1
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Trepte P, Secker C, Olivet J, Blavier J, Kostova S, Maseko SB, Minia I, Silva Ramos E, Cassonnet P, Golusik S, Zenkner M, Beetz S, Liebich MJ, Scharek N, Schütz A, Sperling M, Lisurek M, Wang Y, Spirohn K, Hao T, Calderwood MA, Hill DE, Landthaler M, Choi SG, Twizere JC, Vidal M, Wanker EE. AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor. Mol Syst Biol 2024; 20:428-457. [PMID: 38467836 PMCID: PMC10987651 DOI: 10.1038/s44320-024-00019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 03/13/2024] Open
Abstract
Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.
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Affiliation(s)
- Philipp Trepte
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
- Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030, Vienna, Austria.
| | - Christopher Secker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
- Zuse Institute Berlin, Berlin, Germany.
| | - Julien Olivet
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Simona Kostova
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Sibusiso B Maseko
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Igor Minia
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
| | - Eduardo Silva Ramos
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Patricia Cassonnet
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique (CNRS), Université de Paris, Paris, France
| | - Sabrina Golusik
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Martina Zenkner
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Stephanie Beetz
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Mara J Liebich
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Nadine Scharek
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Anja Schütz
- Protein Production & Characterization, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Marcel Sperling
- Multifunctional Colloids and Coating, Fraunhofer Institute for Applied Polymer Research (IAP), 14476, Potsdam-Golm, Germany
| | - Michael Lisurek
- Structural Chemistry and Computational Biophysics, Leibniz-Institut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, 13125, Berlin, Germany
| | - Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium.
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
| | - Erich E Wanker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
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2
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Corneillie L, Lemmens I, Weening K, De Meyer A, Van Houtte F, Tavernier J, Meuleman P. Virus-Host Protein Interaction Network of the Hepatitis E Virus ORF2-4 by Mammalian Two-Hybrid Assays. Viruses 2023; 15:2412. [PMID: 38140653 PMCID: PMC10748205 DOI: 10.3390/v15122412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Throughout their life cycle, viruses interact with cellular host factors, thereby influencing propagation, host range, cell tropism and pathogenesis. The hepatitis E virus (HEV) is an underestimated RNA virus in which knowledge of the virus-host interaction network to date is limited. Here, two related high-throughput mammalian two-hybrid approaches (MAPPIT and KISS) were used to screen for HEV-interacting host proteins. Promising hits were examined on protein function, involved pathway(s), and their relation to other viruses. We identified 37 ORF2 hits, 187 for ORF3 and 91 for ORF4. Several hits had functions in the life cycle of distinct viruses. We focused on SHARPIN and RNF5 as candidate hits for ORF3, as they are involved in the RLR-MAVS pathway and interferon (IFN) induction during viral infections. Knocking out (KO) SHARPIN and RNF5 resulted in a different IFN response upon ORF3 transfection, compared to wild-type cells. Moreover, infection was increased in SHARPIN KO cells and decreased in RNF5 KO cells. In conclusion, MAPPIT and KISS are valuable tools to study virus-host interactions, providing insights into the poorly understood HEV life cycle. We further provide evidence for two identified hits as new host factors in the HEV life cycle.
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Affiliation(s)
- Laura Corneillie
- Laboratory of Liver Infectious Diseases, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Irma Lemmens
- VIB-UGent Center for Medical Biotechnology, Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Karin Weening
- Laboratory of Liver Infectious Diseases, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Amse De Meyer
- Laboratory of Liver Infectious Diseases, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Freya Van Houtte
- Laboratory of Liver Infectious Diseases, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- VIB-UGent Center for Medical Biotechnology, Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Philip Meuleman
- Laboratory of Liver Infectious Diseases, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
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3
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Trepte P, Secker C, Kostova S, Maseko SB, Choi SG, Blavier J, Minia I, Ramos ES, Cassonnet P, Golusik S, Zenkner M, Beetz S, Liebich MJ, Scharek N, Schütz A, Sperling M, Lisurek M, Wang Y, Spirohn K, Hao T, Calderwood MA, Hill DE, Landthaler M, Olivet J, Twizere JC, Vidal M, Wanker EE. AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544560. [PMID: 37398436 PMCID: PMC10312674 DOI: 10.1101/2023.06.14.544560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays and AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.
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Affiliation(s)
- Philipp Trepte
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030, Vienna, Austria
| | - Christopher Secker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- Zuse Institute Berlin, Berlin, Germany
| | - Simona Kostova
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Sibusiso B. Maseko
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Igor Minia
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
| | - Eduardo Silva Ramos
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Patricia Cassonnet
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique (CNRS), Université de Paris, Paris, France
| | - Sabrina Golusik
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Martina Zenkner
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Stephanie Beetz
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Mara J. Liebich
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Nadine Scharek
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Anja Schütz
- Protein Production & Characterization, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Marcel Sperling
- Multifunctional Colloids and Coating, Fraunhofer Institute for Applied Polymer Research (IAP), 14476, Potsdam-Golm, Germany
| | - Michael Lisurek
- Structural Chemistry and Computational Biophysics, Leibniz-Institut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Michael A. Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E. Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, 13125, Berlin, Germany
| | - Julien Olivet
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Erich E. Wanker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
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Pérez-Rodríguez D, Penedo MA, Rivera-Baltanás T, Peña-Centeno T, Burkhardt S, Fischer A, Prieto-González JM, Olivares JM, López-Fernández H, Agís-Balboa RC. MiRNA Differences Related to Treatment-Resistant Schizophrenia. Int J Mol Sci 2023; 24:ijms24031891. [PMID: 36768211 PMCID: PMC9916039 DOI: 10.3390/ijms24031891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
Schizophrenia (SZ) is a serious mental disorder that is typically treated with antipsychotic medication. Treatment-resistant schizophrenia (TRS) is the condition where symptoms remain after pharmacological intervention, resulting in long-lasting functional and social impairments. As the identification and treatment of a TRS patient requires previous failed treatments, early mechanisms of detection are needed in order to quicken the access to effective therapy, as well as improve treatment adherence. In this study, we aim to find a microRNA (miRNA) signature for TRS, as well as to shed some light on the molecular pathways potentially involved in this severe condition. To do this, we compared the blood miRNAs of schizophrenia patients that respond to medication and TRS patients, thus obtaining a 16-miRNA TRS profile. Then, we assessed the ability of this signature to separate responders and TRS patients using hierarchical clustering, observing that most of them are grouped correctly (~70% accuracy). We also conducted a network, pathway analysis, and bibliography search to spot molecular pathways potentially altered in TRS. We found that the response to stress seems to be a key factor in TRS and that proteins p53, SIRT1, MDM2, and TRIM28 could be the potential mediators of such responses. Finally, we suggest a molecular pathway potentially regulated by the miRNAs of the TRS profile.
