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Mishra V, Re DB, Le Verche V, Alvarez MJ, Vasciaveo A, Jacquier A, Doulias PT, Greco TM, Nizzardo M, Papadimitriou D, Nagata T, Rinchetti P, Perez-Torres EJ, Politi KA, Ikiz B, Clare K, Than ME, Corti S, Ischiropoulos H, Lotti F, Califano A, Przedborski S. Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow. Nat Commun 2020; 11:5579. [PMID: 33149111 PMCID: PMC7642391 DOI: 10.1038/s41467-020-19177-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/02/2020] [Indexed: 12/31/2022] Open
Abstract
Cell-to-cell communications are critical determinants of pathophysiological phenotypes, but methodologies for their systematic elucidation are lacking. Herein, we propose an approach for the Systematic Elucidation and Assessment of Regulatory Cell-to-cell Interaction Networks (SEARCHIN) to identify ligand-mediated interactions between distinct cellular compartments. To test this approach, we selected a model of amyotrophic lateral sclerosis (ALS), in which astrocytes expressing mutant superoxide dismutase-1 (mutSOD1) kill wild-type motor neurons (MNs) by an unknown mechanism. Our integrative analysis that combines proteomics and regulatory network analysis infers the interaction between astrocyte-released amyloid precursor protein (APP) and death receptor-6 (DR6) on MNs as the top predicted ligand-receptor pair. The inferred deleterious role of APP and DR6 is confirmed in vitro in models of ALS. Moreover, the DR6 knockdown in MNs of transgenic mutSOD1 mice attenuates the ALS-like phenotype. Our results support the usefulness of integrative, systems biology approach to gain insights into complex neurobiological disease processes as in ALS and posit that the proposed methodology is not restricted to this biological context and could be used in a variety of other non-cell-autonomous communication mechanisms.
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Affiliation(s)
- Vartika Mishra
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Spark Therapeutics, 3737 Market Street, Philadelphia, PA, 19104, USA
| | - Diane B Re
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Department of Environmental Health Sciences, Columbia University, New York, NY, 10032, USA
| | - Virginia Le Verche
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Center for Gene Therapy, City of Hope, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- DarwinHealth Inc., New York, NY, 10032, USA
| | - Alessandro Vasciaveo
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Arnaud Jacquier
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217 - Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Paschalis-Tomas Doulias
- Department of Pediatrics, Children's Hospital of Philadelphia Research Institute and the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Todd M Greco
- Department of Pediatrics, Children's Hospital of Philadelphia Research Institute and the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Molecular Biology, Princeton University, Princeton, USA
| | - Monica Nizzardo
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Dimitra Papadimitriou
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Henry Dunant Hospital, BRFAA, Athens, Greece
| | - Tetsuya Nagata
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Paola Rinchetti
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Eduardo J Perez-Torres
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
| | - Kristin A Politi
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
| | - Burcin Ikiz
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
| | - Kevin Clare
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
- New York Medical College, Valhalla, NY, 10595, USA
| | - Manuel E Than
- Protein Crystallography Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745, Jena, Germany
| | - Stefania Corti
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Harry Ischiropoulos
- Department of Pediatrics, Children's Hospital of Philadelphia Research Institute and the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Francesco Lotti
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA
| | - Andrea Califano
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA.
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- J.P. Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| | - Serge Przedborski
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
- Center for Motor Neuron Biology and Diseases, Columbia University, New York, NY, 10032, USA.
- Departments of Neurology and Neuroscience, Columbia University, New York, NY, 10032, USA.
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