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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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2
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Buffart TE, van den Oord RAHM, van den Berg A, Hilhorst R, Bastiaensen N, Pruijt HFM, van den Brule A, Nooijen P, Labots M, de Goeij-de Haas RR, Dekker H, Piersma SR, Pham TV, van der Leij T, de Wijn R, Ruijtenbeek R, Jiménez CR, Verheul HMW. Time dependent effect of cold ischemia on the phosphoproteome and protein kinase activity in fresh-frozen colorectal cancer tissue obtained from patients. Clin Proteomics 2021; 18:8. [PMID: 33602116 PMCID: PMC7893972 DOI: 10.1186/s12014-020-09306-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background Based on their potential to analyze aberrant cellular signaling in relation to biological function, kinase activity profiling in tumor biopsies by peptide microarrays and mass spectrometry-based phosphoproteomics may guide selection of protein kinase inhibitors in patients with cancer. Variable tissue handling procedures in clinical practice may influence protein phosphorylation status and kinase activity and therewith may hamper biomarker discovery. Here, the effect of cold ischemia time (CIT) on the stability of kinase activity and protein phosphorylation status in fresh-frozen clinical tissue samples was studied using peptide microarrays and mass spectrometry-based phosphoproteomics. Methods Biopsies of colorectal cancer resection specimens from five patients were collected and snap frozen immediately after surgery and at 6 additional time points between 0 and 180 min of CIT. Kinase activity profiling was performed for all samples using a peptide microarray. MS-based global phosphoproteomics was performed in tumors from 3 patients at 4 time points. Statistical and cluster analyses were performed to analyze changes in kinase activity and phosphoproteome resulting from CIT. Results Unsupervised cluster analysis of kinase activity and phosphoproteome data revealed that samples from the same patients cluster together. Continuous ANOVA analysis of all 7 time points for 5 patient samples resulted in 4 peptides out of 210 (2%) with significantly (p < 0.01 and fold change > 2) altered signal intensity in time. In 4 out of 5 patients tumor kinase activity was stable with CIT. MS-based phosphoproteomics resulted in the detection of 10,488 different phosphopeptides with on average 6044 phosphopeptides per tumor sample. 2715 phosphopeptides were detected in all samples at time point 0, of which 90 (3.3%) phosphopeptides showed significant changes in intensity with CIT (p < 0.01). Only two phosphopeptides were significantly changed in all time points, including one peptide (PKP3) with a fold change > 2. Conclusions The vast majority of the phosphoproteome as well as the activity of protein kinases in colorectal cancer resection tissue is stable up to 180 min of CIT and reflects tumor characteristics. However, specific changes in kinase activity with increasing CIT were observed. Therefore, stringent tissue collection procedures are advised to minimize changes in kinase activity during CIT.
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Affiliation(s)
- Tineke E Buffart
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rosanne A H M van den Oord
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Department of Medical Oncology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | | | - Riet Hilhorst
- PamGene International BV, 'S-Hertogenbosch, The Netherlands
| | | | - Hans F M Pruijt
- Department of Medical Oncology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Adriaan van den Brule
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Peet Nooijen
- Department of Pathology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Henk Dekker
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Rik de Wijn
- PamGene International BV, 'S-Hertogenbosch, The Netherlands
| | - Rob Ruijtenbeek
- PamGene International BV, 'S-Hertogenbosch, The Netherlands.,GenMab BV, Utrecht, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands. .,Department of Medical Oncology, Radboud University Medical Center, Geert Grooteplein 10, 6525GA, Nijmegen, The Netherlands.
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Tahiri A, Tekpli X, Satheesh SV, DeWijn R, Lüders T, Bukholm IR, Hurtado A, Geisler J, Kristensen VN. Loss of progesterone receptor is associated with distinct tyrosine kinase profiles in breast cancer. Breast Cancer Res Treat 2020; 183:585-598. [PMID: 32710281 PMCID: PMC7497693 DOI: 10.1007/s10549-020-05763-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/20/2020] [Indexed: 11/30/2022]
Abstract
PURPOSE The aim of this study was to assess protein tyrosine kinase profiles in primary breast cancer samples in correlation with the distinct hormone and growth receptor profiles ER, PR, and HER2. EXPERIMENTAL DESIGN Pamchip® microarrays were used to measure the phosphorylation of 144 tyrosine kinase substrates in 29 ER+ breast cancer samples and cell lines MCF7, BT474 and ZR75-1. mRNA expression data from the METABRIC cohort and publicly available PR chip-sequencing data were used for validation purposes, together with RT-PCR. RESULTS In ER+ breast tumors and cell lines, we observed that the loss of PR expression correlated to higher kinase activity in samples and cell lines that were HER2-. A number of kinases, representing mostly proteins within the PI3K/AKT pathway, were identified as responsible for the differential phosphorylation between PR- and PR+ in ER+/HER2- tumors. We used the METABRIC cohort to analyze mRNA expression from 977 ER+/HER2- breast cancers. Twenty four kinase-encoding genes were identified as differentially expressed between PR+ and PR-, dividing ER+/HER2- samples in two distinct clusters with significant differences in survival (p < 0.05). Four kinase genes, LCK, FRK, FGFR4, and MST1R, were identified as potential direct targets of PR. CONCLUSIONS Our results suggest that the PR status has a profound effect on tyrosine kinases, especially for FGFR4 and LCK genes, in ER+/HER2- breast cancer patients. The influence of these genes on the PI3K/AKT signaling pathway may potentially lead to novel drug targets for ER+/PR- breast cancer patients.
