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Zallocchi M, Vijayakumar S, Fleegel J, Batalkina L, Brunette KE, Shukal D, Chen Z, Devuyst O, Liu H, He DZZ, Imami AS, Hamoud ARA, McCullumsmith R, Conda-Sheridan M, De Campos LJ, Zuo J. Piplartine attenuates aminoglycoside-induced TRPV1 activity and protects from hearing loss in mice. Sci Transl Med 2024; 16:eadn2140. [PMID: 39110778 PMCID: PMC11392653 DOI: 10.1126/scitranslmed.adn2140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/17/2024] [Accepted: 06/28/2024] [Indexed: 09/15/2024]
Abstract
Hearing loss is a major health concern in our society, affecting more than 400 million people worldwide. Among the causes, aminoglycoside therapy can result in permanent hearing loss in 40% to 60% of patients receiving treatment, and despite these high numbers, no drug for preventing or treating this type of hearing loss has yet been approved by the US Food and Drug Administration. We have previously conducted high-throughput screenings of bioactive compounds, using zebrafish as our discovery platform, and identified piplartine as a potential therapeutic molecule. In the present study, we expanded this work and characterized piplartine's physicochemical and therapeutic properties. We showed that piplartine had a wide therapeutic window and neither induced nephrotoxicity in vivo in zebrafish nor interfered with aminoglycoside antibacterial activity. In addition, a fluorescence-based assay demonstrated that piplartine did not inhibit cytochrome C activity in microsomes. Coadministration of piplartine protected from kanamycin-induced hair cell loss in zebrafish and protected hearing function, outer hair cells, and presynaptic ribbons in a mouse model of kanamycin ototoxicity. Last, we investigated piplartine's mechanism of action by phospho-omics, immunoblotting, immunohistochemistry, and molecular dynamics experiments. We found an up-regulation of AKT1 signaling in the cochleas of mice cotreated with piplartine. Piplartine treatment normalized kanamycin-induced up-regulation of TRPV1 expression and modulated the gating properties of this receptor. Because aminoglycoside entrance to the inner ear is, in part, mediated by TRPV1, these results suggested that by regulating TRPV1 expression, piplartine blocked aminoglycoside's entrance, thereby preventing the long-term deleterious effects of aminoglycoside accumulation in the inner ear compartment.
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Affiliation(s)
| | | | | | | | | | | | - Zhiyong Chen
- Institute of Physiology, University of Zürich, Zürich CH-8057, Switzerland
| | - Olivier Devuyst
- Institute of Physiology, University of Zürich, Zürich CH-8057, Switzerland
| | - Huizhan Liu
- Creighton University School of Medicine, Omaha, NE 68178, USA
| | - David Z Z He
- Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Ali Sajid Imami
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | | | - Robert McCullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
- Neurosciences Institute, ProMedica, Toledo, OH 43614, USA
| | | | | | - Jian Zuo
- Creighton University School of Medicine, Omaha, NE 68178, USA
- Ting Therapeutics LLC, La Jolla, CA 92037, USA
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2
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Vijayakumar S, DiGuiseppi JA, Dabestani PJ, Ryan WG, Quevedo RV, Li Y, Diers J, Tu S, Fleegel J, Nguyen C, Rhoda LM, Imami AS, Hamoud ARA, Lovas S, McCullumsmith RE, Zallocchi M, Zuo J. In silico transcriptome screens identify epidermal growth factor receptor inhibitors as therapeutics for noise-induced hearing loss. SCIENCE ADVANCES 2024; 10:eadk2299. [PMID: 38896614 PMCID: PMC11186505 DOI: 10.1126/sciadv.adk2299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Noise-induced hearing loss (NIHL) is a common sensorineural hearing impairment that lacks U.S. Food and Drug Administration-approved drugs. To fill the gap in effective screening models, we used an in silico transcriptome-based drug screening approach, identifying 22 biological pathways and 64 potential small molecule treatments for NIHL. Two of these, afatinib and zorifertinib [epidermal growth factor receptor (EGFR) inhibitors], showed efficacy in zebrafish and mouse models. Further tests with EGFR knockout mice and EGF-morpholino zebrafish confirmed their protective role against NIHL. Molecular studies in mice highlighted EGFR's crucial involvement in NIHL and the protective effect of zorifertinib. When given orally, zorifertinib was found in the perilymph with favorable pharmacokinetics. In addition, zorifertinib combined with AZD5438 (a cyclin-dependent kinase 2 inhibitor) synergistically prevented NIHL in zebrafish. Our results underscore the potential for in silico transcriptome-based drug screening in diseases lacking efficient models and suggest EGFR inhibitors as potential treatments for NIHL, meriting clinical trials.
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Affiliation(s)
- Sarath Vijayakumar
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Joseph A. DiGuiseppi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Parinaz Jila Dabestani
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - William G. Ryan
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
| | - Rene Vielman Quevedo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Yuju Li
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jack Diers
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Shu Tu
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jonathan Fleegel
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Cassidy Nguyen
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Lauren M. Rhoda
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Ali Sajid Imami
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
| | | | - Sándor Lovas
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
- Neurosciences Institute, ProMedica, Toledo, OH 43606, USA
| | - Marisa Zallocchi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jian Zuo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
- Ting Therapeutics, University of California San Diego, 9310 Athena Circle, San Diego, CA 92037, USA
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3
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Vijayakumar S, DiGuiseppi JA, Dabestani J, Ryan WG, Vielman Quevedo R, Li Y, Diers J, Tu S, Fleegel J, Nguyen C, Rhoda LM, Imami AS, Hamoud AAR, Lovas S, McCullumsmith R, Zallocchi M, Zuo J. In Silico Transcriptome-based Screens Identify Epidermal Growth Factor Receptor Inhibitors as Therapeutics for Noise-induced Hearing Loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544128. [PMID: 37333346 PMCID: PMC10274759 DOI: 10.1101/2023.06.07.544128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Noise-Induced Hearing Loss (NIHL) represents a widespread disease for which no therapeutics have been approved by the Food and Drug Administration (FDA). Addressing the conspicuous void of efficacious in vitro or animal models for high throughput pharmacological screening, we utilized an in silico transcriptome-oriented drug screening strategy, unveiling 22 biological pathways and 64 promising small molecule candidates for NIHL protection. Afatinib and zorifertinib, both inhibitors of the Epidermal Growth Factor Receptor (EGFR), were validated for their protective efficacy against NIHL in experimental zebrafish and murine models. This protective effect was further confirmed with EGFR conditional knockout mice and EGF knockdown zebrafish, both demonstrating protection against NIHL. Molecular analysis using Western blot and kinome signaling arrays on adult mouse cochlear lysates unveiled the intricate involvement of several signaling pathways, with particular emphasis on EGFR and its downstream pathways being modulated by noise exposure and Zorifertinib treatment. Administered orally, Zorifertinib was successfully detected in the perilymph fluid of the inner ear in mice with favorable pharmacokinetic attributes. Zorifertinib, in conjunction with AZD5438 - a potent inhibitor of cyclin dependent kinase 2 - produced synergistic protection against NIHL in the zebrafish model. Collectively, our findings underscore the potential application of in silico transcriptome-based drug screening for diseases bereft of efficient screening models and posit EGFR inhibitors as promising therapeutic agents warranting clinical exploration for combatting NIHL. Highlights In silico transcriptome-based drug screens identify pathways and drugs against NIHL.EGFR signaling is activated by noise but reduced by zorifertinib in mouse cochleae.Afatinib, zorifertinib and EGFR knockout protect against NIHL in mice and zebrafish.Orally delivered zorifertinib has inner ear PK and synergizes with a CDK2 inhibitor.
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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5
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Ghorbanalipoor S, Emtenani S, Parker M, Kamaguchi M, Osterloh C, Pigors M, Gross N, Khil’chenko S, Kasprick A, Patzelt S, Wortmann D, Ibrahim IO, Izumi K, Goletz S, Boch K, Kalies K, Bieber K, Smith P, Schmidt E, Ludwig RJ. Cutaneous kinase activity correlates with treatment outcomes following PI3K delta inhibition in mice with experimental pemphigoid diseases. Front Immunol 2022; 13:865241. [PMID: 36248903 PMCID: PMC9555174 DOI: 10.3389/fimmu.2022.865241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic blistering at the skin and/or mucous membranes, accompanied by a varying degree of inflammation, is the clinical hallmark of pemphigoid diseases that impose a major medical burden. Pemphigoid diseases are caused by autoantibodies targeting structural proteins of the epithelial basement membrane. One major pathogenic pathway of skin blistering and inflammation is activation of myeloid cells following Fc gamma receptor-dependent binding to the skin-bound immune complexes. This process requires activation of specific kinases, such as PI3Kδ, which have emerged as potential targets for the treatment of pemphigoid diseases. Yet, it is unknown if global cutaneous kinase activity present in lesional pemphigoid disease correlates with therapeutic effects following treatment with a given target-selective kinase inhibitor. To address this, we here first determined the kinase activity in three different mouse models of pemphigoid diseases: Antibody transfer-induced mucous membrane pemphigoid (MMP), antibody transfer-induced epidermolysis bullosa acquisita (EBA) and immunization-induced EBA. Interestingly, the kinome signatures were different among the three models. More specifically, PI3Kδ was within the kinome activation network of antibody transfer-induced MMP and immunization-induced EBA, but not in antibody transfer-induced EBA. Next, the therapeutic impact of the PI3Kδ-selective inhibitor parsaclisib was evaluated in the three model systems. In line with the kinome signatures, parsaclisib had therapeutic effects in antibody transfer-induced MMP and immunization-induced EBA, but not in autoantibody-induced EBA. In conclusion, kinase activation signatures of inflamed skin, herein exemplified by pemphigoid diseases, correlate with the therapeutic outcomes following kinase inhibition, demonstrated here by the PI3Kδ inhibitor parsaclisib.