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Affiliation(s)
- Daniel Pérez-Rodríguez
- NeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
| | - Maria Aránzazu Penedo
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Grupo de Neurofarmacología de Las Adicciones y Los Trastornos Degenerativos (NEUROFAN), Universidad CEU San Pablo, 28925 Madrid, Spain
| | - Tania Rivera-Baltanás
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
| | - Tonatiuh Peña-Centeno
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany
| | - José M. Prieto-González
- NeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Servicio de Neurología, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Grupo Trastornos del Movimiento, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - José Manuel Olivares
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Department of Psychiatry, Área Sanitaria de Vigo, 36312 Vigo, Spain
| | - Hugo López-Fernández
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
- CINBIO, Department of Computer Science, ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain
- Correspondence: (H.L.-F.); (R.C.A.-B.)
| | - Roberto Carlos Agís-Balboa
- NeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Servicio de Neurología, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Grupo Trastornos del Movimiento, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
- Correspondence: (H.L.-F.); (R.C.A.-B.)
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5
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An Unexpected Encounter: Respiratory Syncytial Virus Nonstructural Protein 1 Interacts with Mediator Subunit MED25. J Virol 2022; 96:e0129722. [PMID: 36102648 PMCID: PMC9555202 DOI: 10.1128/jvi.01297-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Innate immune responses, including the production of type I and III interferons, play a crucial role in the first line of defense against RSV infection. However, only a poor induction of type I IFNs is observed during RSV infection, suggesting that RSV has evolved mechanisms to prevent type I IFN expression by the infected host cell.
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6
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Lukinović V, Biggar KK. Deconvoluting complex protein interaction networks through reductionist strategies in peptide biochemistry: Modern approaches and research questions. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110616. [PMID: 34000427 DOI: 10.1016/j.cbpb.2021.110616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
Following the decoding of the first human genome, researchers have vastly improved their understanding of cell biology and its regulation. As a result, it has become clear that it is not merely genetic information, but the aberrant changes in the functionality and connectivity of its encoded proteins that drive cell response to periods of stress and external cues. Therefore, proper utilization of refined methods that help to describe protein signalling or regulatory networks (i.e., functional connectivity), can help us understand how change in the signalling landscape effects the cell. However, given the vast complexity in 'how and when' proteins communicate or interact with each other, it is extremely difficult to define, characterize, and understand these interaction networks in a tangible manner. Herein lies the challenge of tackling the functional proteome; its regulation is encoded in multiple layers of interaction, chemical modification and cell compartmentalization. To address and refine simple research questions, modern reductionist strategies in protein biochemistry have successfully used peptide-based experiments; their summation helping to simplify the overall complexity of these protein interaction networks. In this way, peptides are powerful tools used in fundamental research that can be readily applied to comparative biochemical research. Understanding and defining how proteins interact is one of the key aspects towards understanding how the proteome functions. To date, reductionist peptide-based research has helped to address a wide range of proteome-related research questions, including the prediction of enzymes substrates, identification of posttranslational modifications, and the annotation of protein interaction partners. Peptide arrays have been used to identify the binding specificity of reader domains, which are able to recognise the posttranslational modifications; forming dynamic protein interactions that are dependent on modification state. Finally, representing one of the fastest growing classes of inhibitor molecules, peptides are now begin explored as "disruptors" of protein-protein interactions or enzyme activity. Collectively, this review will discuss the use of peptides, peptide arrays, peptide-oriented computational biochemistry as modern reductionist strategies in deconvoluting the functional proteome.
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Affiliation(s)
- Valentina Lukinović
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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7
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Yao Z, Aboualizadeh F, Kroll J, Akula I, Snider J, Lyakisheva A, Tang P, Kotlyar M, Jurisica I, Boxem M, Stagljar I. Split Intein-Mediated Protein Ligation for detecting protein-protein interactions and their inhibition. Nat Commun 2020; 11:2440. [PMID: 32415080 PMCID: PMC7229206 DOI: 10.1038/s41467-020-16299-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Here, to overcome many limitations accompanying current available methods to detect protein-protein interactions (PPIs), we develop a live cell method called Split Intein-Mediated Protein Ligation (SIMPL). In this approach, bait and prey proteins are respectively fused to an intein N-terminal fragment (IN) and C-terminal fragment (IC) derived from a re-engineered split intein GP41-1. The bait/prey binding reconstitutes the intein, which splices the bait and prey peptides into a single intact protein that can be detected by regular protein detection methods such as Western blot analysis and ELISA, serving as readouts of PPIs. The method is robust and can be applied not only in mammalian cell lines but in animal models such as C. elegans. SIMPL demonstrates high sensitivity and specificity, and enables exploration of PPIs in different cellular compartments and tracking of kinetic interactions. Additionally, we establish a SIMPL ELISA platform that enables high-throughput screening of PPIs and their inhibitors. Protein-protein interactions are fundamental to the regulation of protein activity and cellular phyisology. Here the authors present Split Intein-Mediated Protein Ligation, which uses bait and prey proteins fused to intein fragments to generate single intact proteins upon interaction.