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Affiliation(s)
- Andliena Tahiri
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Rik DeWijn
- PamGene International B.V., 's-Hertogenbosch, The Netherlands
| | - Torben Lüders
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ida R Bukholm
- Helgelandssykehuset HF and Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Antoni Hurtado
- Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, Casanova, Barcelona, Spain.,August Pi I Sunyer Research Center (IDIBAPS), Barcelona, Spain
| | - Jürgen Geisler
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Vessela N Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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Metformin induces lipogenic differentiation in myofibroblasts to reverse lung fibrosis. Nat Commun 2019; 10:2987. [PMID: 31278260 PMCID: PMC6611870 DOI: 10.1038/s41467-019-10839-0] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/03/2019] [Indexed: 01/05/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease in which the intricate alveolar network of the lung is progressively replaced by fibrotic scars. Myofibroblasts are the effector cells that excessively deposit extracellular matrix proteins thus compromising lung structure and function. Emerging literature suggests a correlation between fibrosis and metabolic alterations in IPF. In this study, we show that the first-line antidiabetic drug metformin exerts potent antifibrotic effects in the lung by modulating metabolic pathways, inhibiting TGFβ1 action, suppressing collagen formation, activating PPARγ signaling and inducing lipogenic differentiation in lung fibroblasts derived from IPF patients. Using genetic lineage tracing in a murine model of lung fibrosis, we show that metformin alters the fate of myofibroblasts and accelerates fibrosis resolution by inducing myofibroblast-to-lipofibroblast transdifferentiation. Detailed pathway analysis revealed a two-arm mechanism by which metformin accelerates fibrosis resolution. Our data report an antifibrotic role for metformin in the lung, thus warranting further therapeutic evaluation. Idiopathic pulmonary fibrosis is associated with myofibroblast activation in the lungs and metabolic alterations. Here, the authors show that the antidiabetic drug metformin has antifibrotic effects in human-derived samples and mouse models, by modulating a number of metabolic pathways to induce lipogenic transdifferentiation of myofibroblasts.
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Weiss A, Neubauer MC, Yerabolu D, Kojonazarov B, Schlueter BC, Neubert L, Jonigk D, Baal N, Ruppert C, Dorfmuller P, Pullamsetti SS, Weissmann N, Ghofrani HA, Grimminger F, Seeger W, Schermuly RT. Targeting cyclin-dependent kinases for the treatment of pulmonary arterial hypertension. Nat Commun 2019; 10:2204. [PMID: 31101827 PMCID: PMC6525202 DOI: 10.1038/s41467-019-10135-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/15/2019] [Indexed: 12/21/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a devastating disease with poor prognosis and limited therapeutic options. We screened for pathways that may be responsible for the abnormal phenotype of pulmonary arterial smooth muscle cells (PASMCs), a major contributor of PAH pathobiology, and identified cyclin-dependent kinases (CDKs) as overactivated kinases in specimens derived from patients with idiopathic PAH. This increased CDK activity is confirmed at the level of mRNA and protein expression in human and experimental PAH, respectively. Specific CDK inhibition by dinaciclib and palbociclib decreases PASMC proliferation via cell cycle arrest and interference with the downstream CDK-Rb (retinoblastoma protein)-E2F signaling pathway. In two experimental models of PAH (i.e., monocrotaline and Su5416/hypoxia treated rats) palbociclib reverses the elevated right ventricular systolic pressure, reduces right heart hypertrophy, restores the cardiac index, and reduces pulmonary vascular remodeling. These results demonstrate that inhibition of CDKs by palbociclib may be a therapeutic strategy in PAH. Cells of the pulmonary vasculature show a hyperproliferative phenotype in pulmonary arterial hypertension (PAH), thus contributing to the disease pathogenesis. Here the authors show that cyclin-dependent kinases are overactivated in PAH, and that their pharmacological inhibition attenuates the disease in two independent rodent models
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Affiliation(s)
- Astrid Weiss
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Moritz Christian Neubauer
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Dinesh Yerabolu
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Baktybek Kojonazarov
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Beate Christiane Schlueter
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Lavinia Neubert
- Member of the German Center for Lung Research (DZL), Giessen, Germany.,Institute of Pathology, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, Hannover, 30625, Germany
| | - Danny Jonigk
- Member of the German Center for Lung Research (DZL), Giessen, Germany.,Institute of Pathology, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, Hannover, 30625, Germany
| | - Nelli Baal
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,Institute for Clinical Immunology and Transfusion Medicine, University Hospital Giessen and Marburg (UKGM), Aulweg 128, Giessen, 35392, Germany
| | - Clemens Ruppert
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Peter Dorfmuller
- Member of the German Center for Lung Research (DZL), Giessen, Germany.,Department of Pathology, University Hospital of Giessen and Marburg (UKGM), Langhansstrasse 10, Giessen, 35392, Germany
| | - Soni Savai Pullamsetti
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,Max Planck Institute (MPI) for Heart and Lung Research, Parkstrasse 1, Bad Nauheim, 61231, Germany
| | - Norbert Weissmann
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Hossein-Ardeschir Ghofrani
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,Department of Medicine, Imperial College London, London, UK
| | - Friedrich Grimminger
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,University Hospital Giessen and Marburg (UKGM), Giessen, Germany
| | - Werner Seeger
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,Max Planck Institute (MPI) for Heart and Lung Research, Parkstrasse 1, Bad Nauheim, 61231, Germany.,University Hospital Giessen and Marburg (UKGM), Giessen, Germany
| | - Ralph Theo Schermuly
- Justus-Liebig-University Giessen (JLU), Aulweg 130, Giessen, 35392, Germany. .,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany. .,Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, Giessen, Germany. .,Member of the German Center for Lung Research (DZL), Giessen, Germany.
