1
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Staes A, Boucher K, Dufour S, Maia TM, Timmerman E, Haver DV, Pauwels J, Demol H, Vandenbussche J, Gevaert K, Impens F, Devos S. High-Throughput Nanoflow Proteomics Using a Dual-Column Electrospray Source. Anal Chem 2024; 96:6534-6539. [PMID: 38647218 DOI: 10.1021/acs.analchem.4c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
With current trends in proteomics, especially regarding clinical and low input (to single cell) samples, it is increasingly important to both maximize the throughput of the analysis and maintain as much sensitivity as possible. The new generation of mass spectrometers (MS) are taking a huge leap in sensitivity, allowing analysis of samples with shorter liquid chromatography (LC) methods while digging as deep in the proteome. However, the throughput can be doubled by implementing a dual column nano-LC-MS configuration. For this purpose, we used a dual-column setup with a two-outlet electrospray source and compared it to a classic dual-column setup with a single-outlet source.
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Affiliation(s)
- An Staes
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Katie Boucher
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Sara Dufour
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Teresa Mendes Maia
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Jarne Pauwels
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Hans Demol
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | | | - Kris Gevaert
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Simon Devos
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
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2
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Ferrucci V, Asadzadeh F, Collina F, Siciliano R, Boccia A, Marrone L, Spano D, Carotenuto M, Chiarolla CM, De Martino D, De Vita G, Macrì A, Dassi L, Vandenbussche J, Marino N, Cantile M, Paolella G, D'Andrea F, di Bonito M, Gevaert K, Zollo M. Prune-1 drives polarization of tumor-associated macrophages (TAMs) within the lung metastatic niche in triple-negative breast cancer. iScience 2020; 24:101938. [PMID: 33426510 PMCID: PMC7779777 DOI: 10.1016/j.isci.2020.101938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/22/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
M2-tumor-associated macrophages (M2-TAMs) in the tumor microenvironment represent a prognostic indicator for poor outcome in triple-negative breast cancer (TNBC). Here we show that Prune-1 overexpression in human TNBC patients has positive correlation to lung metastasis and infiltrating M2-TAMs. Thus, we demonstrate that Prune-1 promotes lung metastasis in a genetically engineered mouse model of metastatic TNBC augmenting M2-polarization of TAMs within the tumor microenvironment. Thus, this occurs through TGF-β enhancement, IL-17F secretion, and extracellular vesicle protein content modulation. We also find murine inactivating gene variants in human TNBC patient cohorts that are involved in activation of the innate immune response, cell adhesion, apoptotic pathways, and DNA repair. Altogether, we indicate that the overexpression of Prune-1, IL-10, COL4A1, ILR1, and PDGFB, together with inactivating mutations of PDE9A, CD244, Sirpb1b, SV140, Iqca1, and PIP5K1B genes, might represent a route of metastatic lung dissemination that need future prognostic validations. Prune-1 correlates to M2-TAMs confirming lung metastatic dissemination in GEMM Cytokines and EV proteins are responsible of M2-TAMs polarization processes A small molecule with immunomodulatory properties ameliorates metastatic dissemination Identification of gene variants within immune response and cell adhesion in TNBC
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Affiliation(s)
- Veronica Ferrucci
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy.,European School of Molecular Medicine (SEMM), University of Milan, Milan, Italy
| | - Fatemeh Asadzadeh
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | - Francesca Collina
- Pathology Unit, Istituto Nazionale Tumori-IRCS- Fondazione G.Pascale, Naples 80131, Italy
| | | | | | - Laura Marrone
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | | | - Marianeve Carotenuto
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | | | - Daniela De Martino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | - Gennaro De Vita
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy
| | | | - Luisa Dassi
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy
| | - Jonathan Vandenbussche
- VIB-UGent Centre for Medical Biotechnology, Ghent 9052, Belgium.,Department of Biomolecular Medicine, Ghent University, B9052 Ghent, Belgium
| | - Natascia Marino