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Affiliation(s)
- Saeedeh Ghorbanalipoor
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Shirin Emtenani
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Melissa Parker
- Incyte Research Institute, Wilmington, DE, United States
| | - Mayumi Kamaguchi
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Colin Osterloh
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Manuela Pigors
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Natalie Gross
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Stanislav Khil’chenko
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Anika Kasprick
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Sabrina Patzelt
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Diana Wortmann
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Ibrahim O. Ibrahim
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Kentaro Izumi
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Stephanie Goletz
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Katharina Boch
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Kathrin Kalies
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Paul Smith
- Incyte Research Institute, Wilmington, DE, United States
| | - Enno Schmidt
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Ralf J. Ludwig
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
- *Correspondence: Ralf J. Ludwig,
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6
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Distler O, Ludwig RJ, Niemann S, Riemekasten G, Schreiber S. Editorial: Precision Medicine in Chronic Inflammation. Front Immunol 2021; 12:770462. [PMID: 34630441 PMCID: PMC8495129 DOI: 10.3389/fimmu.2021.770462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 01/12/2023] Open
Affiliation(s)
- Oliver Distler
- Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Zurich, Germany
| | - Stefan Niemann
- Research Center Borstel, Molecular and Experimental Mycobacteriology, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Stefan Schreiber
- Department of Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
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7
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Zillikens H, Kasprick A, Osterloh C, Gross N, Radziewitz M, Hass C, Hartmann V, Behnen-Härer M, Ernst N, Boch K, Vidarsson G, Visser R, Laskay T, Yu X, Petersen F, Ludwig RJ, Bieber K. Topical Application of the PI3Kβ-Selective Small Molecule Inhibitor TGX-221 Is an Effective Treatment Option for Experimental Epidermolysis Bullosa Acquisita. Front Med (Lausanne) 2021; 8:713312. [PMID: 34557502 PMCID: PMC8452940 DOI: 10.3389/fmed.2021.713312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/17/2021] [Indexed: 11/23/2022] Open
Abstract
Class I phosphoinositide 3-kinases (PI3K) have been implemented in pathogenesis of experimental epidermolysis bullosa acquisita (EBA), an autoimmune skin disease caused by type VII collagen (COL7) autoantibodies. Mechanistically, inhibition of specific PI3K isoforms, namely PI3Kβ or PI3Kδ, impaired immune complex (IC)-induced neutrophil activation, a key prerequisite for EBA pathogenesis. Data unrelated to EBA showed that neutrophil activation is also modulated by PI3Kα and γ, but their impact on the EBA has, so far, remained elusive. To address this and to identify potential therapeutic targets, we evaluated the impact of a panel of PI3K isoform-selective inhibitors (PI3Ki) on neutrophil function in vitro, and in pre-clinical EBA mouse models. We document that distinctive, and EBA pathogenesis-related activation-induced neutrophil in vitro functions depend on distinctive PI3K isoforms. When mice were treated with the different PI3Ki, selective blockade of PI3Kα (alpelisib), PI3Kγ (AS-604850), or PI3Kβ (TGX-221) impaired clinical disease manifestation. When applied topically, only TGX-221 impaired induction of experimental EBA. Ultimately, multiplex kinase activity profiling in the presence of disease-modifying PI3Ki identified unique signatures of different PI3K isoform-selective inhibitors on the kinome of IC-activated human neutrophils. Collectively, we here identify topical PI3Kβ inhibition as a potential therapeutic target for the treatment of EBA.
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Affiliation(s)
- Hannah Zillikens
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Anika Kasprick
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Colin Osterloh
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Natalie Gross
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Michael Radziewitz
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Cindy Hass
- Priority Area Asthma and Allergy, Research Center Borstel, Airway Research Center North, German Center for Lung Research, Borstel, Germany
| | - Veronika Hartmann
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Martina Behnen-Härer
- Department for Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Nancy Ernst
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Katharina Boch
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Gestur Vidarsson
- Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Remco Visser
- Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Tamás Laskay
- Department for Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Xinhua Yu
- Priority Area Asthma and Allergy, Research Center Borstel, Airway Research Center North, German Center for Lung Research, Borstel, Germany
| | - Frank Petersen
- Priority Area Asthma and Allergy, Research Center Borstel, Airway Research Center North, German Center for Lung Research, Borstel, Germany
| | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology and Center for Research on Inflammation of the Skin, University of Lübeck, Lübeck, Germany
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Kumar N, Perez-Novo C, Shaw P, Logie E, Privat-Maldonado A, Dewilde S, Smits E, Berghe WV, Bogaerts A. Physical plasma-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death. Free Radic Biol Med 2021; 166:187-200. [PMID: 33636332 DOI: 10.1016/j.freeradbiomed.2021.02.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 12/17/2022]
Abstract
Despite modern therapeutic advances, the survival prospects of pancreatic cancer patients remain poor, due to chemoresistance and dysregulated oncogenic kinase signaling networks. We applied a novel kinome activity-mapping approach using biological peptide targets as phospho-sensors to identify vulnerable kinase dependencies for therapy sensitization by physical plasma. Ser/Thr-kinome specific activity changes were mapped upon induction of ferroptotic cell death in pancreatic tumor cells exposed to reactive oxygen and nitrogen species of plasma-treated water (PTW). This revealed a broad kinome activity response involving the CAMK, the AGC and CMGC family of kinases. This systems-level kinome network response supports stress adaptive switches between chemoresistant anti-oxidant responses of Kelch-like ECH-associated protein 1 (KEAP1)/Heme Oxygenase 1 (HMOX1) and ferroptotic cell death sensitization upon suppression of Nuclear factor (erythroid derived 2)-like 2 (NRF2) and Glutathione peroxidase 4 (GPX4). This is further supported by ex vivo experiments in the chicken chorioallantoic membrane assay, showing decreased GPX4 and Glutathione (GSH) expression as well as increased lipid peroxidation, along with suppressed BxPC-3 tumor growth in response to PTW. Taken all together, we demonstrate that plasma treated water-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death by targeting a NRF2-HMOX1-GPX4 specific kinase signaling network.
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Affiliation(s)
- Naresh Kumar
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Antwerp, 2610, Belgium; National Institute of Pharmaceutical Education and Research, Guwahati, 781125, Guwahati, Assam, India.
| | - Claudina Perez-Novo
- Department of Biomedical Sciences, Laboratory of Protein Science, Proteomics & Epigenetic Signalling, University of Antwerp, Antwerp, 2610, Belgium
| | - Priyanka Shaw
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Antwerp, 2610, Belgium; Solid Tumor Immunology Group, Center for Oncological Research, University of Antwerp, 2610, Belgium
| | - Emilie Logie
- Department of Biomedical Sciences, Laboratory of Protein Science, Proteomics & Epigenetic Signalling, University of Antwerp, Antwerp, 2610, Belgium
| | - Angela Privat-Maldonado
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Antwerp, 2610, Belgium; Solid Tumor Immunology Group, Center for Oncological Research, University of Antwerp, 2610, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, Laboratory of Protein Science, Proteomics & Epigenetic Signalling, University of Antwerp, Antwerp, 2610, Belgium
| | - Evelien Smits
- Solid Tumor Immunology Group, Center for Oncological Research, University of Antwerp, 2610, Belgium
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, Laboratory of Protein Science, Proteomics & Epigenetic Signalling, University of Antwerp, Antwerp, 2610, Belgium.
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Antwerp, 2610, Belgium.
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Covalent Cysteine Targeting of Bruton's Tyrosine Kinase (BTK) Family by Withaferin-A Reduces Survival of Glucocorticoid-Resistant Multiple Myeloma MM1 Cells. Cancers (Basel) 2021; 13:cancers13071618. [PMID: 33807411 PMCID: PMC8037275 DOI: 10.3390/cancers13071618] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy characterized by plasma cells' uncontrolled growth. The major barrier in treating MM is the occurrence of primary and acquired therapy resistance to anticancer drugs. Often, this therapy resistance is associated with constitutive hyperactivation of tyrosine kinase signaling. Novel covalent kinase inhibitors, such as the clinically approved BTK inhibitor ibrutinib (IBR) and the preclinical phytochemical withaferin A (WA), have, therefore, gained pharmaceutical interest. Remarkably, WA is more effective than IBR in killing BTK-overexpressing glucocorticoid (GC)-resistant MM1R cells. To further characterize the kinase inhibitor profiles of WA and IBR in GC-resistant MM cells, we applied phosphopeptidome- and transcriptome-specific tyrosine kinome profiling. In contrast to IBR, WA was found to reverse BTK overexpression in GC-resistant MM1R cells. Furthermore, WA-induced cell death involves covalent cysteine targeting of Hinge-6 domain type tyrosine kinases of the kinase cysteinome classification, including inhibition of the hyperactivated BTK. Covalent interaction between WA and BTK could further be confirmed by biotin-based affinity purification and confocal microscopy. Similarly, molecular modeling suggests WA preferably targets conserved cysteines in the Hinge-6 region of the kinase cysteinome classification, favoring inhibition of multiple B-cell receptors (BCR) family kinases. Altogether, we show that WA's promiscuous inhibition of multiple BTK family tyrosine kinases represents a highly effective strategy to overcome GC-therapy resistance in MM.