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Dussaq AM, Kennell T, Eustace NJ, Anderson JC, Almeida JS, Willey CD. Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data. PLoS One 2018; 13:e0202139. [PMID: 30130366 PMCID: PMC6103510 DOI: 10.1371/journal.pone.0202139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/27/2018] [Indexed: 12/14/2022] Open
Abstract
Kinomics is an emerging field of science that involves the study of global kinase activity. As kinases are essential players in virtually all cellular activities, kinomic testing can directly examine protein function, distinguishing kinomics from more remote, upstream components of the central dogma, such as genomics and transcriptomics. While there exist several different approaches for kinomic research, peptide microarrays are the most widely used and involve kinase activity assessment through measurement of phosphorylation of peptide substrates on the array. Unfortunately, bioinformatic tools for analyzing kinomic data are quite limited necessitating the development of accessible open access software in order to facilitate standardization and dissemination of kinomic data for scientific use. Here, we examine and present tools for data analysis for the popular PamChip® (PamGene International) kinomic peptide microarray. As a result, we propose (1) a procedural optimization of kinetic curve data capture, (2) new methods for background normalization, (3) guidelines for the detection of outliers during parameterization, and (4) a standardized data model to store array data at various analytical points. In order to utilize the new data model, we developed a series of tools to implement the new methods and to visualize the various data models. In the interest of accessibility, we developed this new toolbox as a series of JavaScript procedures that can be utilized as either server side resources (easily packaged as web services) or as client side scripts (web applications running in the browser). The aggregation of these tools within a Kinomics Toolbox provides an extensible web based analytic platform that researchers can engage directly and web programmers can extend. As a proof of concept, we developed three analytical tools, a technical reproducibility visualizer, an ANOVA based detector of differentially phosphorylated peptides, and a heatmap display with hierarchical clustering.
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Affiliation(s)
- Alex M. Dussaq
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy Kennell
- Informatics Institute, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nicholas J. Eustace
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joshua C. Anderson
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jonas S. Almeida
- Department of Biomedical Informatics, Stony Brook University School of Medicine, Stony Brook, New York, United States of America
| | - Christopher D. Willey
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Labots M, Van der Mijn JC, Dekker H, Ruijter R, Pham TV, Van der Vliet HJ, Van der Hoeven JJM, Meijer GA, Verheul HMW. Selection of Protein Kinase Inhibitors Based on Tumor Tissue Kinase Activity Profiles in Patients with Refractory Solid Malignancies: An Interventional Molecular Profiling Study. Oncologist 2018; 23:1135-e118. [PMID: 30018133 PMCID: PMC6263134 DOI: 10.1634/theoncologist.2018-0263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/27/2017] [Indexed: 01/08/2023] Open
Abstract
Lessons Learned. Clinically applicable tools are needed for treatment selection and repurposing of available protein kinase inhibitors (PKIs) in patients with advanced solid tumors refractory to standard treatment. Using a tyrosine kinase peptide substrate microarray, observed inhibitory activity in vitro could not sufficiently predict clinical benefit of treatment with the selected PKI.
Background. This exploratory molecular profiling study determined the feasibility and benefit of the selection of protein kinase inhibitors (PKIs) based on kinase activity profiling in patients with refractory solid malignancies. Methods. Adult patients with biopsy‐accessible refractory solid tumors were eligible. Per patient, the inhibitory potency of sunitinib, dasatinib, erlotinib, sorafenib, everolimus, and lapatinib was determined in tumor lysates from fresh biopsies using a tyrosine kinase peptide substrate microarray. The most active PKI in this in vitro assay was selected for treatment. Results. Thirteen patients were enrolled in the feasibility part and underwent tumor biopsy. Of 12 patients in whom kinase activity profiling was performed, 11 started treatment with a selected PKI: dasatinib in 8, sunitinib in 2, and erlotinib in 1 patient(s). Eight patients were evaluable for response. One patient had stable disease (SD) >4 months on sunitinib; one patient had SD at 6 weeks but progressive disease (PD) at 12 weeks. The remaining patients had PD after 6 weeks of treatment. Conclusion. Kinase inhibition profiles of multiple PKIs can be reliably determined using fresh tumor biopsies from patients with refractory solid tumors. However, the current in vitro microarray selection approach insufficiently predicted clinical benefit of PKI treatment in these patients.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Johannes C Van der Mijn
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Rita Ruijter
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Hans J Van der Vliet
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
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Warmoes M, Lam SW, van der Groep P, Jaspers JE, Smolders YHCM, de Boer L, Pham TV, Piersma SR, Rottenberg S, Boven E, Jonkers J, van Diest PJ, Jimenez CR. Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer. Oncotarget 2018; 7:63537-63548. [PMID: 27566577 PMCID: PMC5325383 DOI: 10.18632/oncotarget.11535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/13/2016] [Indexed: 11/25/2022] Open
Abstract
Breast cancer arising in female BRCA1 mutation carriers is characterized by an aggressive phenotype and early age of onset. We performed tandem mass spectrometry-based proteomics of secretomes and exosome-like extracellular vesicles from BRCA1-deficient and BRCA1-proficient murine breast tumor models to identify extracellular protein biomarkers, which can be used as an adjunct to current diagnostic modalities in patients with BRCA1-deficient breast cancer. We identified 2,107 proteins, of which 215 were highly enriched in the BRCA1-deficient secretome. We demonstrated that BRCA1-deficient secretome proteins could cluster most human BRCA1- and BRCA2-related breast carcinomas at the transcriptome level. Topoisomerase I (TOP1) and P-cadherin (CDH3) expression was investigated by immunohistochemistry on tissue microarrays of a large panel of 253 human breast carcinomas with and without BRCA1/2 mutations. We showed that expression of TOP1 and CDH3 was significantly increased in human BRCA1-related breast carcinomas relative to sporadic cases (p = 0.002 and p < 0.001, respectively). Multiple logistic regression showed that TOP1 (adjusted odds ratio [OR] 3.75; 95% confidence interval [95% CI], 1.85 - 7.71, p < 0.001) as well as CDH3 positivity (adjusted OR 2.45; 95% CI, 1.08 - 5.49, p = 0.032) were associated with BRCA1/2-related breast carcinomas after adjustment for triple-negative phenotype and age. In conclusion, proteome profiling of secretome using murine breast tumor models is a powerful strategy to identify non-invasive candidate biomarkers of BRCA1-deficient breast cancer. We demonstrate that TOP1 and CDH3 are closely associated to BRCA1-deficient breast cancer. These data merit further investigation for early detection of tumors arising in BRCA1 mutation carriers.