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Department of Medicine, Indiana University-Purdue University Indianapolis, Indianapolis 46202, USA
| | - Monica Cantile
- Pathology Unit, Istituto Nazionale Tumori-IRCS- Fondazione G.Pascale, Naples 80131, Italy
| | | | - Francesco D'Andrea
- Dipartimento di Sanità pubblica - AOU, Università; degli Studi di Napoli Federico II, Naples 80131, Italy
| | - Maurizio di Bonito
- Pathology Unit, Istituto Nazionale Tumori-IRCS- Fondazione G.Pascale, Naples 80131, Italy
| | - Kris Gevaert
- VIB-UGent Centre for Medical Biotechnology, Ghent 9052, Belgium.,Department of Biomolecular Medicine, Ghent University, B9052 Ghent, Belgium
| | - Massimo Zollo
- CEINGE, Biotecnologie Avanzate, Naples 80145, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples 80134, Italy.,European School of Molecular Medicine (SEMM), University of Milan, Milan, Italy.,DAI Medicina di Laboratorio e Trasfusionale, AOU Federico II, Naples 80131, Italy
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3
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Corne TDJ, Sieprath T, Vandenbussche J, Mohammed D, Te Lindert M, Gevaert K, Gabriele S, Wolf K, De Vos WH. Deregulation of focal adhesion formation and cytoskeletal tension due to loss of A-type lamins. Cell Adh Migr 2016; 11:447-463. [PMID: 27791462 DOI: 10.1080/19336918.2016.1247144] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The nuclear lamina mechanically integrates the nucleus with the cytoskeleton and extracellular environment and regulates gene expression. These functions are exerted through direct and indirect interactions with the lamina's major constituent proteins, the A-type lamins, which are encoded by the LMNA gene. Using quantitative stable isotope labeling-based shotgun proteomics we have analyzed the proteome of human dermal fibroblasts in which we have depleted A-type lamins by means of a sustained siRNA-mediated LMNA knockdown. Gene ontology analysis revealed that the largest fraction of differentially produced proteins was involved in actin cytoskeleton organization, in particular proteins involved in focal adhesion dynamics, such as actin-related protein 2 and 3 (ACTR2/3), subunits of the ARP2/3 complex, and fascin actin-bundling protein 1 (FSCN1). Functional validation using quantitative immunofluorescence showed a significant reduction in the size of focal adhesion points in A-type lamin depleted cells, which correlated with a reduction in early cell adhesion capacity and an increased cell motility. At the same time, loss of A-type lamins led to more pronounced stress fibers and higher traction forces. This phenotype could not be mimicked or reversed by experimental modulation of the STAT3-IL6 pathway, but it was partly recapitulated by chemical inhibition of the ARP2/3 complex. Thus, our data suggest that the loss of A-type lamins perturbs the balance between focal adhesions and cytoskeletal tension. This imbalance may contribute to mechanosensing defects observed in certain laminopathies.
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Affiliation(s)
- Tobias D J Corne
- a Laboratory of Cell Biology and Histology , Department of Veterinary Sciences, University of Antwerp , Antwerp , Belgium.,b Cell Systems and Imaging Research Group (CSI) , Department of Molecular Biotechnology, Ghent University , Ghent , Belgium
| | - Tom Sieprath
- a Laboratory of Cell Biology and Histology , Department of Veterinary Sciences, University of Antwerp , Antwerp , Belgium.,b Cell Systems and Imaging Research Group (CSI) , Department of Molecular Biotechnology, Ghent University , Ghent , Belgium
| | - Jonathan Vandenbussche
- c Medical Biotechnology Center, VIB , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Danahe Mohammed
- e Mechanobiology & Soft Matter Research Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons , Mons , Belgium
| | - Mariska Te Lindert
- f Department of Cell Biology , Radboud University Medical Center , Nijmegen , The Netherlands
| | - Kris Gevaert
- c Medical Biotechnology Center, VIB , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Sylvain Gabriele
- e Mechanobiology & Soft Matter Research Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons , Mons , Belgium
| | - Katarina Wolf
- f Department of Cell Biology , Radboud University Medical Center , Nijmegen , The Netherlands
| | - Winnok H De Vos
- a Laboratory of Cell Biology and Histology , Department of Veterinary Sciences, University of Antwerp , Antwerp , Belgium.,b Cell Systems and Imaging Research Group (CSI) , Department of Molecular Biotechnology, Ghent University , Ghent , Belgium
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4
