticarcinogenic potential against CRC, but the molecular mechanism underlying this effect and the relation with RTK signaling remain the subject of intense research effort. Therefore, the rapid effects of COX-2 inhibition in CRC on the complement of all cellular kinases were investigated using a kinase substrate peptide array, Western blotting, transfection, small interfering RNA assays, and CRC cell lines. The resulting alterations in the kinome profile revealed that celecoxib, a selective COX-2 inhibitor, impairs phosphorylation of substrates for the RTKs c-Met and insulin-like growth factor receptor, resulting in decreased downstream signaling. The decrease in c-Met activation is accompanied with an increase in glycogen synthase kinase 3beta kinase activity together with a rapid increase in phosphorylation of beta-catenin. In agreement, a significant reduction of beta-catenin-T-cell factor-dependent transcription is observed both with celecoxib and selective inhibition of c-Met phosphorylation by small molecules. Hence, corepression of c-Met-related and beta-catenin-related oncogenic signal transduction seems a major effector of celecoxib in CRC, which provides a rationale to use c-Met inhibitors and celecoxib analogous to target c-Met and Wnt signaling in a therapeutic setting for patients with CRC.
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Affiliation(s)
- Jurriaan B Tuynman
- Laboratory of Experimental Oncology, Department of Surgery, Academic Medical Center, Amsterdam, the Netherlands.
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