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Affiliation(s)
- Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Jason Kroll
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Indira Akula
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Priscilla Tang
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Mike Boxem
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, HR-21000, Split, Croatia.
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8
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Lemmens I, Jansen S, de Rouck S, de Smet AS, Defever D, Neyts J, Dallmeier K, Tavernier J. The Development of RNA-KISS, a Mammalian Three-Hybrid Method to Detect RNA-Protein Interactions in Living Mammalian Cells. J Proteome Res 2020; 19:2529-2538. [PMID: 32216351 DOI: 10.1021/acs.jproteome.0c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA-protein interactions are essential for the regulation of mRNA and noncoding RNA functions and are implicated in many diseases, such as cancer and neurodegenerative disorders. A method that can detect RNA-protein interactions in living mammalian cells on a proteome-wide scale will be an important asset to identify and study these interactions. Here we show that a combination of the mammalian two-hybrid protein-protein detection method KISS (kinase substrate sensor) and the yeast RNA three-hybrid method, utilizing the specific interaction between the MS2 RNA and MS2 coat protein, is capable of detecting RNA-protein interactions in living mammalian cells. For conceptional proof we used the subgenomic flavivirus RNA (sfRNA) of the dengue virus (DENV), a highly structured noncoding RNA derived from the DENV genome known to target host cell proteins involved in innate immunity and antiviral defense, as bait. Using RNA-KISS, we could confirm the previously established interaction between the RNA-binding domain of DDX6 and the DENV sfRNA. Finally, we performed a human proteome-wide screen for DENV sfRNA-binding host factors, identifying several known flavivirus host factors such as DDX6 and PACT, further validating the RNA-KISS method as a robust and high-throughput cell-based RNA-protein interaction screening tool.
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Affiliation(s)
- Irma Lemmens
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Sander Jansen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Steffi de Rouck
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Anne-Sophie de Smet
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Dieter Defever
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Jan Tavernier
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium.,Orionis Biosciences, B-9052 Ghent, Belgium
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9
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Patrício D, Fardilha M. The mammalian two-hybrid system as a powerful tool for high-throughput drug screening. Drug Discov Today 2020; 25:764-771. [PMID: 32032707 DOI: 10.1016/j.drudis.2020.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/13/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are the backbone of signaling pathways, responsible for the basis of cell communication and, when deregulated, several diseases. Consequently, identifying and modulating PPIs can unravel the pathophysiological mechanisms of diseases. The two-hybrid system, particularly the mammalian two-hybrid system (MTH), is an efficient technique to validate PPIs ex vivo. Combining MTH with high-throughput screening has a huge advantage in biomedical research. In this review, we describe methodologies developed from MTH and the role of these adaptations in PPI discovery. We also highlight the powerful contribution of MTH to the identification of disease-related PPIs and its use in the development of potential new drug screens.
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Affiliation(s)
- Daniela Patrício
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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10
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TYK2: An Upstream Kinase of STATs in Cancer. Cancers (Basel) 2019; 11:cancers11111728. [PMID: 31694222 PMCID: PMC6896190 DOI: 10.3390/cancers11111728] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/28/2019] [Accepted: 11/02/2019] [Indexed: 02/07/2023] Open
Abstract
In this review we concentrate on the recent findings describing the oncogenic potential of the protein tyrosine kinase 2 (TYK2). The overview on the current understanding of TYK2 functions in cytokine responses and carcinogenesis focusses on the activation of the signal transducers and activators of transcription (STAT) 3 and 5. Insight gained from loss-of-function (LOF) gene-modified mice and human patients homozygous for Tyk2/TYK2-mutated alleles established the central role in immunological and inflammatory responses. For the description of physiological TYK2 structure/function relationships in cytokine signaling and of overarching molecular and pathologic properties in carcinogenesis, we mainly refer to the most recent reviews. Dysregulated TYK2 activation, aberrant TYK2 protein levels, and gain-of-function (GOF) TYK2 mutations are found in various cancers. We discuss the molecular consequences thereof and briefly describe the molecular means to counteract TYK2 activity under (patho-)physiological conditions by cellular effectors and by pharmacological intervention. For the role of TYK2 in tumor immune-surveillance we refer to the recent Special Issue of Cancers “JAK-STAT Signaling Pathway in Cancer”.
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11
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Shanmugapriya, Othman N, Sasidharan S. Prediction of genes and protein-protein interaction networking for miR-221-5p using bioinformatics analysis. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Choi SG, Olivet J, Cassonnet P, Vidalain PO, Luck K, Lambourne L, Spirohn K, Lemmens I, Dos Santos M, Demeret C, Jones L, Rangarajan S, Bian W, Coutant EP, Janin YL, van der Werf S, Trepte P, Wanker EE, De Las Rivas J, Tavernier J, Twizere JC, Hao T, Hill DE, Vidal M, Calderwood MA, Jacob Y. Maximizing binary interactome mapping with a minimal number of assays. Nat Commun 2019; 10:3907. [PMID: 31467278 PMCID: PMC6715725 DOI: 10.1038/s41467-019-11809-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/02/2019] [Indexed: 02/06/2023] Open
Abstract
Complementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high precision often remains unclear. Here, we propose a framework for binary protein-protein interaction (PPI) mapping based on optimally combining assays and/or assay versions to maximize detection of true positive interactions, while avoiding detection of random protein pairs. We have engineered a novel NanoLuc two-hybrid (N2H) system that integrates 12 different versions, differing by protein expression systems and tagging configurations. The resulting union of N2H versions recovers as many PPIs as 10 distinct assays combined. Thus, to further improve PPI mapping, developing alternative versions of existing assays might be as productive as designing completely new assays. Our findings should be applicable to systematic mapping of other biological landscapes.