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10
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Humrich JY, Bernardes JP, Ludwig RJ, Klatzmann D, Scheffold A. Phenotyping of Adaptive Immune Responses in Inflammatory Diseases. Front Immunol 2020; 11:604464. [PMID: 33324421 PMCID: PMC7723922 DOI: 10.3389/fimmu.2020.604464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
Immunophenotyping on the molecular and cellular level is a central aspect for characterization of patients with inflammatory diseases, both to better understand disease etiopathogenesis and based on this to develop diagnostic and prognostic biomarkers which allow patient stratification and tailor-made treatment strategies. Technology-driven developments have considerably expanded the range of analysis tools. Especially the analysis of adaptive immune responses, often regarded as central though mostly poorly characterized disease drivers, is a major focus of personalized medicine. The identification of the disease-relevant antigens and characterization of corresponding antigen-specific lymphocytes in individual patients benefits significantly from recent developments in cytometry by sequencing and proteomics. The aim of this workshop was to identify the important developments for state-of-the-art immunophenotyping for clinical application and precision medicine. We focused here on recent key developments in analysis of antigen-specific lymphocytes, sequencing, and proteomics approaches, their relevance in precision medicine and the discussion of the major challenges and opportunities for the future.
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Affiliation(s)
- Jens Y. Humrich
- Department of Rheumatology and Clinical Immunology, University Hospital Schleswig-Holstein—Campus Lübeck, Lübeck, Germany
| | - Joana P. Bernardes
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ralf J. Ludwig
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, Lübeck, Germany
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
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11
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Wang J, Pollard K, Allen AN, Tomar T, Pijnenburg D, Yao Z, Rodriguez FJ, Pratilas CA. Combined Inhibition of SHP2 and MEK Is Effective in Models of NF1-Deficient Malignant Peripheral Nerve Sheath Tumors. Cancer Res 2020; 80:5367-5379. [PMID: 33032988 DOI: 10.1158/0008-5472.can-20-1365] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/18/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022]
Abstract
Loss of the RAS GTPase-activating protein (RAS-GAP) NF1 drives aberrant activation of RAS/MEK/ERK signaling and other effector pathways in the majority of malignant peripheral nerve sheath tumors (MPNST). These dysregulated pathways represent potential targets for therapeutic intervention. However, studies of novel single agents including MEK inhibitors (MEKi) have demonstrated limited efficacy both preclinically and clinically, with little advancement in overall patient survival. By interrogation of kinome activity through an unbiased screen and targeted evaluation of the signaling response to MEK inhibition, we have identified global activation of upstream receptor tyrosine kinases (RTK) that converges on activation of RAS as a mechanism to limit sensitivity to MEK inhibition. As no direct inhibitors of pan-RAS were available, an inhibitor of the protein tyrosine phosphatase SHP2, a critical mediator of RAS signal transduction downstream of multiple RTK, represented an alternate strategy. The combination of MEKi plus SHP099 was superior to MEKi alone in models of NF1-MPNST, including those with acquired resistance to MEKi. Our findings have immediate translational implications and may inform future clinical trials for patients with MPNST harboring alterations in NF1. SIGNIFICANCE: Combined inhibition of MEK and SHP2 is effective in models of NF1-MPNST, both those naïve to and those resistant to MEKi, as well as in the MPNST precursor lesion plexiform neurofibroma.
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Affiliation(s)
- Jiawan Wang
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kai Pollard
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Amy N Allen
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tushar Tomar
- PamGene International BV, 's-Hertogenbosch, the Netherlands
| | | | - Zhan Yao
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine A Pratilas
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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12
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Shi J, Ruijtenbeek R, Pieters RJ. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 2019; 28:814-824. [PMID: 29635275 DOI: 10.1093/glycob/cwy031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
O-GlcNAcylation, analogous to phosphorylation, is an essential post-translational modification of proteins at Ser/Thr residues with a single β-N-acetylglucosamine moiety. This dynamic protein modification regulates many fundamental cellular processes and its deregulation has been linked to chronic diseases such as cancer, diabetes and neurodegenerative disorders. Reversible attachment and removal of O-GlcNAc is governed only by O-GlcNAc transferase and O-GlcNAcase, respectively. Peptide substrates, derived from natural O-GlcNAcylation targets, function in the catalytic cores of these two enzymes by maintaining interactions between enzyme and substrate, which makes them ideal models for the study of O-GlcNAcylation and deglycosylation. These peptides provide valuable tools for a deeper understanding of O-GlcNAc processing enzymes. By taking advantage of peptide chemistry, recent progress in the study of activity and regulatory mechanisms of these two enzymes has advanced our understanding of their fundamental specificities as well as their potential as therapeutic targets. Hence, this review summarizes the recent achievements on this modification studied at the peptide level, focusing on enzyme activity, enzyme specificity, direct function, site-specific antibodies and peptide substrate-inspired inhibitors.
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Affiliation(s)
- Jie Shi
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands.,PamGene International BV, HH's-Hertogenbosch, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
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13
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Chirumamilla CS, Fazil MHUT, Perez-Novo C, Rangarajan S, de Wijn R, Ramireddy P, Verma NK, Vanden Berghe W. Profiling Activity of Cellular Kinases in Migrating T-Cells. Methods Mol Biol 2019; 1930:99-113. [PMID: 30610604 DOI: 10.1007/978-1-4939-9036-8_13] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
T-Lymphocyte kinases are important checkpoints that control T-cell motility by regulating a diverse range of signal transduction pathways. The distinct configuration of kinase events in T-cell could be used to fingerprint the status of T-cells. However, only small fraction human kinases have been characterized so far and little is known about the dynamics of the kinome in motile T-cells. Although several direct and indirect strategies exist to characterize cellular kinase activities, such as RNA interference, antibody arrays, enzyme kinetics, and mass spectrometry, this chapter focuses on an alternative multiplex phosphopeptide array-based methodology, which allows the kinome-wide identification of hyper-activated kinases involved in the regulation of T-cell migration.
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Affiliation(s)
- Chandra Sekhar Chirumamilla
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerpen, Belgium
| | - Mobashar Hussain Urf Turabe Fazil
- Lymphocyte Signalling Research Laboratory, Lee Kong Chain School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore.
| | - Claudina Perez-Novo
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerpen, Belgium
| | | | - Rik de Wijn
- PamGene International B.V., 5200 BJ 's-Hertogenbosch, The Netherlands
| | - Padma Ramireddy
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerpen, Belgium
| | - Navin Kumar Verma
- Lee Kong Chain School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerpen, Belgium
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14
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Signal-Targeted Therapies and Resistance Mechanisms in Pancreatic Cancer: Future Developments Reside in Proteomics. Cancers (Basel) 2018; 10:cancers10060174. [PMID: 29865155 PMCID: PMC6025626 DOI: 10.3390/cancers10060174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
For patients with metastatic pancreatic cancer that are not eligible for surgery, signal-targeted therapies have so far failed to significantly improve survival. These therapeutic options have been tested in phase II/III clinical trials mostly in combination with the reference treatment gemcitabine. Innovative therapies aim to annihilate oncogenic dependency, or to normalize the tumoural stroma to allow immune cells to function and/or re-vascularisation to occur. Large scale transcriptomic and genomic analysis revealed that pancreatic cancers display great heterogeneity but failed to clearly delineate specific oncogene dependency, besides oncogenic Kras. Beyond these approaches, proteomics appears to be an appropriate approach to classify signal dependency and to identify specific alterations at the targetable level. However, due to difficulties in sampling, proteomic data for this pathology are scarce. In this review, we will discuss the current state of clinical trials for targeted therapies against pancreatic cancer. We will then highlight the most recent proteomic data for pancreatic tumours and their metastasis, which could help to identify major oncogenic signalling dependencies, as well as provide future leads to explain why pancreatic tumours are intrinsically resistant to signal-targeted therapies. We will finally discuss how studies on phosphatidylinositol-3-kinase (PI3K) signalling, as the paradigmatic pro-tumoural signal downstream of oncogenic Kras in pancreatic cancer, would benefit from exploratory proteomics to increase the efficiency of targeted therapies.