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Affiliation(s)
- Marc Warmoes
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Siu W Lam
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Petra van der Groep
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Janneke E Jaspers
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yvonne H C M Smolders
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leon de Boer
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Epie Boven
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Connie R Jimenez
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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9
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Large-scale reduction of tyrosine kinase activities in human monocytes stimulated in vitro with N. meningitidis. PLoS One 2018; 13:e0181912. [PMID: 29357362 PMCID: PMC5774972 DOI: 10.1371/journal.pone.0181912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 07/10/2017] [Indexed: 01/07/2023] Open
Abstract
N. meningitidis induces extensive gene expression changes in human monocytes, suggesting that complex networks of signaling pathways are activated during meningococcal sepsis. These effects are modulated by the anti-inflammatory cytokine interleukin-10 (IL-10). To further study changes in signal transduction suggested by mRNA data, we used kinase substrate arrays to identify composite kinase activities induced by lysates from a primary human monocyte model system. Cell lysates were prepared from monocytes treated with the following experimental conditions: 106 N. meningitidis/mL, 25 ng/mL IL-10, 106 N. meningitidis/mL in combination with 25 ng/mL IL-10, and vehicle. Lysates were subjected to kinase activity profiling with Tyrosine Kinase PamChip® arrays containing 144 kinase peptide substrates. In our experimental model, we were not able to detect a statistically significant large-scale change in ex vivo array peptide phosphorylation by lysates from monocytes treated for 15 minutes. Targets of the IL-10 anti-inflammatory response were not identified. A profound inhibition of array peptide phosphorylation by monocytes treated for 60 minutes was identified, suggesting low activity of a large number of kinases associated with different signaling pathways and immune cell functions, including STAT3 activity, Nf-κB and VEGF signaling, and PTEN signaling activity. The peptide representing ZBTB16, which was reduced in phosphorylation by lysates from all three experimental conditions, was in Ingenuity Pathway Analysis identified to be linked to reduced cytokine release and mRNA levels of tumor necrosis factor (TNF), IL-6, and CXCL10. Further studies should investigate changes in tyrosine kinase-mediated signal transduction in human immune cells, in order to evaluate the potential clinical application of kinome profiling in the study of systemic inflammatory responses to pathogens.
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10
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Labots M, Gotink KJ, Dekker H, Azijli K, van der Mijn JC, Huijts CM, Piersma SR, Jiménez CR, Verheul HMW. Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer. Exp Mol Med 2016; 48:e279. [PMID: 27980342 PMCID: PMC5192072 DOI: 10.1038/emm.2016.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/19/2016] [Accepted: 06/11/2016] [Indexed: 01/05/2023] Open
Abstract
Personalized cancer medicine aims to accurately predict the response of individual patients to targeted therapies, including tyrosine kinase inhibitors (TKIs). Clinical implementation of this concept requires a robust selection tool. Here, using both cancer cell lines and tumor tissue from patients, we evaluated a high-throughput tyrosine kinase peptide substrate array to determine its readiness as a selection tool for TKI therapy. We found linearly increasing phosphorylation signal intensities of peptides representing kinase activity along the kinetic curve of the assay with 7.5–10 μg of lysate protein and up to 400 μM adenosine triphosphate (ATP). Basal kinase activity profiles were reproducible with intra- and inter-experiment coefficients of variation of <15% and <20%, respectively. Evaluation of 14 tumor cell lines and tissues showed similar consistently high phosphorylated peptides in their basal profiles. Incubation of four patient-derived tumor lysates with the TKIs dasatinib, sunitinib, sorafenib and erlotinib primarily caused inhibition of substrates that were highly phosphorylated in the basal profile analyses. Using recombinant Src and Axl kinase, relative substrate specificity was demonstrated for a subset of peptides, as their phosphorylation was reverted by co-incubation with a specific inhibitor. In conclusion, we demonstrated robust technical specifications of this high-throughput tyrosine kinase peptide microarray. These features required as little as 5–7 μg of protein per sample, facilitating clinical implementation as a TKI selection tool. However, currently available peptide substrates can benefit from an enhancement of the differential potential for complex samples such as tumor lysates. We propose that mass spectrometry-based phosphoproteomics may provide such an enhancement by identifying more discriminative peptides.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Kristy J Gotink
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Kaamar Azijli
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Charlotte M Huijts
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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11
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Ree AH, Redalen KR. Personalized radiotherapy: concepts, biomarkers and trial design. Br J Radiol 2015; 88:20150009. [PMID: 25989697 DOI: 10.1259/bjr.20150009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In the past decade, and pointing onwards to the immediate future, clinical radiotherapy has undergone considerable developments, essentially including technological advances to sculpt radiation delivery, the demonstration of the benefit of adding concomitant cytotoxic agents to radiotherapy for a range of tumour types and, intriguingly, the increasing integration of targeted therapeutics for biological optimization of radiation effects. Recent molecular and imaging insights into radiobiology will provide a unique opportunity for rational patient treatment, enabling the parallel design of next-generation trials that formally examine the therapeutic outcome of adding targeted drugs to radiation, together with the critically important assessment of radiation volume and dose-limiting treatment toxicities. In considering the use of systemic agents with presumed radiosensitizing activity, this may also include the identification of molecular, metabolic and imaging markers of treatment response and tolerability, and will need particular attention on patient eligibility. In addition to providing an overview of clinical biomarker studies relevant for personalized radiotherapy, this communication will highlight principles in addressing clinical evaluation of combined-modality-targeted therapeutics and radiation. The increasing number of translational studies that bridge large-scale omics sciences with quality-assured phenomics end points-given the imperative development of open-source data repositories to allow investigators the access to the complex data sets-will enable radiation oncology to continue to position itself with the highest level of evidence within existing clinical practice.