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Affiliation(s)
- Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Julien Olivet
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.,Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Groupe Interdisciplinaire de Génomique Appliquée (GIGA Institute), University of Liège, 7 Place du 20 Août, 4000, Liège, Belgium
| | - Patricia Cassonnet
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, Sorbonne Paris Cité, 28 rue du Docteur Roux, 75015, Paris, France
| | - Pierre-Olivier Vidalain
- Équipe Chimie, Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), UMR8601, CNRS, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France
| | - Katja Luck
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Irma Lemmens
- Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie (VIB), 3 Albert Baertsoenkaai, 9000, Ghent, Belgium.,Cytokine Receptor Laboratory (CRL), Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 3 Albert Baertsoenkaai, 9000, Ghent, Belgium
| | - Mélanie Dos Santos
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, Sorbonne Paris Cité, 28 rue du Docteur Roux, 75015, Paris, France
| | - Caroline Demeret
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, Sorbonne Paris Cité, 28 rue du Docteur Roux, 75015, Paris, France
| | - Louis Jones
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, 28 rue du Docteur Roux, 75015, Paris, France
| | - Sudharshan Rangarajan
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Wenting Bian
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Eloi P Coutant
- Département de Biologie Structurale et Chimie, Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523, CNRS, 28 rue du Docteur Roux, 75015, Paris, France
| | - Yves L Janin
- Département de Biologie Structurale et Chimie, Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523, CNRS, 28 rue du Docteur Roux, 75015, Paris, France
| | - Sylvie van der Werf
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, Sorbonne Paris Cité, 28 rue du Docteur Roux, 75015, Paris, France
| | - Philipp Trepte
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, 10 Robert-Rössle-Str., 13125, Berlin, Germany.,Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 3 Dr. Bohr-Gasse, 1030, Vienna, Austria
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, 10 Robert-Rössle-Str., 13125, Berlin, Germany
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Jan Tavernier
- Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie (VIB), 3 Albert Baertsoenkaai, 9000, Ghent, Belgium.,Cytokine Receptor Laboratory (CRL), Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 3 Albert Baertsoenkaai, 9000, Ghent, Belgium
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Groupe Interdisciplinaire de Génomique Appliquée (GIGA Institute), University of Liège, 7 Place du 20 Août, 4000, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA. .,Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
| | - Yves Jacob
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA. .,Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, Sorbonne Paris Cité, 28 rue du Docteur Roux, 75015, Paris, France.
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13
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Young D, Pedre B, Ezeriņa D, De Smet B, Lewandowska A, Tossounian MA, Bodra N, Huang J, Astolfi Rosado L, Van Breusegem F, Messens J. Protein Promiscuity in H 2O 2 Signaling. Antioxid Redox Signal 2019; 30:1285-1324. [PMID: 29635930 DOI: 10.1089/ars.2017.7013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE Decrypting the cellular response to oxidative stress relies on a comprehensive understanding of the redox signaling pathways stimulated under oxidizing conditions. Redox signaling events can be divided into upstream sensing of oxidants, midstream redox signaling of protein function, and downstream transcriptional redox regulation. Recent Advances: A more and more accepted theory of hydrogen peroxide (H2O2) signaling is that of a thiol peroxidase redox relay, whereby protein thiols with low reactivity toward H2O2 are instead oxidized through an oxidative relay with thiol peroxidases. CRITICAL ISSUES These ultrareactive thiol peroxidases are the upstream redox sensors, which form the first cellular port of call for H2O2. Not all redox-regulated interactions between thiol peroxidases and cellular proteins involve a transfer of oxidative equivalents, and the nature of redox signaling is further complicated through promiscuous functions of redox-regulated "moonlighting" proteins, of which the precise cellular role under oxidative stress can frequently be obscured by "polygamous" interactions. An ultimate goal of redox signaling is to initiate a rapid response, and in contrast to prokaryotic oxidant-responsive transcription factors, mammalian systems have developed redox signaling pathways, which intersect both with kinase-dependent activation of transcription factors, as well as direct oxidative regulation of transcription factors through peroxiredoxin (Prx) redox relays. FUTURE DIRECTIONS We highlight that both transcriptional regulation and cell fate can be modulated either through oxidative regulation of kinase pathways, or through distinct redox-dependent associations involving either Prxs or redox-responsive moonlighting proteins with functional promiscuity. These protein associations form systems of crossregulatory networks with multiple nodes of potential oxidative regulation for H2O2-mediated signaling.
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Affiliation(s)
- David Young
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Brandan Pedre
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daria Ezeriņa
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Barbara De Smet
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Aleksandra Lewandowska
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria-Armineh Tossounian
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nandita Bodra
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jingjing Huang
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Leonardo Astolfi Rosado
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank Van Breusegem
- 2 Brussels Center for Redox Biology, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Joris Messens
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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14
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Fumagalli A, Zarca A, Neves M, Caspar B, Hill SJ, Mayor F, Smit MJ, Marin P. CXCR4/ACKR3 Phosphorylation and Recruitment of Interacting Proteins: Key Mechanisms Regulating Their Functional Status. Mol Pharmacol 2019; 96:794-808. [PMID: 30837297 DOI: 10.1124/mol.118.115360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/21/2019] [Indexed: 01/14/2023] Open
Abstract
The C-X-C motif chemokine receptor type 4 (CXCR4) and the atypical chemokine receptor 3 (ACKR3/CXCR7) are class A G protein-coupled receptors (GPCRs). Accumulating evidence indicates that GPCR subcellular localization, trafficking, transduction properties, and ultimately their pathophysiological functions are regulated by both interacting proteins and post-translational modifications. This has encouraged the development of novel techniques to characterize the GPCR interactome and to identify residues subjected to post-translational modifications, with a special focus on phosphorylation. This review first describes state-of-the-art methods for the identification of GPCR-interacting proteins and GPCR phosphorylated sites. In addition, we provide an overview of the current knowledge of CXCR4 and ACKR3 post-translational modifications and an exhaustive list of previously identified CXCR4- or ACKR3-interacting proteins. We then describe studies highlighting the importance of the reciprocal influence of CXCR4/ACKR3 interactomes and phosphorylation states. We also discuss their impact on the functional status of each receptor. These studies suggest that deeper knowledge of the CXCR4/ACKR3 interactomes along with their phosphorylation and ubiquitination status would shed new light on their regulation and pathophysiological functions.