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Walton A, Stes E, Goeminne G, Braem L, Vuylsteke M, Matthys C, De Cuyper C, Staes A, Vandenbussche J, Boyer FD, Vanholme R, Fromentin J, Boerjan W, Gevaert K, Goormachtig S. The Response of the Root Proteome to the Synthetic Strigolactone GR24 in Arabidopsis. Mol Cell Proteomics 2016; 15:2744-55. [PMID: 27317401 DOI: 10.1074/mcp.m115.050062] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/06/2022] Open
Abstract
Strigolactones are plant metabolites that act as phytohormones and rhizosphere signals. Whereas most research on unraveling the action mechanisms of strigolactones is focused on plant shoots, we investigated proteome adaptation during strigolactone signaling in the roots of Arabidopsis thaliana. Through large-scale, time-resolved, and quantitative proteomics, the impact of the strigolactone analog rac-GR24 was elucidated on the root proteome of the wild type and the signaling mutant more axillary growth 2 (max2). Our study revealed a clear MAX2-dependent rac-GR24 response: an increase in abundance of enzymes involved in flavonol biosynthesis, which was reduced in the max2-1 mutant. Mass spectrometry-driven metabolite profiling and thin-layer chromatography experiments demonstrated that these changes in protein expression lead to the accumulation of specific flavonols. Moreover, quantitative RT-PCR revealed that the flavonol-related protein expression profile was caused by rac-GR24-induced changes in transcript levels of the corresponding genes. This induction of flavonol production was shown to be activated by the two pure enantiomers that together make up rac-GR24. Finally, our data provide much needed clues concerning the multiple roles played by MAX2 in the roots and a comprehensive view of the rac-GR24-induced response in the root proteome.
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Affiliation(s)
- Alan Walton
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elisabeth Stes
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Geert Goeminne
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lukas Braem
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | | | - Cedrick Matthys
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Carolien De Cuyper
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - An Staes
- ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Jonathan Vandenbussche
- ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - François-Didier Boyer
- ‡‡Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, 78026 Versailles, France; §§AgroParisTech, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, 78026 Versailles, France; ¶¶Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, Unité Propre de Recherche 2301, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France
| | - Ruben Vanholme
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Justine Fromentin
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; ‖‖Laboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441, Institut National de la Recherche Agronomique, 31326 Castanet-Tolosan, France; and Laboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 2594, Centre National de la Recherche Scientifique, 31326 Castanet-Tolosan, France
| | - Wout Boerjan
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium;
| | - Sofie Goormachtig
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
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5
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Dooley J, Tian L, Schonefeldt S, Delghingaro-Augusto V, Garcia-Perez JE, Pasciuto E, Di Marino D, Carr EJ, Oskolkov N, Lyssenko V, Franckaert D, Lagou V, Overbergh L, Vandenbussche J, Allemeersch J, Chabot-Roy G, Dahlstrom JE, Laybutt DR, Petrovsky N, Socha L, Gevaert K, Jetten AM, Lambrechts D, Linterman MA, Goodnow CC, Nolan CJ, Lesage S, Schlenner SM, Liston A. Genetic predisposition for beta cell fragility underlies type 1 and type 2 diabetes. Nat Genet 2016; 48:519-27. [PMID: 26998692 DOI: 10.1038/ng.3531] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/26/2016] [Indexed: 12/12/2022]
Abstract
Type 1 (T1D) and type 2 (T2D) diabetes share pathophysiological characteristics, yet mechanistic links have remained elusive. T1D results from autoimmune destruction of pancreatic beta cells, whereas beta cell failure in T2D is delayed and progressive. Here we find a new genetic component of diabetes susceptibility in T1D non-obese diabetic (NOD) mice, identifying immune-independent beta cell fragility. Genetic variation in Xrcc4 and Glis3 alters the response of NOD beta cells to unfolded protein stress, enhancing the apoptotic and senescent fates. The same transcriptional relationships were observed in human islets, demonstrating the role of beta cell fragility in genetic predisposition to diabetes.