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15
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Arni S, Le THN, de Wijn R, Garcia-Villegas R, Dankers M, Weder W, Hillinger S. Ex vivo multiplex profiling of protein tyrosine kinase activities in early stages of human lung adenocarcinoma. Oncotarget 2017; 8:68599-68613. [PMID: 28978141 PMCID: PMC5620281 DOI: 10.18632/oncotarget.19803] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 07/17/2017] [Indexed: 11/25/2022] Open
Abstract
Despite constant improvement in existing therapeutic efforts, the overall survival rate of lung cancer patients remains low. Enzyme activities may identify new therapeutically targetable biomarkers and overcome the marked lack of correlation between cellular abundance of translated proteins and corresponding mRNA expression levels. We analysed tyrosine kinase activities to classify lung adenocarcinoma (LuAdCa) resection specimens based on their underlying changes in cellular processes and pathways that are agents of or result from malignant transformation. We characterised 71 same-patient pairs of early-stage LuAdCa and non-neoplastic LuAdCa resection specimen lysates in the presence or absence of a tyrosine kinase inhibitor. We performed ex vivo multiplex tyrosine phosphorylation assays using 144 selected microarrayed kinase substrates. The obtained 76 selected phosphotyrosine signature peptides were subsequently analysed in terms of follow-up treatments and outcomes recorded in the patient files. For tumour, node, metastasis (TNM) stage 1 LuAdCa patients, we noticed a larger tyrosine kinase inhibitor-induced decrease in tyrosine phosphorylation for long-term as opposed to short-term disease survivors, for which 26 of 76 selected peptides were significantly (p < 0.01, FDR < 3%) more inhibited in the long-term survivors. Using statistical class prediction analysis, we obtained a 'prognostic-signature' for long- versus short-term disease survivors and correctly predicted the survival status of 73% of our patients. Our translational approach may assist clinical disease management after surgical resection and may help to direct patients for an optimal treatment strategy.
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Affiliation(s)
- Stephan Arni
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Thi Hong Nhung Le
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Rik de Wijn
- PamGene International B.V., 's-Hertogenbosch, The Netherlands
| | - Refugio Garcia-Villegas
- Department of Physiology, Biophysics and Neuroscience, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico
| | - Martjin Dankers
- PamGene International B.V., 's-Hertogenbosch, The Netherlands
| | - Walter Weder
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Sven Hillinger
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
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16
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Huhtinen A, Hongisto V, Laiho A, Löyttyniemi E, Pijnenburg D, Scheinin M. Gene expression profiles and signaling mechanisms in α 2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells. BMC SYSTEMS BIOLOGY 2017; 11:65. [PMID: 28659168 PMCID: PMC5490158 DOI: 10.1186/s12918-017-0439-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 06/09/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND α2-adrenoceptors are important regulators of vascular tone and blood pressure. Regulation of cell proliferation is a less well investigated consequence of α2-adrenoceptor activation. We have previously shown that α2B-adrenoceptor activation stimulates proliferation of vascular smooth muscle cells (VSMCs). This may be important for blood vessel development and plasticity and for the pathology and therapeutics of cardiovascular disorders. The underlying cellular mechanisms have remained mostly unknown. This study explored pathways of regulation of gene expression and intracellular signaling related to α2B-adrenoceptor-evoked VSMC proliferation. RESULTS The cellular mechanisms and signaling pathways of α2B-adrenoceptor-evoked proliferation of VSMCs are complex and include redundancy. Functional enrichment analysis and pathway analysis identified differentially expressed genes associated with α2B-adrenoceptor-regulated VSMC proliferation. They included the upregulated genes Egr1, F3, Ptgs2 and Serpine1 and the downregulated genes Cx3cl1, Cav1, Rhoa, Nppb and Prrx1. The most highly upregulated gene, Lypd8, represents a novel finding in the VSMC context. Inhibitor library screening and kinase activity profiling were applied to identify kinases in the involved signaling pathways. Putative upstream kinases identified by two different screens included PKC, Raf-1, Src, the MAP kinases p38 and JNK and the receptor tyrosine kinases EGFR and HGF/HGFR. As a novel finding, the Src family kinase Lyn was also identified as a putative upstream kinase. CONCLUSIONS α2B-adrenoceptors may mediate their pro-proliferative effects in VSMCs by promoting the activity of bFGF and PDGF and the growth factor receptors EGFR, HGFR and VEGFR-1/2. The Src family kinase Lyn was also identified as a putative upstream kinase. Lyn is known to be expressed in VSMCs and has been identified as an important regulator of GPCR trafficking and GPCR effects on cell proliferation. Identified Ser/Thr kinases included several PKC isoforms and the β-adrenoceptor kinases 1 and 2. Cross-talk between the signaling mechanisms involved in α2B-adrenoceptor-evoked VSMC proliferation thus appears to involve PKC activation, subsequent changes in gene expression, transactivation of EGFR, and modulation of kinase activities and growth factor-mediated signaling. While many of the identified individual signals were relatively small in terms of effect size, many of them were validated by combining pathway analysis and our integrated screening approach.
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Affiliation(s)
- Anna Huhtinen
- Department of Pharmacology, Drug Development and Therapeutics, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
- Unit of Clinical Pharmacology, Turku University Hospital, Turku, Finland
| | - Vesa Hongisto
- Toxicology Division, Misvik Biology Oy, Turku, Finland
| | - Asta Laiho
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Eliisa Löyttyniemi
- Department of Biostatistics, Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Dirk Pijnenburg
- PamGene International BV, Wolvenhoek 10, 5211HH s’Hertogenbosch, The Netherlands
| | - Mika Scheinin
- Department of Pharmacology, Drug Development and Therapeutics, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
- Unit of Clinical Pharmacology, Turku University Hospital, Turku, Finland
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17
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Rosenberger AFN, Hilhorst R, Coart E, García Barrado L, Naji F, Rozemuller AJM, van der Flier WM, Scheltens P, Hoozemans JJM, van der Vies SM. Protein Kinase Activity Decreases with Higher Braak Stages of Alzheimer's Disease Pathology. J Alzheimers Dis 2016; 49:927-43. [PMID: 26519433 PMCID: PMC4927853 DOI: 10.3233/jad-150429] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alzheimer’s disease (AD) is characterized by a long pre-clinical phase (20–30 years), during which significant brain pathology manifests itself. Disease mechanisms associated with pathological hallmarks remain elusive. Most processes associated with AD pathogenesis, such as inflammation, synaptic dysfunction, and hyper-phosphorylation of tau are dependent on protein kinase activity. The objective of this study was to determine the involvement of protein kinases in AD pathogenesis. Protein kinase activity was determined in postmortem hippocampal brain tissue of 60 patients at various stages of AD and 40 non-demented controls (Braak stages 0-VI) using a peptide-based microarray platform. We observed an overall decrease of protein kinase activity that correlated with disease progression. The phosphorylation of 96.7% of the serine/threonine peptides and 37.5% of the tyrosine peptides on the microarray decreased significantly with increased Braak stage (p-value <0.01). Decreased activity was evident at pre-clinical stages of AD pathology (Braak I-II). Increased phosphorylation was not observed for any peptide. STRING analysis in combination with pathway analysis and identification of kinases responsible for peptide phosphorylation showed the interactions between well-known proteins in AD pathology, including the Ephrin-receptor A1 (EphA1), a risk gene for AD, and sarcoma tyrosine kinase (Src), which is involved in memory formation. Additionally, kinases that have not previously been associated with AD were identified, e.g., protein tyrosine kinase 6 (PTK6/BRK), feline sarcoma oncogene kinase (FES), and fyn-associated tyrosine kinase (FRK). The identified protein kinases are new biomarkers and potential drug targets for early (pre-clinical) intervention.
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Affiliation(s)
- Andrea F N Rosenberger
- Alzheimer Center & Department of Neurology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Riet Hilhorst
- PamGene International BV, 's-Hertogenbosch, The Netherlands
| | - Elisabeth Coart
- International Drug Development Institute, Louvain-la-Neuve, Belgium
| | | | - Faris Naji
- PamGene International BV, 's-Hertogenbosch, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center & Department of Neurology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.,Department of Epidemiology and Biostatistics, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Philip Scheltens
- Alzheimer Center & Department of Neurology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Jeroen J M Hoozemans
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Saskia M van der Vies
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
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18
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Shi J, Sharif S, Ruijtenbeek R, Pieters RJ. Activity Based High-Throughput Screening for Novel O-GlcNAc Transferase Substrates Using a Dynamic Peptide Microarray. PLoS One 2016; 11:e0151085. [PMID: 26960196 PMCID: PMC4784888 DOI: 10.1371/journal.pone.0151085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
O-GlcNAcylation is a reversible and dynamic protein post-translational modification in mammalian cells. The O-GlcNAc cycle is catalyzed by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). O-GlcNAcylation plays important role in many vital cellular events including transcription, cell cycle regulation, stress response and protein degradation, and altered O-GlcNAcylation has long been implicated in cancer, diabetes and neurodegenerative diseases. Recently, numerous approaches have been developed to identify OGT substrates and study their function, but there is still a strong demand for highly efficient techniques. Here we demonstrated the utility of the peptide microarray approach to discover novel OGT substrates and study its specificity. Interestingly, the protein RBL-2, which is a key regulator of entry into cell division and may function as a tumor suppressor, was identified as a substrate for three isoforms of OGT. Using peptide Ala scanning, we found Ser 420 is one possible O-GlcNAc site in RBL-2. Moreover, substitution of Ser 420, on its own, inhibited OGT activity, raising the possibility of mechanism-based development for selective OGT inhibitors. This approach will prove useful for both discovery of novel OGT substrates and studying OGT specificity.