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Affiliation(s)
- A H Ree
- 1 Department of Oncology, Akershus University Hospital, Lørenskog, Norway.,2 Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - K R Redalen
- 1 Department of Oncology, Akershus University Hospital, Lørenskog, Norway
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12
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Ree AH, Flatmark K, Saelen MG, Folkvord S, Dueland S, Geisler J, Redalen KR. Tumor phosphatidylinositol 3-kinase signaling in therapy resistance and metastatic dissemination of rectal cancer: opportunities for signaling-adapted therapies. Crit Rev Oncol Hematol 2015; 95:114-24. [PMID: 25624177 DOI: 10.1016/j.critrevonc.2015.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/18/2014] [Accepted: 01/06/2015] [Indexed: 02/06/2023] Open
Abstract
Locally advanced rectal cancer (LARC) comprises heterogeneous tumors with predominant hypoxic components, a hallmark of the tumor microenvironment and determinant of resistance to cytotoxic therapies, local recurrence, and metastatic progression. A rational integration of molecularly targeted agents in established combined-modality treatment regimens may improve local and systemic disease control, but will require a clear definition of functional biomarkers for patient stratification. In a prospective study of LARC patients given neoadjuvant chemotherapy and radiation, we applied a kinase substrate array technology to analyze the patients' tumor biopsies sampled at the time of diagnosis, and observed that receptor tyrosine kinase activities integrated by high phosphatidylinositol 3-kinase signaling were correlated both with poor tumor response to the neoadjuvant treatment and adverse progression-free survival. Conceptually, the specific tumor signature of phosphatidylinositol 3-kinase signaling activity may point to actionable therapy targets in LARC patients with unfavorable disease features. Clinical trial registration number NCT00278694.
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Affiliation(s)
- Anne Hansen Ree
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478 Lørenskog, Norway; Institute of Clinical Medicine, University of Oslo, P.O. Box 1171 Blindern, 0318 Oslo, Norway.
| | - Kjersti Flatmark
- Department of Tumor Biology, Oslo University Hospital, P.O. Box 4956 Nydalen, 0424 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, P.O. Box 1171 Blindern, 0318 Oslo, Norway; Department of Gastroenterological Surgery, Oslo University Hospital, P.O. Box 4956 Nydalen, 0424 Oslo, Norway.
| | - Marie Grøn Saelen
- Department of Tumor Biology, Oslo University Hospital, P.O. Box 4956 Nydalen, 0424 Oslo, Norway.
| | - Sigurd Folkvord
- Department of Tumor Biology, Oslo University Hospital, P.O. Box 4956 Nydalen, 0424 Oslo, Norway.
| | - Svein Dueland
- Department of Oncology, Oslo University Hospital, P.O. Box 4956 Nydalen, 0424 Oslo, Norway.
| | - Jürgen Geisler
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478 Lørenskog, Norway; Institute of Clinical Medicine, University of Oslo, P.O. Box 1171 Blindern, 0318 Oslo, Norway.
| | - Kathrine Røe Redalen
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478 Lørenskog, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, P.O. Box 1000, 1478 Lørenskog, Norway.
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13
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van der Mijn JC, Sol N, Mellema W, Jimenez CR, Piersma SR, Dekker H, Schutte LM, Smit EF, Broxterman HJ, Skog J, Tannous BA, Wurdinger T, Verheul HMW. Analysis of AKT and ERK1/2 protein kinases in extracellular vesicles isolated from blood of patients with cancer. J Extracell Vesicles 2014; 3:25657. [PMID: 25491250 PMCID: PMC4261239 DOI: 10.3402/jev.v3.25657] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/27/2014] [Accepted: 11/12/2014] [Indexed: 01/03/2023] Open
Abstract
Background Extracellular vesicles (EVs) are small nanometre-sized vesicles that are circulating in blood. They are released by multiple cells, including tumour cells. We hypothesized that circulating EVs contain protein kinases that may be assessed as biomarkers during treatment with tyrosine kinase inhibitors. Methods EVs released by U87 glioma cells, H3255 and H1650 non-small-cell lung cancer (NSCLC) cells were profiled by tandem mass spectrometry. Total AKT/protein kinase B and extracellular signal regulated kinase 1/2 (ERK1/2) levels as well as their relative phosphorylation were measured by western blot in isogenic U87 cells with or without mutant epidermal growth factor receptor (EGFRvIII) and their corresponding EVs. To assess biomarker potential, plasma samples from 24 healthy volunteers and 42 patients with cancer were used. Results In total, 130 different protein kinases were found to be released in EVs including multiple drug targets, such as mammalian target of rapamycin (mTOR), AKT, ERK1/2, AXL and EGFR. Overexpression of EGFRvIII in U87 cells results in increased phosphorylation of EGFR, AKT and ERK1/2 in cells and EVs, whereas a decreased phosphorylation was noted upon treatment with the EGFR inhibitor erlotinib. EV samples derived from patients with cancer contained significantly more protein (p=0.0067) compared to healthy donors. Phosphorylation of AKT and ERK1/2 in plasma EVs from both healthy donors and patients with cancer was relatively low compared to levels in cancer cells. Preliminary analysis of total AKT and ERK1/2 levels in plasma EVs from patients with NSCLC before and after sorafenib/metformin treatment (n=12) shows a significant decrease in AKT levels among patients with a favourable treatment response (p<0.005). Conclusion Phosphorylation of protein kinases in EVs reflects their phosphorylation in tumour cells. Total AKT protein levels may allow monitoring of kinase inhibitor responses in patients with cancer.