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Affiliation(s)
- James Dooley
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Lei Tian
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Susann Schonefeldt
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | | | - Josselyn E Garcia-Perez
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Emanuela Pasciuto
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Daniele Di Marino
- Department of Informatics, Università della Svizzera Italiana, Lugano, Switzerland
| | - Edward J Carr
- Lymphocyte Signaling and Development Institute Strategic Programme, Babraham Institute, Cambridge, UK
| | - Nikolay Oskolkov
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden.,Department of Translational Pathophysiology, Steno Diabetes Center, Gentofte, Denmark
| | - Dean Franckaert
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Vasiliki Lagou
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.,Department of Neurosciences, University of Leuven, Leuven, Belgium
| | - Lut Overbergh
- Department of Clinical and Experimental Medicine, University of Leuven, Leuven, Belgium
| | - Jonathan Vandenbussche
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | - Genevieve Chabot-Roy
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jane E Dahlstrom
- Australian National University Medical School, Canberra, Australian Capital Territory, Australia.,Department of Anatomical Pathology, Canberra Hospital, Garran, Australian Capital Territory, Australia
| | - D Ross Laybutt
- Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Nikolai Petrovsky
- Department of Endocrinology, Flinders University, Adelaide, South Australia, Australia
| | - Luis Socha
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Anton M Jetten
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium.,Department of Oncology, University of Leuven, Leuven, Belgium
| | - Michelle A Linterman
- Lymphocyte Signaling and Development Institute Strategic Programme, Babraham Institute, Cambridge, UK
| | - Chris C Goodnow
- Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Christopher J Nolan
- Australian National University Medical School, Canberra, Australian Capital Territory, Australia.,Department of Endocrinology, Canberra Hospital, Garran, Australian Capital Territory, Australia
| | - Sylvie Lesage
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Susan M Schlenner
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Adrian Liston
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
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6
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Kohout M, Vandenbussche J, Roller A, Tůma J, Bogaerts J, Bultinck P, Herrebout W, Lindner W. Absolute configuration of the antimalarial erythro-mefloquine – vibrational circular dichroism and X-ray diffraction studies of mefloquine and its thiourea derivative. RSC Adv 2016. [DOI: 10.1039/c6ra19367f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The long-standing discussion of the absolute configuration of erythro-mefloquine is revisited, showcasing the strength of a combination of experimental and calculated vibrational circular dichroism spectroscopy.
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Affiliation(s)
- M. Kohout
- Department of Organic Chemistry
- University of Chemistry and Technology Prague
- Technická 5
- 166 28 Prague
- Czech Republic
| | - J. Vandenbussche
- Department of Inorganic and Physical Chemistry
- Ghent University
- 9000 Ghent
- Belgium
| | - A. Roller
- Institute of Inorganic Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - J. Tůma
- Department of Organic Chemistry
- University of Chemistry and Technology Prague
- Technická 5
- 166 28 Prague
- Czech Republic
| | - J. Bogaerts
- Department of Chemistry
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - P. Bultinck
- Department of Inorganic and Physical Chemistry
- Ghent University
- 9000 Ghent
- Belgium
| | - W. Herrebout
- Department of Chemistry
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - W. Lindner
- Institute of Analytical Chemistry
- University of Vienna
- 1090 Vienna
- Austria
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7
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Kelchtermans P, Silva ASC, Argentini A, Staes A, Vandenbussche J, Laukens K, Valkenborg D, Martens L. Open-Source, Platform-Independent Library and Online Scripting Environment for Accessing Thermo Scientific RAW Files. J Proteome Res 2015; 14:4940-3. [DOI: 10.1021/acs.jproteome.5b00778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pieter Kelchtermans