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Affiliation(s)
- Jie Shi
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
| | - Suhela Sharif
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
- PamGene International BV, ‘s-Hertogenbosch, The Netherlands
| | - Roland J. Pieters
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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19
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Hovestad-Bijl L, van Ameijde J, Pijnenburg D, Hilhorst R, Liskamp R, Ruijtenbeek R. Peptide Microarrays for Real-Time Kinetic Profiling of Tyrosine Phosphatase Activity of Recombinant Phosphatases and Phosphatases in Lysates of Cells or Tissue Samples. Methods Mol Biol 2016; 1447:67-78. [PMID: 27514800 DOI: 10.1007/978-1-4939-3746-2_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A high-throughput method for the determination of the kinetics of protein tyrosine phosphatase (PTP) activity in a microarray format is presented, allowing real-time monitoring of the dephosphorylation of a 3-nitro-phosphotyrosine residue. The 3-nitro-phosphotyrosine residue is incorporated in potential PTP substrates. The peptide substrates are immobilized onto a porous surface in discrete spots. After dephosphorylation by a PTP, a 3-nitrotyrosine residue is formed that can be detected by a specific, sequence-independent antibody. The rate of dephosphorylation can be measured simultaneously on 12 microarrays, each comprising three concentrations of 48 clinically relevant peptides, using 1.0-5.0 μg of protein from a cell or tissue lysate or 0.1-2.0 μg of purified phosphatase. The data obtained compare well with solution phase assays involving the corresponding unmodified phosphotyrosine substrates. This technology, characterized by high-throughput (12 assays in less than 2 h), multiplexing and low sample requirements, facilitates convenient and unbiased investigation of the enzymatic activity of the PTP enzyme family, for instance by profiling of PTP substrate specificities, evaluation of PTP inhibitors and pinpointing changes in PTP activity in biological samples related to diseases.
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Affiliation(s)
| | | | - Dirk Pijnenburg
- PamGene International BV, 1345, 5200 BJ, 's-Hertogenbosch, The Netherlands
| | - Riet Hilhorst
- PamGene International BV, 1345, 5200 BJ, 's-Hertogenbosch, The Netherlands
| | - Rob Liskamp
- School of Chemistry, University of Glasgow, Glasgow, UK
- Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- PamGene International BV, 1345, 5200 BJ, 's-Hertogenbosch, The Netherlands.
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20
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Ferguson BD, Carol Tan YH, Kanteti RS, Liu R, Gayed MJ, Vokes EE, Ferguson MK, John Iafrate A, Gill PS, Salgia R. Novel EPHB4 Receptor Tyrosine Kinase Mutations and Kinomic Pathway Analysis in Lung Cancer. Sci Rep 2015; 5:10641. [PMID: 26073592 PMCID: PMC4466581 DOI: 10.1038/srep10641] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 04/28/2015] [Indexed: 12/11/2022] Open
Abstract
Lung cancer outcomes remain poor despite the identification of several potential therapeutic targets. The EPHB4 receptor tyrosine kinase (RTK) has recently emerged as an oncogenic factor in many cancers, including lung cancer. Mutations of EPHB4 in lung cancers have previously been identified, though their significance remains unknown. Here, we report the identification of novel EPHB4 mutations that lead to putative structural alterations as well as increased cellular proliferation and motility. We also conducted a bioinformatic analysis of these mutations to demonstrate that they are mutually exclusive from other common RTK variants in lung cancer, that they correspond to analogous sites of other RTKs’ variations in cancers, and that they are predicted to be oncogenic based on biochemical, evolutionary, and domain-function constraints. Finally, we show that EPHB4 mutations can induce broad changes in the kinome signature of lung cancer cells. Taken together, these data illuminate the role of EPHB4 in lung cancer and further identify EPHB4 as a potentially important therapeutic target.
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Affiliation(s)
- Benjamin D Ferguson
- Department of Surgery, University of Chicago, Chicago, Illinois, United States of America
| | - Yi-Hung Carol Tan
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Rajani S Kanteti
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Ren Liu
- Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, California, United States of America
| | - Matthew J Gayed
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Everett E Vokes
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Mark K Ferguson
- Department of Surgery, University of Chicago, Chicago, Illinois, United States of America.,Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, United States of America
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Parkash S Gill
- Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, California, United States of America
| | - Ravi Salgia
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America.,Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, United States of America
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21
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Ikeda H, Yayama Y, Hata A, Kamimoto J, Yamamoto T, Mori T, Katayama Y. PNA-tagged peptide microarrays for ratiometric activity detection of cellular protein kinases. ANAL SCI 2015; 30:631-5. [PMID: 24919666 DOI: 10.2116/analsci.30.631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Peptide microarrays can be used to measure the activity of multiple protein kinases (PKs), which can be used to elucidate kinomics for drug discovery and diagnosis. Here we demonstrated a new microarray for ratiometric detection of the activity of PKs using peptide nucleic acid (PNA)-tagged peptides labeled with two different fluorophores, Cy3 and Cy5. We successfully detected cellular PK activities based on ratiometry, and applied the system for evaluation of an inhibitory drug.
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Affiliation(s)
- Hiromu Ikeda
- Department of Applied Chemistry, Kyushu University
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22
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Hamid Mujawar L, van Amerongen A, Norde W. Influence of Pluronic F127 on the distribution and functionality of inkjet-printed biomolecules in porous nitrocellulose substrates. Talanta 2015; 131:541-7. [DOI: 10.1016/j.talanta.2014.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/30/2014] [Accepted: 08/02/2014] [Indexed: 10/24/2022]
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Sanz Sanz A, Niranjan Y, Hammarén H, Ungureanu D, Ruijtenbeek R, Touw IP, Silvennoinen O, Hilhorst R. The JH2 domain and SH2-JH2 linker regulate JAK2 activity: A detailed kinetic analysis of wild type and V617F mutant kinase domains. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1835-41. [PMID: 25107665 DOI: 10.1016/j.bbapap.2014.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/19/2014] [Accepted: 07/07/2014] [Indexed: 12/31/2022]
Abstract
JAK2 tyrosine kinase regulates many cellular functions. Its activity is controlled by the pseudokinase (JH2) domain by still poorly understood mechanisms. The V617F mutation in the pseudokinase domain activates JAK2 and causes myeloproliferative neoplasms. We conducted a detailed kinetic analysis of recombinant JAK2 tyrosine kinase domain (JH1) and wild-type and V617F tandem kinase (JH1JH2) domains using peptide microarrays to define the functions of the kinase domains. The results show that i) JAK2 follows a random Bi-Bi reaction mechanism ii) JH2 domain restrains the activity of the JH1 domain by reducing the affinity for ATP and ATP competitive inhibitors iii) V617F decreases affinity for ATP but increases catalytic activity compared to wild-type and iv) the SH2-JH2 linker region participates in controlling activity by reducing the affinity for ATP.
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Affiliation(s)
- Arturo Sanz Sanz
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Yashavanthi Niranjan
- Institute of Biomedical Technology, School of Medicine, University of Tampere, 33014 Tampere, Finland
| | - Henrik Hammarén
- Institute of Biomedical Technology, School of Medicine, University of Tampere, 33014 Tampere, Finland
| | - Daniela Ungureanu
- Institute of Biomedical Technology, School of Medicine, University of Tampere, 33014 Tampere, Finland
| | - Rob Ruijtenbeek
- PamGene International BV, 5200 BJ 's-Hertogenbosch, The Netherlands
| | - Ivo P Touw
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Olli Silvennoinen
- Institute of Biomedical Technology, School of Medicine, University of Tampere, 33014 Tampere, Finland; Department of Internal Medicine, Tampere University Hospital, 33520 Tampere, Finland.
| | - Riet Hilhorst
- PamGene International BV, 5200 BJ 's-Hertogenbosch, The Netherlands.
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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McCullumsmith RE, Hammond JH, Shan D, Meador-Woodruff JH. Postmortem brain: an underutilized substrate for studying severe mental illness. Neuropsychopharmacology 2014; 39:65-87. [PMID: 24091486 PMCID: PMC3857666 DOI: 10.1038/npp.2013.239] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 02/08/2023]
Abstract
We propose that postmortem tissue is an underutilized substrate that may be used to translate genetic and/or preclinical studies, particularly for neuropsychiatric illnesses with complex etiologies. Postmortem brain tissues from subjects with schizophrenia have been extensively studied, and thus serve as a useful vehicle for illustrating the challenges associated with this biological substrate. Schizophrenia is likely caused by a combination of genetic risk and environmental factors that combine to create a disease phenotype that is typically not apparent until late adolescence. The complexity of this illness creates challenges for hypothesis testing aimed at understanding the pathophysiology of the illness, as postmortem brain tissues collected from individuals with schizophrenia reflect neuroplastic changes from a lifetime of severe mental illness, as well as treatment with antipsychotic medications. While there are significant challenges with studying postmortem brain, such as the postmortem interval, it confers a translational element that is difficult to recapitulate in animal models. On the other hand, data derived from animal models typically provide specific mechanistic and behavioral measures that cannot be generated using human subjects. Convergence of these two approaches has led to important insights for understanding molecular deficits and their causes in this illness. In this review, we discuss the problem of schizophrenia, review the common challenges related to postmortem studies, discuss the application of biochemical approaches to this substrate, and present examples of postmortem schizophrenia studies that illustrate the role of the postmortem approach for generating important new leads for understanding the pathophysiology of severe mental illness.