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Affiliation(s)
| | - Nik Sol
- Neuro-Oncology Research Group, Department of Neurosurgery, VU University Medical Center, Amsterdam, The Netherlands
| | - Wouter Mellema
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Lisette M Schutte
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Egbert F Smit
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk J Broxterman
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Johan Skog
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Bakhos A Tannous
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Thomas Wurdinger
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands;
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14
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Kindrachuk J, Wahl-Jensen V, Safronetz D, Trost B, Hoenen T, Arsenault R, Feldmann F, Traynor D, Postnikova E, Kusalik A, Napper S, Blaney JE, Feldmann H, Jahrling PB. Ebola virus modulates transforming growth factor β signaling and cellular markers of mesenchyme-like transition in hepatocytes. J Virol 2014; 88:9877-92. [PMID: 24942569 PMCID: PMC4136307 DOI: 10.1128/jvi.01410-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/09/2014] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED Ebola virus (EBOV) causes a severe hemorrhagic disease in humans and nonhuman primates, with a median case fatality rate of 78.4%. Although EBOV is considered a public health concern, there is a relative paucity of information regarding the modulation of the functional host response during infection. We employed temporal kinome analysis to investigate the relative early, intermediate, and late host kinome responses to EBOV infection in human hepatocytes. Pathway overrepresentation analysis and functional network analysis of kinome data revealed that transforming growth factor (TGF-β)-mediated signaling responses were temporally modulated in response to EBOV infection. Upregulation of TGF-β signaling in the kinome data sets correlated with the upregulation of TGF-β secretion from EBOV-infected cells. Kinase inhibitors targeting TGF-β signaling, or additional cell receptors and downstream signaling pathway intermediates identified from our kinome analysis, also inhibited EBOV replication. Further, the inhibition of select cell signaling intermediates identified from our kinome analysis provided partial protection in a lethal model of EBOV infection. To gain perspective on the cellular consequence of TGF-β signaling modulation during EBOV infection, we assessed cellular markers associated with upregulation of TGF-β signaling. We observed upregulation of matrix metalloproteinase 9, N-cadherin, and fibronectin expression with concomitant reductions in the expression of E-cadherin and claudin-1, responses that are standard characteristics of an epithelium-to-mesenchyme-like transition. Additionally, we identified phosphorylation events downstream of TGF-β that may contribute to this process. From these observations, we propose a model for a broader role of TGF-β-mediated signaling responses in the pathogenesis of Ebola virus disease. IMPORTANCE Ebola virus (EBOV), formerly Zaire ebolavirus, causes a severe hemorrhagic disease in humans and nonhuman primates and is the most lethal Ebola virus species, with case fatality rates of up to 90%. Although EBOV is considered a worldwide concern, many questions remain regarding EBOV molecular pathogenesis. As it is appreciated that many cellular processes are regulated through kinase-mediated phosphorylation events, we employed temporal kinome analysis to investigate the functional responses of human hepatocytes to EBOV infection. Administration of kinase inhibitors targeting signaling pathway intermediates identified in our kinome analysis inhibited viral replication in vitro and reduced EBOV pathogenesis in vivo. Further analysis of our data also demonstrated that EBOV infection modulated TGF-β-mediated signaling responses and promoted "mesenchyme-like" phenotypic changes. Taken together, these results demonstrated that EBOV infection specifically modulates TGF-β-mediated signaling responses in epithelial cells and may have broader implications in EBOV pathogenesis.
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Affiliation(s)
- Jason Kindrachuk
- Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Victoria Wahl-Jensen
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA National Biodefense Analysis and Countermeasures Center, Frederick, Maryland, USA
| | - David Safronetz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Brett Trost
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Thomas Hoenen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Ryan Arsenault
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Dawn Traynor
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Scott Napper
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Joseph E Blaney
- Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Peter B Jahrling
- Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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15
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Ko CC, Chen YJ, Chen CT, Liu YC, Cheng FC, Hsu KC, Chow LP. Chemical proteomics identifies heterogeneous nuclear ribonucleoprotein (hnRNP) A1 as the molecular target of quercetin in its anti-cancer effects in PC-3 cells. J Biol Chem 2014; 289:22078-89. [PMID: 24962584 DOI: 10.1074/jbc.m114.553248] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Quercetin, a flavonoid abundantly present in plants, is widely used as a phytotherapy in prostatitis and prostate cancer. Although quercetin has been reported to have a number of therapeutic effects, the cellular target(s) responsible for its anti-cancer action has not yet been clearly elucidated. Here, employing affinity chromatography and mass spectrometry, we identified heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) as a direct target of quercetin. A specific interaction between quercetin and hnRNPA1 was validated by immunoblotting and in vitro binding experiments. We found that quercetin bound the C-terminal region of hnRNPA1, impairing the ability of hnRNPA1 to shuttle between the nucleus and cytoplasm and ultimately resulting in its cytoplasmic retention. In addition, hnRNPA1 was recruited to stress granules after treatment of cells with quercetin for up to 48 h, and the levels of cIAP1 (cellular inhibitor of apoptosis), an internal ribosome entry site translation-dependent protein, were reduced by hnRNPA1 regulation. This is the first report that anti-cancer effects of quercetin are mediated, in part, by impairing functions of hnRNPA1, insights that were obtained using a chemical proteomics strategy.