- Medical
Biotechnology Center, VIB, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, 9000 Ghent, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Ana S. C. Silva
- Medical
Biotechnology Center, VIB, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, 9000 Ghent, Belgium
| | - Andrea Argentini
- Medical
Biotechnology Center, VIB, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, 9000 Ghent, Belgium
| | - An Staes
- Medical
Biotechnology Center, VIB, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Jonathan Vandenbussche
- Medical
Biotechnology Center, VIB, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Kris Laukens
- Department
of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Biomedical
Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, 2020 Antwerp, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium
- CFP, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- I-BioStat, Hasselt University, Agoralaan, Building D, 3590 Diepenbeek, Belgium
| | - Lennart Martens
- Medical
Biotechnology Center, VIB, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, 9000 Ghent, Belgium
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8
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Di Michele M, Stes E, Vandermarliere E, Arora R, Astorga-Wells J, Vandenbussche J, van Heerde E, Zubarev R, Bonnet P, Linders JTM, Jacoby E, Brehmer D, Martens L, Gevaert K. Limited Proteolysis Combined with Stable Isotope Labeling Reveals Conformational Changes in Protein (Pseudo)kinases upon Binding Small Molecules. J Proteome Res 2015; 14:4179-93. [PMID: 26293246 DOI: 10.1021/acs.jproteome.5b00282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Likely due to conformational rearrangements, small molecule inhibitors may stabilize the active conformation of protein kinases and paradoxically promote tumorigenesis. We combined limited proteolysis with stable isotope labeling MS to monitor protein conformational changes upon binding of small molecules. Applying this method to the human serine/threonine kinase B-Raf, frequently mutated in cancer, we found that binding of ATP or its nonhydrolyzable analogue AMP-PNP, but not ADP, stabilized the structure of both B-Raf(WT) and B-Raf(V600E). The ATP-competitive type I B-Raf inhibitor vemurafenib and the type II inhibitor sorafenib stabilized the kinase domain (KD) but had distinct effects on the Ras-binding domain. Stabilization of the B-Raf(WT) KD was confirmed by hydrogen/deuterium exchange MS and molecular dynamics simulations. Our results are further supported by cellular assays in which we assessed cell viability and phosphorylation profiles in cells expressing B-Raf(WT) or B-Raf(V600E) in response to vemurafenib or sorafenib. Our data indicate that an overall stabilization of the B-Raf structure by specific inhibitors activates MAPK signaling and increases cell survival, helping to explain clinical treatment failure. We also applied our method to monitor conformational changes upon nucleotide binding of the pseudokinase KSR1, which holds high potential for inhibition in human diseases.
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Affiliation(s)
- Michela Di Michele
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Elien Vandermarliere
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Rohit Arora
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans , Pôle de chimie, Rue de Chartres, 45100 Orléans, France
| | | | - Jonathan Vandenbussche
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Erika van Heerde
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Roman Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Scheelelaberatoriet Scheeles väg 2, SE-171 77 Stockholm, Sweden
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans , Pôle de chimie, Rue de Chartres, 45100 Orléans, France
| | - Joannes T M Linders
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Edgar Jacoby
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Dirk Brehmer
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
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9