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Affiliation(s)
| | - John H Hammond
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Dan Shan
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
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Comparative characterization of direct and indirect substrate probes for on-chip transamidating activity assay of transglutaminases. J Biotechnol 2013; 168:324-30. [DOI: 10.1016/j.jbiotec.2013.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 10/05/2013] [Accepted: 10/08/2013] [Indexed: 01/11/2023]
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van Ameijde J, Overvoorde J, Knapp S, den Hertog J, Ruijtenbeek R, Liskamp RMJ. Real-Time Monitoring of the Dephosphorylating Activity of Protein Tyrosine Phosphatases Using Microarrays with 3-Nitrophosphotyrosine Substrates. Chempluschem 2013; 78:1349-1357. [PMID: 31986648 DOI: 10.1002/cplu.201300299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Indexed: 11/10/2022]
Abstract
Phosphatases and kinases regulate the crucial phosphorylation post-translational modification. In spite of their similarly important role in many diseases and therapeutic potential, phosphatases have received arguably less attention. One reason for this is a scarcity of high-throughput phosphatase assays. Herein, a new real-time, dynamic protein tyrosine phosphatase (PTP) substrate microarray assay measuring product formation is described. PTP substrates comprising a novel 3-nitrophosphotyrosine residue are immobilized in discrete spots. After reaction catalyzed by a PTP a 3-nitrotyrosine residue is formed that can be detected by specific, sequence-independent antibodies. The resulting microarray was successfully evaluated with a panel of recombinant PTPs and cell lysates, which afforded results comparable to data from other assays. Its parallel nature, convenience, and low sample requirements facilitate investigation of the therapeutically relevant PTP enzyme family.
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Affiliation(s)
- Jeroen van Ameijde
- Medicinal Chemistry and Chemical Biology, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht (The Netherlands), Fax: (+31) (0)30-253-6655.,Netherlands Proteomics Centre, Padualaan 8, 3584 CA Utrecht (The Netherlands)
| | - John Overvoorde
- Hubrecht Institute, KNAW and University Medical Centre, Uppsalalaan 8, 3508 AD Utrecht (The Netherlands)
| | - Stefan Knapp
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Headington, Oxford OX3 7DQ (U.K.)
| | - Jeroen den Hertog
- Hubrecht Institute, KNAW and University Medical Centre, Uppsalalaan 8, 3508 AD Utrecht (The Netherlands).,Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden (The Netherlands)
| | - Rob Ruijtenbeek
- Pamgene International Ltd. Wolvenhoek 10, 5200 BJ Den Bosch (The Netherlands)
| | - Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht (The Netherlands), Fax: (+31) (0)30-253-6655.,School of Chemistry, Joseph Black Building, Glasgow University, University Avenue, Glasgow G12 8QQ (U.K.)
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Aarts JMMJG, Wang S, Houtman R, van Beuningen RMGJ, Westerink WMA, Van De Waart BJ, Rietjens IMCM, Bovee TFH. Robust array-based coregulator binding assay predicting ERα-agonist potency and generating binding profiles reflecting ligand structure. Chem Res Toxicol 2013; 26:336-46. [PMID: 23383871 DOI: 10.1021/tx300463b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Testing chemicals for their endocrine-disrupting potential, including interference with estrogen receptor (ER) signaling, is an important aspect of chemical safety testing. Because of the practical drawbacks of animal testing, the development of in vitro alternatives for the uterotrophic assay and other in vivo (anti)estrogenicity tests has high priority. It was previously demonstrated that an in vitro assay that profiles ligand-induced binding of ERα to a microarray of coregulator-derived peptides might be a valuable candidate for a panel of in vitro assays aiming at an ultimate replacement of the uterotrophic assay. In the present study, the reproducibility and robustness of this coregulator binding assay was determined by measuring the binding profiles of 14 model compounds that are recommended by the Office of Prevention, Pesticides and Toxic Substances for testing laboratory proficiency in estrogen receptor transactivation assays. With a median coefficient of variation of 5.0% and excellent correlation (R(2) = 0.993) between duplicate measurements, the reproducibility of the ERα-coregulator binding assay was better than the reproducibility of other commonly used in vitro ER functional assays. In addition, the coregulator binding assay is correctly predicting the estrogenicity for 13 out of 14 compounds tested. When the potency of the ER-agonists to induce ERα-coregulator binding was compared to their ER binding affinity, their ranking was similar, and the correlation between the EC50 values was excellent (R(2) = 0.96), as was the correlation with their potency in a transactivation assay (R(2) = 0.94). Moreover, when the ERα-coregulator binding profiles were hierarchically clustered using Euclidian cluster distance, the structurally related compounds were found to cluster together, whereas the steroid test compounds having an aromatic A-ring were separated from those with a cyclohexene A-ring. We concluded that this assay is capable of distinguishing ERα agonists and antagonists and that it even reflects the structural similarity of ERα agonists, indicating a potential to achieve identification and classification of ERα endocrine disruptors with high fidelity.
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Affiliation(s)
- Jac M M J G Aarts
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety, Wageningen University and Research Centre , Akkermaalsbos 2, Wageningen, The Netherlands
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Differential phosphorylation of perilipin 1A at the initiation of lipolysis revealed by novel monoclonal antibodies and high content analysis. PLoS One 2013; 8:e55511. [PMID: 23405163 PMCID: PMC3566132 DOI: 10.1371/journal.pone.0055511] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 01/02/2013] [Indexed: 12/03/2022] Open
Abstract
Lipolysis in adipocytes is regulated by phosphorylation of lipid droplet-associated proteins, including perilipin 1A and hormone-sensitive lipase (HSL). Perilipin 1A is potentially phosphorylated by cAMP(adenosine 3′,5′-cyclic monophosphate)-dependent protein kinase (PKA) on several sites, including conserved C-terminal residues, serine 497 (PKA-site 5) and serine 522 (PKA-site 6). To characterize perilipin 1A phosphorylation, novel monoclonal antibodies were developed, which selectively recognize perilipin 1A phosphorylation at PKA-site 5 and PKA-site 6. Utilizing these novel antibodies, as well as antibodies selectively recognizing HSL phosphorylation at serine 563 or serine 660, we used high content analysis to examine the phosphorylation of perilipin 1A and HSL in adipocytes exposed to lipolytic agents. We found that perilipin PKA-site 5 and HSL-serine 660 were phosphorylated to a similar extent in response to forskolin (FSK) and L-γ-melanocyte stimulating hormone (L-γ-MSH). In contrast, perilipin PKA-site 6 and HSL-serine 563 were phosphorylated more slowly and L-γ-MSH was a stronger agonist for these sites compared to FSK. When a panel of lipolytic agents was tested, including multiple concentrations of isoproterenol, FSK, and L-γ-MSH, the pattern of results was virtually identical for perilipin PKA-site 5 and HSL-serine 660, whereas a distinct pattern was observed for perilipin PKA-site 6 and HSL-serine 563. Notably, perilipin PKA-site 5 and HSL-serine 660 feature two arginine residues upstream from the phospho-acceptor site, which confers high affinity for PKA, whereas perilipin PKA-site 6 and HSL-serine 563 feature only a single arginine. Thus, we suggest perilipin 1A and HSL are differentially phosphorylated in a similar manner at the initiation of lipolysis and arginine residues near the target serines may influence this process.
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Rose HM, Stuiver M, Thongwichian R, Theillet FX, Feller SM, Selenko P. Quantitative NMR analysis of Erk activity and inhibition by U0126 in a panel of patient-derived colorectal cancer cell lines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1396-401. [PMID: 23360766 DOI: 10.1016/j.bbapap.2013.01.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/11/2013] [Accepted: 01/18/2013] [Indexed: 01/01/2023]
Abstract
We comparatively analyzed the basal activity of extra-cellular signal-regulated kinase (Erk1/2) in lysates of 10 human colorectal cancer cell lines by semi-quantitative Western blotting and time-resolved NMR spectroscopy. Both methods revealed heterogeneous levels of endogenous Erk1/2 activities in a highly consistent manner. Upon treatment with U0126, an inhibitor of mitogen-activated protein kinase kinase (MEK) acting upstream of Erk1/2, Western-blotting and NMR congruently reported specific modulations of cellular phospho-Erk levels that translated into reduced kinase activities. Results obtained in this study highlight the complementary nature of antibody- and NMR-based phospho-detection techniques. They further exemplify the usefulness of time-resolved NMR measurements in providing fast and quantitative readouts of kinase activities and kinase inhibitor efficacies in native cellular environments. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Honor May Rose
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology FMP Berlin, Robert-Rössle Strasse 10, 13125 Berlin, Germany
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31
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Hilhorst R, Houkes L, Mommersteeg M, Musch J, van den Berg A, Ruijtenbeek R. Peptide microarrays for profiling of serine/threonine kinase activity of recombinant kinases and lysates of cells and tissue samples. Methods Mol Biol 2013; 977:259-71. [PMID: 23436369 DOI: 10.1007/978-1-62703-284-1_21] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptide microarray technology can be used to identify substrates for recombinant kinases, to measure kinase activity and changes thereof in cell lysates and lysates from fresh frozen (tumor) tissue. The effect of kinase inhibitors on the kinase activities in relevant tissues can be investigated as well. The method for performing experiments on dynamic peptide microarrays with real-time readout is described, as well as the influence of assay parameters and suggestions for optimization of experiments.