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Affiliation(s)
- Chia-Chen Ko
- From the Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and
| | - Yun-Ju Chen
- From the Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and
| | - Chih-Ta Chen
- From the Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and
| | - Yu-Chih Liu
- From the Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and
| | - Fong-Chi Cheng
- Eurofins Panlabs Taiwan Ltd., 158 Li-Teh Road, Peitou, Taipei 112, Taiwan
| | - Kai-Chao Hsu
- From the Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and
| | - Lu-Ping Chow
- From the Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and
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16
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Liu Y, Guo M. Chemical proteomic strategies for the discovery and development of anticancer drugs. Proteomics 2014; 14:399-411. [DOI: 10.1002/pmic.201300261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/26/2013] [Accepted: 10/11/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Yuanzhen Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
- The Keck School of Medicine; University of Southern California; Los Angeles CA USA
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17
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Development and validation of an indirect pulsed electrochemical detection method for monitoring the inhibition of Abl1 tyrosine kinase. J Pharm Biomed Anal 2014; 90:52-7. [DOI: 10.1016/j.jpba.2013.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/15/2013] [Accepted: 11/17/2013] [Indexed: 01/02/2023]
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18
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Molecular mechanisms underlying the antitumor activity of 3-aminopropanamide irreversible inhibitors of the epidermal growth factor receptor in non-small cell lung cancer. Neoplasia 2013; 15:61-72. [PMID: 23359111 DOI: 10.1593/neo.121434] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/31/2012] [Accepted: 11/12/2012] [Indexed: 01/05/2023] Open
Abstract
Overcoming the emergence of acquired resistance to clinically approved epidermal growth factor receptor (EGFR) inhibitors is a major challenge in the treatment of advanced non-small cell lung cancer (NSCLC). The aim of this study was to investigate the effects of a series of novel compounds affecting viability of NSCLC NCI-H1975 cells (carrying the EGFR T790M mutation). The inhibition of the autophosphorylation of EGFR occurred at nanomolar concentrations and both UPR1282 and UPR1268 caused a significant induction of apoptosis. Targeting of EGFR and downstream pathways was confirmed by a peptide substrate array, which highlighted the inhibition of other kinases involved in NSCLC cell aggressive behavior. Accordingly, the drugs inhibited migration (about 30% vs. control), which could be, in part, explained also by the increase of E-cadherin expression. Additionally, we observed a contraction of the volume of H1975 spheroids, associated with the reduction of the cancer stem-like cell hallmark CD133. The activity of UPR1282 was retained in H1975 xenograft models where it determined tumor shrinkage (P < .05) and resulted well tolerated compared to canertinib. Of note, the kinase activity profile of UPR1282 on xenograft tumor tissues showed overlapping results with respect to the activity in H1975 cells, unraveling the inhibition of kinases involved in pivotal proliferation and invasive signaling pathways. In conclusion, UPR1282 and UPR1268 are effective against various processes involved in malignancy transformation and progression and may be promising compounds for the future treatment of gefitinib-resistant NSCLCs.
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Guo S, Zou J, Wang G. Advances in the proteomic discovery of novel therapeutic targets in cancer. DRUG DESIGN DEVELOPMENT AND THERAPY 2013; 7:1259-71. [PMID: 24187485 PMCID: PMC3810204 DOI: 10.2147/dddt.s52216] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteomic approaches are continuing to make headways in cancer research by helping to elucidate complex signaling networks that underlie tumorigenesis and disease progression. This review describes recent advances made in the proteomic discovery of drug targets for therapeutic development. A variety of technical and methodological advances are overviewed with a critical assessment of challenges and potentials. A number of potential drug targets, such as baculoviral inhibitor of apoptosis protein repeat-containing protein 6, macrophage inhibitory cytokine 1, phosphoglycerate mutase 1, prohibitin 1, fascin, and pyruvate kinase isozyme 2 were identified in the proteomic analysis of drug-resistant cancer cells, drug action, and differential disease state tissues. Future directions for proteomics-based target identification and validation to be more translation efficient are also discussed.