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Andries V, Vandepoele K, Staes K, Berx G, Bogaert P, Van Isterdael G, Ginneberge D, Parthoens E, Vandenbussche J, Gevaert K, van Roy F. NBPF1, a tumor suppressor candidate in neuroblastoma, exerts growth inhibitory effects by inducing a G1 cell cycle arrest. BMC Cancer 2015; 15:391. [PMID: 25958384 PMCID: PMC4440459 DOI: 10.1186/s12885-015-1408-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 04/29/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND NBPF1 (Neuroblastoma Breakpoint Family, member 1) was originally identified in a neuroblastoma patient on the basis of its disruption by a chromosomal translocation t(1;17)(p36.2;q11.2). Considering this genetic defect and the frequent genomic alterations of the NBPF1 locus in several cancer types, we hypothesized that NBPF1 is a tumor suppressor. Decreased expression of NBPF1 in neuroblastoma cell lines with loss of 1p36 heterozygosity and the marked decrease of anchorage-independent clonal growth of DLD1 colorectal carcinoma cells with induced NBPF1 expression further suggest that NBPF1 functions as tumor suppressor. However, little is known about the mechanisms involved. METHODS Expression of NBPF was analyzed in human skin and human cervix by immunohistochemistry. The effects of NBPF1 on the cell cycle were evaluated by flow cytometry. We investigated by real-time quantitative RT-PCR the expression profile of a panel of genes important in cell cycle regulation. Protein levels of CDKN1A-encoded p21(CIP1/WAF1) were determined by western blotting and the importance of p53 was shown by immunofluorescence and by a loss-of-function approach. LC-MS/MS analysis was used to investigate the proteome of DLD1 colon cancer cells with induced NBPF1 expression. Possible biological interactions between the differentially regulated proteins were investigated with the Ingenuity Pathway Analysis tool. RESULTS We show that NBPF is expressed in the non-proliferative suprabasal layers of squamous stratified epithelia of human skin and cervix. Forced expression of NBPF1 in HEK293T cells resulted in a G1 cell cycle arrest that was accompanied by upregulation of the cyclin-dependent kinase inhibitor p21(CIP1/WAF1) in a p53-dependent manner. Additionally, forced expression of NBPF1 in two p53-mutant neuroblastoma cell lines also resulted in a G1 cell cycle arrest and CDKN1A upregulation. However, CDKN1A upregulation by NBPF1 was not observed in the DLD1 cells, which demonstrates that NBPF1 exerts cell-specific effects. In addition, proteome analysis of NBPF1-overexpressing DLD1 cells identified 32 differentially expressed proteins, of which several are implicated in carcinogenesis. CONCLUSIONS We demonstrated that NBPF1 exerts different tumor suppressive effects, depending on the cell line analyzed, and provide new clues into the molecular mechanism of the enigmatic NBPF proteins.
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Affiliation(s)
- Vanessa Andries
- Inflammation Research Center, VIB, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, B-9052, Ghent, Zwijnaarde, Belgium.
| | - Karl Vandepoele
- Inflammation Research Center, VIB, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, B-9052, Ghent, Zwijnaarde, Belgium. .,Laboratory for Molecular Diagnostics - Hematology, Ghent University Hospital, Ghent, Belgium.
| | | | - Geert Berx
- Inflammation Research Center, VIB, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, B-9052, Ghent, Zwijnaarde, Belgium.
| | - Pieter Bogaert
- Inflammation Research Center, VIB, Ghent, Belgium. .,BARC Global Central Laboratory, Ghent, Zwijnaarde, Belgium.
| | - Gert Van Isterdael
- Inflammation Research Center, VIB, Ghent, Belgium. .,Department of Internal Medicine, Ghent University, Ghent, Belgium.
| | | | - Eef Parthoens
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, B-9052, Ghent, Zwijnaarde, Belgium. .,BioImaging Core, VIB, Ghent, Belgium.
| | - Jonathan Vandenbussche
- Department of Medical Protein Research, VIB, Ghent, Belgium. .,Department of Biochemistry, Ghent University, Ghent, Belgium.
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium. .,Department of Biochemistry, Ghent University, Ghent, Belgium.
| | - Frans van Roy
- Inflammation Research Center, VIB, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, B-9052, Ghent, Zwijnaarde, Belgium.
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10
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Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HWP, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJR, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics 2014; 13:1905-13. [PMID: 24760958 PMCID: PMC4125725 DOI: 10.1074/mcp.m113.035907] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 03/13/2014] [Indexed: 12/22/2022] Open
Abstract
Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml.