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Affiliation(s)
- Amos Fumagalli
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
| | - Aurélien Zarca
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
| | - Maria Neves
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
| | - Birgit Caspar
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
| | - Stephen J Hill
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
| | - Federico Mayor
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
| | - Martine J Smit
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
| | - Philippe Marin
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France (A.F., P.M.); Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (A.Z., M.J.S.); Departamento de Biología Molecular and Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Madrid, Spain (M.N., F.M.); CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (M.N., F.M.); and Division of Physiology, Pharmacology and Neuroscience, Medical School, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (B.C., S.J.H.)
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15
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Zabeau L, Wauman J, Dam J, Van Lint S, Burg E, De Geest J, Rogge E, Silva A, Jockers R, Tavernier J. A novel leptin receptor antagonist uncouples leptin's metabolic and immune functions. Cell Mol Life Sci 2019; 76:1201-1214. [PMID: 30659329 PMCID: PMC11105424 DOI: 10.1007/s00018-019-03004-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/28/2018] [Accepted: 01/02/2019] [Indexed: 12/19/2022]
Abstract
Leptin links body energy stores to high energy demanding processes like reproduction and immunity. Based on leptin's role in autoimmune diseases and cancer, several leptin and leptin receptor (LR) antagonists have been developed, but these intrinsically lead to unwanted weight gain. Here, we report on the uncoupling of leptin's metabolic and immune functions based on the cross talk with the epidermal growth factor receptor (EGFR). We show that both receptors spontaneously interact and, remarkably, that this complex can partially overrule the lack of LR activation by a leptin antagonistic mutein. Moreover, this leptin mutant induces EGFR phosphorylation comparable to wild-type leptin. Exploiting this non-canonical leptin signalling pathway, we identified a camelid single-domain antibody that selectively inhibits this LR-EGFR cross talk without interfering with homotypic LR signalling. Administration in vivo showed that this single-domain antibody did not interfere with leptin's metabolic functions, but could reverse the leptin-driven protection against starvation-induced thymic and splenic atrophy. These findings offer new opportunities for the design and clinical application of selective leptin and LR antagonists that avoid unwanted metabolic side effects.
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Affiliation(s)
- Lennart Zabeau
- Faculty of Medicine and Health Sciences, VIB-UGent Center for Medical Biotechnology, Flanders Institute for Biotechnology, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Joris Wauman
- Faculty of Medicine and Health Sciences, VIB-UGent Center for Medical Biotechnology, Flanders Institute for Biotechnology, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Julie Dam
- Inserm U1016, CNRS UMR 8104, Univ. Paris Descartes, Sorbonne Paris Cité, Institut Cochin, 22 rue Méchain, 75014, Paris, France
| | - Sandra Van Lint
- Faculty of Medicine and Health Sciences, VIB-UGent Center for Medical Biotechnology, Flanders Institute for Biotechnology, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Elianne Burg
- Faculty of Medicine and Health Sciences, VIB-UGent Center for Medical Biotechnology, Flanders Institute for Biotechnology, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Jennifer De Geest
- Faculty of Medicine and Health Sciences, VIB-UGent Center for Medical Biotechnology, Flanders Institute for Biotechnology, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Elke Rogge
- Faculty of Medicine and Health Sciences, VIB-UGent Center for Medical Biotechnology, Flanders Institute for Biotechnology, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Anisia Silva
- Inserm U1016, CNRS UMR 8104, Univ. Paris Descartes, Sorbonne Paris Cité, Institut Cochin, 22 rue Méchain, 75014, Paris, France
| | - Ralf Jockers
- Inserm U1016, CNRS UMR 8104, Univ. Paris Descartes, Sorbonne Paris Cité, Institut Cochin, 22 rue Méchain, 75014, Paris, France
| | - Jan Tavernier
- Faculty of Medicine and Health Sciences, VIB-UGent Center for Medical Biotechnology, Flanders Institute for Biotechnology, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium.
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16
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Yakubu RR, Nieves E, Weiss LM. The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:169-198. [PMID: 31347048 DOI: 10.1007/978-3-030-15950-4_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass Spectrometry (MS) has revolutionized the way we study biomolecules, especially proteins, their interactions and posttranslational modifications (PTM). As such MS has established itself as the leading tool for the analysis of PTMs mainly because this approach is highly sensitive, amenable to high throughput and is capable of assigning PTMs to specific sites in the amino acid sequence of proteins and peptides. Along with the advances in MS methodology there have been improvements in biochemical, genetic and cell biological approaches to mapping the interactome which are discussed with consideration for both the practical and technical considerations of these techniques. The interactome of a species is generally understood to represent the sum of all potential protein-protein interactions. There are still a number of barriers to the elucidation of the human interactome or any other species as physical contact between protein pairs that occur by selective molecular docking in a particular spatiotemporal biological context are not easily captured and measured.PTMs massively increase the complexity of organismal proteomes and play a role in almost all aspects of cell biology, allowing for fine-tuning of protein structure, function and localization. There are an estimated 300 PTMS with a predicted 5% of the eukaryotic genome coding for enzymes involved in protein modification, however we have not yet been able to reliably map PTM proteomes due to limitations in sample preparation, analytical techniques, data analysis, and the substoichiometric and transient nature of some PTMs. Improvements in proteomic and mass spectrometry methods, as well as sample preparation, have been exploited in a large number of proteome-wide surveys of PTMs in many different organisms. Here we focus on previously published global PTM proteome studies in the Apicomplexan parasites T. gondii and P. falciparum which offer numerous insights into the abundance and function of each of the studied PTM in the Apicomplexa. Integration of these datasets provide a more complete picture of the relative importance of PTM and crosstalk between them and how together PTM globally change the cellular biology of the Apicomplexan protozoa. A multitude of techniques used to investigate PTMs, mostly techniques in MS-based proteomics, are discussed for their ability to uncover relevant biological function.