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Affiliation(s)
- Riet Hilhorst
- PamGene International BV, 's-Hertogenbosch, The Netherlands
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32
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Ree AH, Kristensen AT, Saelen MG, de Wijn R, Edvardsen H, Jovanovic J, Abrahamsen TW, Dueland S, Flatmark K. Tumor phosphatidylinositol-3-kinase signaling and development of metastatic disease in locally advanced rectal cancer. PLoS One 2012; 7:e50806. [PMID: 23226389 PMCID: PMC3511283 DOI: 10.1371/journal.pone.0050806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/25/2012] [Indexed: 02/02/2023] Open
Abstract
Background Recognizing EGFR as key orchestrator of the metastatic process in colorectal cancer, but also the substantial heterogeneity of responses to anti-EGFR therapy, we examined the pattern of composite tumor kinase activities governed by EGFR-mediated signaling that might be implicated in development of metastatic disease. Patients and Methods Point mutations in KRAS, BRAF, and PIK3CA and ERBB2 amplification were determined in primary tumors from 63 patients with locally advanced rectal cancer scheduled for radical treatment. Using peptide arrays with tyrosine kinase substrates, ex vivo phosphopeptide profiles were generated from the same baseline tumor samples and correlated to metastasis-free survival. Results Unsupervised clustering analysis of the resulting phosphorylation of 102 array substrates defined two tumor classes, both consisting of cases with and without KRAS/BRAF mutations. The smaller cluster group of patients, with tumors generating high ex vivo phosphorylation of phosphatidylinositol-3-kinase-related substrates, had a particularly aggressive disease course, with almost a half of patients developing metastatic disease within one year of follow-up. Conclusion High phosphatidylinositol-3-kinase-mediated signaling activity of the primary tumor, rather than KRAS/BRAF mutation status, was identified as a hallmark of poor metastasis-free survival in patients with locally advanced rectal cancer undergoing radical treatment of the pelvic cavity.
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Affiliation(s)
- Anne Hansen Ree
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway.
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33
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van Wandelen LTM, van Ameijde J, Mady ASA, Wammes AEM, Bode A, Poot AJ, Ruijtenbeek R, Liskamp RMJ. Directed modulation of protein kinase C isozyme selectivity with bisubstrate-based inhibitors. ChemMedChem 2012; 7:2113-21. [PMID: 23139239 DOI: 10.1002/cmdc.201200349] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/09/2012] [Indexed: 11/11/2022]
Abstract
Kinases present an attractive target for drug development, since they are involved in vital cellular processes and are implicated in a variety of diseases, such as cancer and diabetes. However, obtaining selectivity for a specific kinase over others is difficult since many current kinase inhibitors exclusively target the highly conserved kinase ATP binding domain. Previously, a microarray-based strategy to discover so-called bisubstrate-based inhibitors that target the more specific peptide binding groove in addition to the ATP binding site was described. One attractive feature of this strategy is the opportunity to tune the selectivity of these inhibitors by systematically varying components. In an extension to this previous work, this study explores the potential of this guided selectivity modulation, leading to a series of inhibitors with different selectivity profiles against highly homologous protein kinase C (PKC) isozymes. Of the inhibitors studied, most exhibited improved potency and selectivity compared with their constituent parts. Furthermore, the selectivity was found to be tunable either through modification of the pseudosubstrate peptide (peptide binding groove) or the ATP-competitive part (ATP binding site). In a number of cases, the selectivity of the construct could be predicted from the initial peptide substrate profiling experiment. Since this strategy is applicable to all kinase sets, it could be used to rapidly develop uniquely selective inhibitors.
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Affiliation(s)
- Loek T M van Wandelen
- Medicinal Chemistry and Chemical Biology, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
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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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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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Houtman R, de Leeuw R, Rondaij M, Melchers D, Verwoerd D, Ruijtenbeek R, Martens JW, Neefjes J, Michalides R. Serine-305 Phosphorylation Modulates Estrogen Receptor Alpha Binding to a Coregulator Peptide Array, with Potential Application in Predicting Responses to Tamoxifen. Mol Cancer Ther 2012; 11:805-16. [DOI: 10.1158/1535-7163.mct-11-0855] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Tournoij E, Koekman CA, Du VX, Roest M, Ruijtenbeek R, Moll FL, Akkerman JWN. The platelet P2Y12 receptor contributes to granule secretion through Ephrin A4 receptor. Platelets 2012; 23:617-25. [PMID: 22273509 DOI: 10.3109/09537104.2011.645924] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The main responses of P2Y(1) ligation are platelet shape change and transient aggregation while P2Y(12) ligation amplifies P2Y(1)-induced aggregation and accelerates aggregation, secretion and thromboxane A(2) production induced by other agonist-receptor complexes. We searched for new targets of P2Y signalling using micro-arrays with 144 peptides representing known phosphosites of protein tyrosine kinases. ADP induced phosphorylation of peptides representing surface receptors, second messenger enzymes and cytoskeletal proteins. Strong phosphorylation was found in peptides representing Ephrin-receptor family members. Blockade of P2Y(1/12) inhibited phosphorylation of EphA4- and EphB1-peptides on micro-arrays. The EphA2/4 inhibitor 2,5-dimethylpyrrolyl benzoic acid derivative interfered with P2Y(1/12)-induced EphA4 phosphorylation, left P2Y(1)-induced aggregation unchanged but inhibited with P2Y(12)-induced secretion, second phase aggregation and thrombus formation on collagen at 1600 s(-1). These results show that platelet EphA4 is an important intermediate in P2Y(12)-induced granule secretion.
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Affiliation(s)
- Erik Tournoij
- Laboratory for Thrombosis and Haemostasis, Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
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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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Arsenault R, Griebel P, Napper S. Peptide arrays for kinome analysis: New opportunities and remaining challenges. Proteomics 2011; 11:4595-609. [DOI: 10.1002/pmic.201100296] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/28/2011] [Accepted: 10/04/2011] [Indexed: 01/08/2023]
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Thilakarathne PJ, Clement L, Lin D, Shkedy Z, Kasim A, Talloen W, Versele M, Verbeke G. The use of semiparametric mixed models to analyze PamChip(R) peptide array data: an application to an oncology experiment. ACTA ACUST UNITED AC 2011; 27:2859-65. [PMID: 21846736 DOI: 10.1093/bioinformatics/btr475] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Phosphorylation by protein kinases is a central theme in biological systems. Aberrant protein kinase activity has been implicated in a variety of human diseases (e.g. cancer). Therefore, modulation of kinase activity represents an attractive therapeutic approach for the treatment of human illnesses. Thus, identification of signature peptides is crucial for protein kinase targeting and can be achieved by using PamChip(®) microarray technology. We propose a flexible semiparametric mixed model for analyzing PamChip(®) data. This approach enables the estimation of the phosphorylation rate (Velocity) as a function of time together with pointwise confidence intervals. RESULTS Using a publicly available dataset, we show that our model is capable of adequately fitting the kinase activity profiles and provides velocity estimates over time. Moreover, it allows to test for differences in the velocity of kinase inhibition between responding and non-responding cell lines. This can be done at individual time point as well as for the entire velocity profile. CONTACT pushpike@med.kuleuven.be SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pushpike J Thilakarathne
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Katholieke Universiteit Leuven, B3000 Leuven, Belgium.
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Ingham CJ, ter Maat J, de Vos WM. Where bio meets nano: the many uses for nanoporous aluminum oxide in biotechnology. Biotechnol Adv 2011; 30:1089-99. [PMID: 21856400 DOI: 10.1016/j.biotechadv.2011.08.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 07/28/2011] [Accepted: 08/03/2011] [Indexed: 01/17/2023]
Abstract
Porous aluminum oxide (PAO) is a ceramic formed by an anodization process of pure aluminum that enables the controllable assembly of exceptionally dense and regular nanopores in a planar membrane. As a consequence, PAO has a high porosity, nanopores with high aspect ratio, biocompatibility and the potential for high sensitivity imaging and diverse surface modifications. These properties have made this unusual material attractive to a disparate set of applications. This review examines how the structure and properties of PAO connect with its present and potential uses within research and biotechnology. The role of PAO is covered in areas including microbiology, mammalian cell culture, sensitive detection methods, microarrays and other molecular assays, and in creating new nanostructures with further uses within biology.