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Affiliation(s)
- Shanchun Guo
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Clark Atlanta University, Atlanta, GA, USA
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20
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Zhang L, Holmes IP, Hochgräfe F, Walker SR, Ali NA, Humphrey ES, Wu J, de Silva M, Kersten WJA, Connor T, Falk H, Allan L, Street IP, Bentley JD, Pilling PA, Monahan BJ, Peat TS, Daly RJ. Characterization of the novel broad-spectrum kinase inhibitor CTx-0294885 as an affinity reagent for mass spectrometry-based kinome profiling. J Proteome Res 2013; 12:3104-16. [PMID: 23692254 DOI: 10.1021/pr3008495] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Kinase enrichment utilizing broad-spectrum kinase inhibitors enables the identification of large proportions of the expressed kinome by mass spectrometry. However, the existing inhibitors are still inadequate in covering the entire kinome. Here, we identified a novel bisanilino pyrimidine, CTx-0294885, exhibiting inhibitory activity against a broad range of kinases in vitro, and further developed it into a Sepharose-supported kinase capture reagent. Use of a quantitative proteomics approach confirmed the selectivity of CTx-0294885-bound beads for kinase enrichment. Large-scale CTx-0294885-based affinity purification followed by LC-MS/MS led to the identification of 235 protein kinases from MDA-MB-231 cells, including all members of the AKT family that had not been previously detected by other broad-spectrum kinase inhibitors. Addition of CTx-0294885 to a mixture of three kinase inhibitors commonly used for kinase-enrichment increased the number of kinase identifications to 261, representing the largest kinome coverage from a single cell line reported to date. Coupling phosphopeptide enrichment with affinity purification using the four inhibitors enabled the identification of 799 high-confidence phosphosites on 183 kinases, ∼10% of which were localized to the activation loop, and included previously unreported phosphosites on BMP2K, MELK, HIPK2, and PRKDC. Therefore, CTx-0294885 represents a powerful new reagent for analysis of kinome signaling networks that may facilitate development of targeted therapeutic strategies. Proteomics data have been deposited to the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository with the data set identifier PXD000239.
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Affiliation(s)
- Luxi Zhang
- Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, New South Wales 2010, Australia
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Miao Q, Zhang CC, Kast J. Chemical proteomics and its impact on the drug discovery process. Expert Rev Proteomics 2013; 9:281-91. [PMID: 22809207 DOI: 10.1586/epr.12.22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Despite the rapid growth of postgenomic data and fast-paced technology advancement, drug discovery is still a lengthy and difficult process. More effective drug design requires a better understanding of the interaction between drug candidates and their targets/off-targets in various situations. The ability of chemical proteomics to integrate a multiplicity of disciplines enables the direct analysis of protein activities on a proteome-wide scale, which has enormous potential to facilitate drug target elucidation and lead drug verification. Over recent years, chemical proteomics has experienced rapid growth and provided a valuable method for drug target identification and inhibitor discovery. This review introduces basic concepts and technologies of different popular chemical proteomic approaches. It also covers the essential features and recent advances of each approach while underscoring their potentials in drug discovery and development.
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Affiliation(s)
- Qing Miao
- The Biomedical Research Centre, University of British Columbia, Room #401, 2222 Health Sciences Mall, Vancouver, BC, V6T1Z3 Canada
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22
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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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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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Kindrachuk J, Arsenault R, Kusalik A, Kindrachuk KN, Trost B, Napper S, Jahrling PB, Blaney JE. Systems kinomics demonstrates Congo Basin monkeypox virus infection selectively modulates host cell signaling responses as compared to West African monkeypox virus. Mol Cell Proteomics 2012; 11:M111.015701. [PMID: 22205724 PMCID: PMC3433897 DOI: 10.1074/mcp.m111.015701] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/19/2011] [Indexed: 01/04/2023] Open
Abstract
Monkeypox virus (MPXV) is comprised of two clades: Congo Basin MPXV, with an associated case fatality rate of 10%, and Western African MPXV, which is associated with less severe infection and minimal lethality. We thus postulated that Congo Basin and West African MPXV would differentially modulate host cell responses and, as many host responses are regulated through phosphorylation independent of transcription or translation, we employed systems kinomics with peptide arrays to investigate these functional host responses. Using this approach we have demonstrated that Congo Basin MPXV infection selectively down-regulates host responses as compared with West African MPXV, including growth factor- and apoptosis-related responses. These results were confirmed using fluorescence-activated cell sorting analysis demonstrating that West African MPXV infection resulted in a significant increase in apoptosis in human monocytes as compared with Congo Basin MPXV. Further, differentially phosphorylated kinases were identified through comparison of our MPXV data sets and validated as potential targets for pharmacological inhibition of Congo Basin MPXV infection, including increased Akt S473 phosphorylation and decreased p53 S15 phosphorylation. Inhibition of Akt S473 phosphorylation resulted in a significant decrease in Congo Basin MPXV virus yield (261-fold) but did not affect West African MPXV. In addition, treatment with staurosporine, an apoptosis activator resulted in a 49-fold greater decrease in Congo Basin MPXV yields as compared with West African MPXV. Thus, using a systems kinomics approach, our investigation demonstrates that West African and Congo Basin MPXV differentially modulate host cell responses and has identified potential host targets of therapeutic interest.
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Affiliation(s)
- Jason Kindrachuk
- Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Peptide Arrays. MICROARRAYS IN DIAGNOSTICS AND BIOMARKER DEVELOPMENT 2012. [PMCID: PMC7193736 DOI: 10.1007/978-3-642-28203-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite the concern over the potential loss of structural information as a result of the use of peptides as opposed to proteins as molecular probes, peptide arrays have been implemented in a broad range of applications including antibody screening and epitope mapping, characterization of molecular interactions, and enzymatic activity profiling, and they have become a valuable tool for proteomics research. In this chapter, we first (Sect. 7.1) recapitulate the development of these arrays and highlight a couple of key improvements in the array production and the application in proteomics research. For clinical and biomarker development applications, it is important to measure entities that are directly related to physiological function (and dysfunction). In this respect, the assessment of enzymatic activities is obviously preferable to genotyping, expression profiling, or even measurement of protein amounts. In Sect. 7.2, an original technology based on peptides arrayed onto a porous support allows detailed profiling of kinase activities in a biological sample. The applications described range from kinase characterization to inhibition profiles, detection of off-target effects, and drug response prediction in a clinical setting, allowing rational choice of the drug to be used. Such directly functional approaches will have an important role in the transition to more personalized medicine. Finally, in Sect. 7.3, a recently developed method for “laser printing” of peptide arrays that will make these approaches much more practical is presented.
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