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Affiliation(s)
- Rama R Yakubu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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17
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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18
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Proteomics. Mol Biol 2019. [DOI: 10.1016/b978-0-12-813288-3.00015-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Abstract
Discovering and characterizing protein–protein interactions (PPI s) that contribute to cellular homeostasis, development, and disease is a key priority in proteomics. Numerous assays for protein–protein interactions have been developed, but each one comes with its own strengths, weaknesses, and false‐positive/false‐negative rates. Therefore, it seems rather intuitive that combining multiple assays is beneficial for robust and reliable discovery of interactions. Along those lines, in their recent study, Wanker and colleagues (Trepte et al , 2018 ) combined two complementary and quantitative interaction assays in one pot. One assay is luminescence‐based and depends on protein proximity in living cells, while the other relies on formation of more stable complexes detected by co‐precipitation with a luminescence‐based readout, which facilitates confident identification and quantitation of interactions in high throughput.
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Affiliation(s)
- Mikko Taipale
- Department of Molecular GeneticsDonnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
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20
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Trepte P, Kruse S, Kostova S, Hoffmann S, Buntru A, Tempelmeier A, Secker C, Diez L, Schulz A, Klockmeier K, Zenkner M, Golusik S, Rau K, Schnoegl S, Garner CC, Wanker EE. LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells. Mol Syst Biol 2018; 14:e8071. [PMID: 29997244 PMCID: PMC6039870 DOI: 10.15252/msb.20178071] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 06/08/2018] [Accepted: 06/15/2018] [Indexed: 12/12/2022] Open
Abstract
Information on protein-protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double-readout bioluminescence-based two-hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence-based co-precipitation (LuC). The double-readout procedure detects interactions with higher sensitivity than traditional single-readout methods and is broadly applicable, for example, for detecting the effects of small molecules or disease-causing mutations on PPIs. Applying LuTHy in a focused screen, we identified 42 interactions for the presynaptic chaperone CSPα, causative to adult-onset neuronal ceroid lipofuscinosis (ANCL), a progressive neurodegenerative disease. Nearly 50% of PPIs were found to be affected when studying the effect of the disease-causing missense mutations L115R and ∆L116 in CSPα with LuTHy. Our study presents a robust, sensitive research tool with high utility for investigating the molecular mechanisms by which disease-associated mutations impair protein activity in biological systems.
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Affiliation(s)
- Philipp Trepte
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sabrina Kruse
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Simona Kostova
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sheila Hoffmann
- Synaptopathy, German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Alexander Buntru
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Anne Tempelmeier
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
- Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Lisa Diez
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Aline Schulz
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Konrad Klockmeier
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sabrina Golusik
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Kirstin Rau
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Craig C Garner
- Synaptopathy, German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
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21
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Abstract
Comprehensive identification of direct, physical interactions between biological macromolecules, such as protein-protein, protein-DNA, and protein-RNA interactions, is critical for our understanding of the function of gene products as well as the global organization and interworkings of various molecular machines within the cell. The accurate and comprehensive detection of direct interactions, however, remains a huge challenge due to the inherent structural complexity arising from various post-transcriptional and translational modifications coupled with huge heterogeneity in concentration, affinity, and subcellular location differences existing for any interacting molecules. This has created a need for developing multiple orthogonal and complementary assays for detecting various types of biological interactions. In this introduction, we discuss the methods developed for measuring different types of molecular interactions with an emphasis on direct protein-protein interactions, critical issues for generating high-quality interactome datasets, and the insights into biological networks and human diseases that current interaction mapping efforts provide. Further, we will discuss what future might lie ahead for the continued evolution of two-hybrid methods and the role of interactomics for expanding the advancement of biomedical science.
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Affiliation(s)
- Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Aaron Richardson
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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22
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KISS: A Mammalian Two-Hybrid Method for In Situ Analysis of Protein-Protein Interactions. Methods Mol Biol 2018; 1794:269-278. [PMID: 29855964 DOI: 10.1007/978-1-4939-7871-7_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
KISS (KInase Substrate Sensor) is a recently developed two-hybrid technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges. Here, we describe a detailed step-by-step protocol for the detection of an interaction between two proteins of interest using KISS.
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23
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Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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24
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Hess GT, Tycko J, Yao D, Bassik MC. Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes. Mol Cell 2017; 68:26-43. [PMID: 28985508 PMCID: PMC5997582 DOI: 10.1016/j.molcel.2017.09.029] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022]
Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - David Yao
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA.
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25
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Gagarinova A, Phanse S, Cygler M, Babu M. Insights from protein-protein interaction studies on bacterial pathogenesis. Expert Rev Proteomics 2017; 14:779-797. [DOI: 10.1080/14789450.2017.1365603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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26
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Kashima D, Kawade R, Nagamune T, Kawahara M. A Chemically Inducible Helper Module for Detecting Protein–Protein Interactions with Tunable Sensitivity Based on KIPPIS. Anal Chem 2017; 89:4824-4830. [DOI: 10.1021/acs.analchem.6b04063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Daiki Kashima
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Raiji Kawade
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and
Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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27
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Lievens S, Van der Heyden J, Masschaele D, De Ceuninck L, Petta I, Gupta S, De Puysseleyr V, Vauthier V, Lemmens I, De Clercq DJH, Defever D, Vanderroost N, De Smet AS, Eyckerman S, Van Calenbergh S, Martens L, De Bosscher K, Libert C, Hill DE, Vidal M, Tavernier J. Proteome-scale Binary Interactomics in Human Cells. Mol Cell Proteomics 2016; 15:3624-3639. [PMID: 27803151 DOI: 10.1074/mcp.m116.061994] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/23/2016] [Indexed: 12/11/2022] Open
Abstract
Because proteins are the main mediators of most cellular processes they are also prime therapeutic targets. Identifying physical links among proteins and between drugs and their protein targets is essential in order to understand the mechanisms through which both proteins themselves and the molecules they are targeted with act. Thus, there is a strong need for sensitive methods that enable mapping out these biomolecular interactions. Here we present a robust and sensitive approach to screen proteome-scale collections of proteins for binding to proteins or small molecules using the well validated MAPPIT (Mammalian Protein-Protein Interaction Trap) and MASPIT (Mammalian Small Molecule-Protein Interaction Trap) assays. Using high-density reverse transfected cell microarrays, a close to proteome-wide collection of human ORF clones can be screened for interactors at high throughput. The versatility of the platform is demonstrated through several examples. With MAPPIT, we screened a 15k ORF library for binding partners of RNF41, an E3 ubiquitin protein ligase implicated in receptor sorting, identifying known and novel interacting proteins. The potential related to the fact that MAPPIT operates in living human cells is illustrated in a screen where the protein collection is scanned for interactions with the glucocorticoid receptor (GR) in its unliganded versus dexamethasone-induced activated state. Several proteins were identified the interaction of which is modulated upon ligand binding to the GR, including a number of previously reported GR interactors. Finally, the screening technology also enables detecting small molecule target proteins, which in many drug discovery programs represents an important hurdle. We show the efficiency of MASPIT-based target profiling through screening with tamoxifen, a first-line breast cancer drug, and reversine, an investigational drug with interesting dedifferentiation and antitumor activity. In both cases, cell microarray screens yielded known and new potential drug targets highlighting the utility of the technology beyond fundamental biology.