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42
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Sanz A, Ungureanu D, Pekkala T, Ruijtenbeek R, Touw IP, Hilhorst R, Silvennoinen O. Analysis of Jak2 catalytic function by peptide microarrays: the role of the JH2 domain and V617F mutation. PLoS One 2011; 6:e18522. [PMID: 21533163 PMCID: PMC3078918 DOI: 10.1371/journal.pone.0018522] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 03/10/2011] [Indexed: 12/27/2022] Open
Abstract
Janus kinase 2 (JAK2) initiates signaling from several cytokine receptors and is required for biological responses such as erythropoiesis. JAK2 activity is controlled by regulatory proteins such as Suppressor of Cytokine Signaling (SOCS) proteins and protein tyrosine phosphatases. JAK2 activity is also intrinsically controlled by regulatory domains, where the pseudokinase (JAK homology 2, JH2) domain has been shown to play an essential role. The physiological role of the JH2 domain in the regulation of JAK2 activity was highlighted by the discovery of the acquired missense point mutation V617F in myeloproliferative neoplasms (MPN). Hence, determining the precise role of this domain is critical for understanding disease pathogenesis and design of new treatment modalities. Here, we have evaluated the effect of inter-domain interactions in kinase activity and substrate specificity. By using for the first time purified recombinant JAK2 proteins and a novel peptide micro-array platform, we have determined initial phosphorylation rates and peptide substrate preference for the recombinant kinase domain (JH1) of JAK2, and two constructs comprising both the kinase and pseudokinase domains (JH1-JH2) of JAK2. The data demonstrate that (i) JH2 drastically decreases the activity of the JAK2 JH1 domain, (ii) JH2 increased the Km for ATP (iii) JH2 modulates the peptide preference of JAK2 (iv) the V617F mutation partially releases this inhibitory mechanism but does not significantly affect substrate preference or Km for ATP. These results provide the biochemical basis for understanding the interaction between the kinase and the pseudokinase domain of JAK2 and identify a novel regulatory role for the JAK2 pseudokinase domain. Additionally, this method can be used to identify new regulatory mechanisms for protein kinases that provide a better platform for designing specific strategies for therapeutic approaches.
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Affiliation(s)
- Arturo Sanz
- Department of Hematology, Erasmus MC, Rotterdam, Netherlands
| | - Daniela Ungureanu
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
| | - Tuija Pekkala
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
| | | | - Ivo P. Touw
- Department of Hematology, Erasmus MC, Rotterdam, Netherlands
| | - Riet Hilhorst
- PamGene International BV, 's-Hertogenbosch, The Netherlands
| | - Olli Silvennoinen
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
- * E-mail:
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Harmsen S, Dolman MEM, Nemes Z, Lacombe M, Szokol B, Pató J, Kéri G, Őrfi L, Storm G, Hennink WE, Kok RJ. Development of a Cell-Selective and Intrinsically Active Multikinase Inhibitor Bioconjugate. Bioconjug Chem 2011; 22:540-5. [DOI: 10.1021/bc1005637] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Harmsen
- Department of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - M. Emmy M. Dolman
- Department of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Zoltan Nemes
- Department of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Marie Lacombe
- Kreatech Biotechnology BV, Amsterdam, The Netherlands
| | | | | | - György Kéri
- Vichem Chemie, Budapest, Hungary
- Pathobiochemistry Research Group of Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | | | - Gert Storm
- Department of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Wim E. Hennink
- Department of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Robbert J. Kok
- Department of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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Plaza-Menacho I, Morandi A, Mologni L, Boender P, Gambacorti-Passerini C, Magee AI, Hofstra RMW, Knowles P, McDonald NQ, Isacke CM. Focal adhesion kinase (FAK) binds RET kinase via its FERM domain, priming a direct and reciprocal RET-FAK transactivation mechanism. J Biol Chem 2011; 286:17292-302. [PMID: 21454698 DOI: 10.1074/jbc.m110.168500] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Whether RET is able to directly phosphorylate and activate downstream targets independently of the binding of proteins that contain Src homology 2 or phosphotyrosine binding domains and whether mechanisms in trans by cytoplasmic kinases can modulate RET function and signaling remain largely unexplored. In this study, oligopeptide arrays were used to screen substrates directly phosphorylated by purified recombinant wild-type and oncogenic RET kinase domain in the presence or absence of small molecule inhibitors. The results of the peptide array were validated by enzyme kinetics, in vitro kinase, and cell-based experiments. The identification of focal adhesion kinase (FAK) as a direct substrate for RET kinase revealed (i) a RET-FAK transactivation mechanism consisting of direct phosphorylation of FAK Tyr-576/577 by RET and a reciprocal phosphorylation of RET by FAK, which crucially is able to rescue the kinase-impaired RET K758M mutant and (ii) that FAK binds RET via its FERM domain. Interestingly, this interaction is abolished upon RET phosphorylation, indicating that RET binding to the FERM domain of FAK is a priming step for RET-FAK transactivation. Finally, our data indicate that FAK inhibitors could be used as potential therapeutic agents for patients with multiple endocrine neoplasia type 2 tumors because both, treatment with the FAK kinase inhibitor NVP-TAE226 and FAK down-regulation by siRNA reduced RET phosphorylation and signaling as well as the proliferation and survival of tumor and transfected cell lines expressing oncogenic RET.
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Affiliation(s)
- Iván Plaza-Menacho
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom.
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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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Monton MRN, Lebert JM, Little JRL, Nair JJ, McNulty J, Brennan JD. A Sol−Gel-Derived Acetylcholinesterase Microarray for Nanovolume Small-Molecule Screening. Anal Chem 2010; 82:9365-73. [PMID: 20949898 DOI: 10.1021/ac101949s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Rowena N. Monton
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - Julie M. Lebert
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - Jessamyn R. L. Little
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - Jerald James Nair
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - James McNulty
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - John D. Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
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Prediction of response to preoperative chemoradiotherapy in rectal cancer by multiplex kinase activity profiling. Int J Radiat Oncol Biol Phys 2010; 78:555-62. [PMID: 20675069 DOI: 10.1016/j.ijrobp.2010.04.036] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 04/09/2010] [Accepted: 04/14/2010] [Indexed: 11/23/2022]
Abstract
PURPOSE Tumor response of rectal cancer to preoperative chemoradiotherapy (CRT) varies considerably. In experimental tumor models and clinical radiotherapy, activity of particular subsets of kinase signaling pathways seems to predict radiation response. This study aimed to determine whether tumor kinase activity profiles might predict tumor response to preoperative CRT in locally advanced rectal cancer (LARC). METHODS AND MATERIALS Sixty-seven LARC patients were treated with a CRT regimen consisting of radiotherapy, fluorouracil, and, where possible, oxaliplatin. Pretreatment tumor biopsy specimens were analyzed using microarrays with kinase substrates, and the resulting substrate phosphorylation patterns were correlated with tumor response to preoperative treatment as assessed by histomorphologic tumor regression grade (TRG). A predictive model for TRG scores from phosphosubstrate signatures was obtained by partial-least-squares discriminant analysis. Prediction performance was evaluated by leave-one-out cross-validation and use of an independent test set. RESULTS In the patient population, 73% and 15% were scored as good responders (TRG 1-2) or intermediate responders (TRG 3), whereas 12% were assessed as poor responders (TRG 4-5). In a subset of 7 poor responders and 12 good responders, treatment outcome was correctly predicted for 95%. Application of the prediction model on the remaining patient samples resulted in correct prediction for 85%. Phosphosubstrate signatures generated by poor-responding tumors indicated high kinase activity, which was inhibited by the kinase inhibitor sunitinib, and several discriminating phosphosubstrates represented proteins derived from signaling pathways implicated in radioresistance. CONCLUSIONS Multiplex kinase activity profiling may identify functional biomarkers predictive of tumor response to preoperative CRT in LARC.
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Parera Pera N, Branderhorst HM, Kooij R, Maierhofer C, van der Kaaden M, Liskamp RMJ, Wittmann V, Ruijtenbeek R, Pieters RJ. Rapid Screening of Lectins for Multivalency Effects with a Glycodendrimer Microarray. Chembiochem 2010; 11:1896-904. [DOI: 10.1002/cbic.201000340] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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50
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van Ameijde J, Poot AJ, van Wandelen LTM, Wammes AEM, Ruijtenbeek R, Rijkers DTS, Liskamp RMJ. Preparation of novel alkylated arginine derivatives suitable for click-cycloaddition chemistry and their incorporation into pseudosubstrate- and bisubstrate-based kinase inhibitors. Org Biomol Chem 2010; 8:1629-39. [PMID: 20237675 DOI: 10.1039/b922928k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient strategies for the introduction of arginine residues featuring acetylene or azide moieties in their side chains are described. The substituents are introduced in a way that maintains the basicity of the guanidine moiety. The methodology can be used e.g. for non-invasive labeling of arginine-containing peptides. Its applicability is demonstrated by the introduction of 'click' handles into a Protein Kinase C (PKC) pseudosubstrate peptide, and the subsequent preparation and evaluation of a novel bisubstrate-based inhibitor based on such a peptide.
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Affiliation(s)
- Jeroen van Ameijde
- Medicinal Chemistry and Chemical Biology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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