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Affiliation(s)
- Mathias Walzer
- From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany
| | - Lucia Espona Pernas
- §Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland
| | - Sara Nasso
- ¶Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; §Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland
| | - Wout Bittremieux
- ‖Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; **Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium
| | - Sven Nahnsen
- From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany
| | - Pieter Kelchtermans
- ‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; ¶¶Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol Belgium
| | - Peter Pichler
- ‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Henk W P van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - An Staes
- ‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jonathan Vandenbussche
- ‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Michael Mazanek
- ‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Thomas Taus
- ‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Richard A Scheltema
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom; Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Stephan Aiche
- Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
| | - Dirk Valkenborg
- ¶¶Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol Belgium; I-BioStat, Hasselt University, Belgium; CFP-CeProMa, University of Antwerp, Belgium
| | - Kris Laukens
- ‖Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; **Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Karl Mechtler
- ‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Kris Gevaert
- ‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Oliver Kohlbacher
- From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany
| | - Lennart Martens
- ‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium;
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11
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De Antonellis P, Carotenuto M, Vandenbussche J, De Vita G, Ferrucci V, Medaglia C, Boffa I, Galiero A, Di Somma S, Magliulo D, Aiese N, Alonzi A, Spano D, Liguori L, Chiarolla C, Verrico A, Schulte JH, Mestdagh P, Vandesompele J, Gevaert K, Zollo M. Early targets of miR-34a in neuroblastoma. Mol Cell Proteomics 2014; 13:2114-31. [PMID: 24912852 DOI: 10.1074/mcp.m113.035808] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Several genes encoding for proteins involved in proliferation, invasion, and apoptosis are known to be direct miR-34a targets. Here, we used proteomics to screen for targets of miR-34a in neuroblastoma (NBL), a childhood cancer that originates from precursor cells of the sympathetic nervous system. We examined the effect of miR-34a overexpression using a tetracycline inducible system in two NBL cell lines (SHEP and SH-SY5Y) at early time points of expression (6, 12, and 24 h). Proteome analysis using post-metabolic labeling led to the identification of 2,082 proteins, and among these 186 were regulated (112 proteins down-regulated and 74 up-regulated). Prediction of miR-34a targets via bioinformatics showed that 32 transcripts held miR-34a seed sequences in their 3'-UTR. By combining the proteomics data with Kaplan Meier gene-expression studies, we identified seven new gene products (ALG13, TIMM13, TGM2, ABCF2, CTCF, Ki67, and LYAR) that were correlated with worse clinical outcomes. These were further validated in vitro by 3'-UTR seed sequence regulation. In addition, Michigan Molecular Interactions searches indicated that together these proteins affect signaling pathways that regulate cell cycle and proliferation, focal adhesions, and other cellular properties that overall enhance tumor progression (including signaling pathways such as TGF-β, WNT, MAPK, and FAK). In conclusion, proteome analysis has here identified early targets of miR-34a with relevance to NBL tumorigenesis. Along with the results of previous studies, our data strongly suggest miR-34a as a useful tool for improving the chance of therapeutic success with NBL.
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Affiliation(s)
- Pasqualino De Antonellis
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Marianeve Carotenuto
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Jonathan Vandenbussche
- ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; **Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Gennaro De Vita
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Veronica Ferrucci
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Chiara Medaglia
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Iolanda Boffa
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Alessandra Galiero
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Sarah Di Somma
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Daniela Magliulo
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Nadia Aiese
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Alessandro Alonzi
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Daniela Spano
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Lucia Liguori
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Cristina Chiarolla
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Antonio Verrico
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy; ‡‡Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, 80131 Naples, Italy
| | | | - Pieter Mestdagh
- ¶¶Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Jo Vandesompele
- ¶¶Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Kris Gevaert
- ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; **Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Massimo Zollo
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy; ‖‖Centro di Medicina Trasfusionale, Azienda Ospedaliera Federico II, 80131 Naples, Italy
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12
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Staes A, Vandenbussche J, Demol H, Goethals M, Yilmaz Ş, Hulstaert N, Degroeve S, Kelchtermans P, Martens L, Gevaert K. Asn3, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS. Anal Chem 2013; 85:11054-60. [PMID: 24134513 DOI: 10.1021/ac4027093] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of internal calibrants (the so-called lock mass approach) provides much greater accuracy in mass spectrometry based proteomics. However, the polydimethylcyclosiloxane (PCM) peaks commonly used for this purpose are quite unreliable, leading to missing calibrant peaks in spectra and correspondingly lower mass measurement accuracy. Therefore, we here introduce a universally applicable and robust internal calibrant, the tripeptide Asn3. We show that Asn3 is a substantial improvement over PCM both in terms of consistent detection and resulting mass measurement accuracy. Asn3 is also very easy to adopt in the lab, as it requires only minor adjustments to the analytical setup.
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Affiliation(s)
- An Staes
- Department of Medical Protein Research, VIB , B-9000 Ghent, Belgium
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