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Affiliation(s)
- Sam Lievens
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - José Van der Heyden
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Delphine Masschaele
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Leentje De Ceuninck
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Ioanna Petta
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium.,‖Inflammation Research Center, VIB, Ghent, Belgium.,**Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Surya Gupta
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Veronic De Puysseleyr
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Virginie Vauthier
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | - Dieter Defever
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Nele Vanderroost
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Anne-Sophie De Smet
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | - Lennart Martens
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Claude Libert
- ‖Inflammation Research Center, VIB, Ghent, Belgium.,**Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - David E Hill
- ‡‡Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,§§Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Marc Vidal
- ‡‡Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,§§Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jan Tavernier
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium; .,§Department of Biochemistry, Ghent University, Ghent, Belgium
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28
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De Clercq DJH, Tavernier J, Lievens S, Van Calenbergh S. Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling. ACS Chem Biol 2016; 11:2075-90. [PMID: 27267544 DOI: 10.1021/acschembio.5b00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
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Affiliation(s)
- Dries J. H. De Clercq
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Lievens
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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29
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Ivan T, Enkvist E, Viira B, Manoharan GB, Raidaru G, Pflug A, Alam KA, Zaccolo M, Engh RA, Uri A. Bifunctional Ligands for Inhibition of Tight-Binding Protein-Protein Interactions. Bioconjug Chem 2016; 27:1900-10. [PMID: 27389935 DOI: 10.1021/acs.bioconjchem.6b00293] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The acknowledged potential of small-molecule therapeutics targeting disease-related protein-protein interactions (PPIs) has promoted active research in this field. The strategy of using small molecule inhibitors (SMIs) to fight strong (tight-binding) PPIs tends to fall short due to the flat and wide interfaces of PPIs. Here we propose a biligand approach for disruption of strong PPIs. The potential of this approach was realized for disruption of the tight-binding (KD = 100 pM) tetrameric holoenzyme of cAMP-dependent protein kinase (PKA). Supported by X-ray analysis of cocrystals, bifunctional inhibitors (ARC-inhibitors) were constructed that simultaneously associated with both the ATP-pocket and the PPI interface area of the catalytic subunit of PKA (PKAc). Bifunctional inhibitor ARC-1411, possessing a KD value of 3 pM toward PKAc, induced the dissociation of the PKA holoenzyme with a low-nanomolar IC50, whereas the ATP-competitive inhibitor H89 bound to the PKA holoenzyme without disruption of the protein tetramer.
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Affiliation(s)
- Taavi Ivan
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | - Birgit Viira
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | | | - Gerda Raidaru
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | - Alexander Pflug
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø , N-9019 Tromsø, Norway
| | - Kazi Asraful Alam
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø , N-9019 Tromsø, Norway
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford , OX1 3QX Oxford, United Kingdom
| | - Richard Alan Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø , N-9019 Tromsø, Norway
| | - Asko Uri
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
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30
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Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J. Trapping mammalian protein complexes in viral particles. Nat Commun 2016; 7:11416. [PMID: 27122307 PMCID: PMC4853472 DOI: 10.1038/ncomms11416] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 03/22/2016] [Indexed: 01/22/2023] Open
Abstract
Cell lysis is an inevitable step in classical mass spectrometry–based strategies to analyse protein complexes. Complementary lysis conditions, in situ cross-linking strategies and proximal labelling techniques are currently used to reduce lysis effects on the protein complex. We have developed Virotrap, a viral particle sorting approach that obviates the need for cell homogenization and preserves the protein complexes during purification. By fusing a bait protein to the HIV-1 GAG protein, we show that interaction partners become trapped within virus-like particles (VLPs) that bud from mammalian cells. Using an efficient VLP enrichment protocol, Virotrap allows the detection of known binary interactions and MS-based identification of novel protein partners as well. In addition, we show the identification of stimulus-dependent interactions and demonstrate trapping of protein partners for small molecules. Virotrap constitutes an elegant complementary approach to the arsenal of methods to study protein complexes. A large portion of the proteome carries out its cellular function as part of macromolecular complexes. Here the authors describe Virotrap, a novel lysis-free approach for the isolation and identification of biologically relevant protein-protein and small molecule-protein interactions.
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Affiliation(s)
- Sven Eyckerman
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Kevin Titeca
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Emmy Van Quickelberghe
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Eva Cloots
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Annick Verhee
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Noortje Samyn
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Leentje De Ceuninck
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Evy Timmerman
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Delphine De Sutter
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Sam Lievens
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, Ghent B-9000, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Jan Tavernier
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
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31
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Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I. Fundamentals of protein interaction network mapping. Mol Syst Biol 2015; 11:848. [PMID: 26681426 PMCID: PMC4704491 DOI: 10.15252/msb.20156351] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map interactomes. In this review, we highlight basic principles of interactome mapping. Specifically, we discuss the strengths and weaknesses of individual assays, how to select a method appropriate for the problem being studied, and provide general guidelines for carrying out the necessary follow‐up analyses. In addition, we discuss computational methods to predict, map, and visualize interactomes, and provide a summary of some of the most important interactome resources. We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research.
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Affiliation(s)
- Jamie Snider
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Max Kotlyar
- Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada
| | - Punit Saraon
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhong Yao
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada
| | - Igor Stagljar
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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32
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Trepte P, Buntru A, Klockmeier K, Willmore L, Arumughan A, Secker C, Zenkner M, Brusendorf L, Rau K, Redel A, Wanker EE. DULIP: A Dual Luminescence-Based Co-Immunoprecipitation Assay for Interactome Mapping in Mammalian Cells. J Mol Biol 2015; 427:3375-88. [PMID: 26264872 DOI: 10.1016/j.jmb.2015.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 12/30/2022]
Abstract
Mapping of protein-protein interactions (PPIs) is critical for understanding protein function and complex biological processes. Here, we present DULIP, a dual luminescence-based co-immunoprecipitation assay, for systematic PPI mapping in mammalian cells. DULIP is a second-generation luminescence-based PPI screening method for the systematic and quantitative analysis of co-immunoprecipitations using two different luciferase tags. Benchmarking studies with positive and negative PPI reference sets revealed that DULIP allows the detection of interactions with high sensitivity and specificity. Furthermore, the analysis of a PPI reference set with known binding affinities demonstrated that both low- and high-affinity interactions can be detected with DULIP assays. Finally, using the well-characterized interaction between Syntaxin-1 and Munc18, we found that DULIP is capable of detecting the effects of point mutations on interaction strength. Taken together, our studies demonstrate that DULIP is a sensitive and reliable method of great utility for systematic interactome research. It can be applied for interaction screening and validation of PPIs in mammalian cells. Moreover, DULIP permits the specific analysis of mutation-dependent binding patterns.
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Affiliation(s)
- Philipp Trepte
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Alexander Buntru
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Konrad Klockmeier
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Lindsay Willmore
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Anup Arumughan
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Lydia Brusendorf
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Kirstin Rau
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Alexandra Redel
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany.
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33
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Koos B, Cane G, Grannas K, Löf L, Arngården L, Heldin J, Clausson CM, Klaesson A, Hirvonen MK, de Oliveira FMS, Talibov VO, Pham NT, Auer M, Danielson UH, Haybaeck J, Kamali-Moghaddam M, Söderberg O. Proximity-dependent initiation of hybridization chain reaction. Nat Commun 2015; 6:7294. [PMID: 26065580 PMCID: PMC4490387 DOI: 10.1038/ncomms8294] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/24/2015] [Indexed: 11/09/2022] Open
Abstract
Sensitive detection of protein interactions and post-translational modifications of native proteins is a challenge for research and diagnostic purposes. A method for this, which could be used in point-of-care devices and high-throughput screening, should be reliable, cost effective and robust. To achieve this, here we design a method (proxHCR) that combines the need for proximal binding with hybridization chain reaction (HCR) for signal amplification. When two oligonucleotide hairpins conjugated to antibodies bind in close proximity, they can be activated to reveal an initiator sequence. This starts a chain reaction of hybridization events between a pair of fluorophore-labelled oligonucleotide hairpins, generating a fluorescent product. In conclusion, we show the applicability of the proxHCR method for the detection of protein interactions and posttranslational modifications in microscopy and flow cytometry. As no enzymes are needed, proxHCR may be an inexpensive and robust alternative to proximity ligation assays. Proximity ligation assays are a sensitive method for detecting protein interactions, but require the addition of enzymes. Here the authors introduce proxHCR, an enzyme-free method of detecting interactions in close proximity by inducing a hybribization chain reaction (HCR) of fluorescently labelled oligonucleotides.
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Affiliation(s)
- Björn Koos
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Gaëlle Cane
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Karin Grannas
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Liza Löf
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Linda Arngården
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Johan Heldin
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Carl-Magnus Clausson
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Axel Klaesson
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - M Karoliina Hirvonen
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Felipe M S de Oliveira
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Vladimir O Talibov
- Department of Chemistry-BMC, Box 256, Uppsala University, SE-75123 Uppsala, Sweden
| | - Nhan T Pham
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, C H Waddington Building, Max Born Cresent, Kings Buildings, Edinburgh EH9 3BF, UK
| | - Manfred Auer
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, C H Waddington Building, Max Born Cresent, Kings Buildings, Edinburgh EH9 3BF, UK
| | - U Helena Danielson
- Department of Chemistry-BMC, Box 256, Uppsala University, SE-75123 Uppsala, Sweden
| | - Johannes Haybaeck
- Institute of Pathology, Medical University of Graz, A-8036 Graz, Austria
| | - Masood Kamali-Moghaddam
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Ola Söderberg
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
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34
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Application guide for omics approaches to cell signaling. Nat Chem Biol 2015; 11:387-97. [DOI: 10.1038/nchembio.1809] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/31/2015] [Indexed: 01/18/2023]
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35
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De Clercq DJH, Risseeuw MDP, Karalic I, De Smet AS, Defever D, Tavernier J, Lievens S, Van Calenbergh S. Alternative Reagents for Methotrexate as Immobilizing Anchor Moieties in the Optimization of MASPIT: Synthesis and Biological Evaluation. Chembiochem 2015; 16:834-43. [DOI: 10.1002/cbic.201402702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Indexed: 11/10/2022]
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36
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Feng S, Zhou L, Huang C, Xie K, Nice EC. Interactomics: toward protein function and regulation. Expert Rev Proteomics 2015; 12:37-60. [DOI: 10.1586/14789450.2015.1000870] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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37
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Protein interactions in situ. Nat Methods 2014; 11:1093. [DOI: 10.1038/nmeth.3165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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