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Kennedy KE, Kerlero de Rosbo N, Uccelli A, Cellerino M, Ivaldi F, Contini P, De Palma R, Harbo HF, Berge T, Bos SD, Høgestøl EA, Brune-Ingebretsen S, de Rodez Benavent SA, Paul F, Brandt AU, Bäcker-Koduah P, Behrens J, Kuchling J, Asseyer S, Scheel M, Chien C, Zimmermann H, Motamedi S, Kauer-Bonin J, Saez-Rodriguez J, Rinas M, Alexopoulos LG, Andorra M, Llufriu S, Saiz A, Blanco Y, Martinez-Heras E, Solana E, Pulido-Valdeolivas I, Martinez-Lapiscina EH, Garcia-Ojalvo J, Villoslada P. Multiscale networks in multiple sclerosis. PLoS Comput Biol 2024; 20:e1010980. [PMID: 38329927 PMCID: PMC10852301 DOI: 10.1371/journal.pcbi.1010980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 12/12/2023] [Indexed: 02/10/2024] Open
Abstract
Complex diseases such as Multiple Sclerosis (MS) cover a wide range of biological scales, from genes and proteins to cells and tissues, up to the full organism. In fact, any phenotype for an organism is dictated by the interplay among these scales. We conducted a multilayer network analysis and deep phenotyping with multi-omics data (genomics, phosphoproteomics and cytomics), brain and retinal imaging, and clinical data, obtained from a multicenter prospective cohort of 328 patients and 90 healthy controls. Multilayer networks were constructed using mutual information for topological analysis, and Boolean simulations were constructed using Pearson correlation to identified paths within and among all layers. The path more commonly found from the Boolean simulations connects protein MK03, with total T cells, the thickness of the retinal nerve fiber layer (RNFL), and the walking speed. This path contains nodes involved in protein phosphorylation, glial cell differentiation, and regulation of stress-activated MAPK cascade, among others. Specific paths identified were subsequently analyzed by flow cytometry at the single-cell level. Combinations of several proteins (GSK3AB, HSBP1 or RS6) and immune cells (Th17, Th1 non-classic, CD8, CD8 Treg, CD56 neg, and B memory) were part of the paths explaining the clinical phenotype. The advantage of the path identified from the Boolean simulations is that it connects information about these known biological pathways with the layers at higher scales (retina damage and disability). Overall, the identified paths provide a means to connect the molecular aspects of MS with the overall phenotype.
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Affiliation(s)
- Keith E. Kennedy
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicole Kerlero de Rosbo
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
- TomaLab, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche (CNR), Rome, Italy
| | - Antonio Uccelli
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Maria Cellerino
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Federico Ivaldi
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Paola Contini
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Raffaele De Palma
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Hanne F. Harbo
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Tone Berge
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | - Steffan D. Bos
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Einar A. Høgestøl
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Synne Brune-Ingebretsen
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Sigrid A. de Rodez Benavent
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Friedemann Paul
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Alexander U. Brandt
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
- Department of Neurology, University of California, Irvine, California, United States of America
| | - Priscilla Bäcker-Koduah
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Janina Behrens
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Joseph Kuchling
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Susanna Asseyer
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Michael Scheel
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Claudia Chien
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Hanna Zimmermann
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Seyedamirhosein Motamedi
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Josef Kauer-Bonin
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Melanie Rinas
- Institute for Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Leonidas G. Alexopoulos
- ProtATonce Ltd, Athens, Greece
- School of Mechanical Engineering, National Technical University of Athens, Zografou, Greece
| | - Magi Andorra
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Sara Llufriu
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Albert Saiz
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Yolanda Blanco
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Eloy Martinez-Heras
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Elisabeth Solana
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Irene Pulido-Valdeolivas
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Elena H. Martinez-Lapiscina
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Pablo Villoslada
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Neurology, Hospital del Mar Research Institute, Barcelona, Spain
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Malagarriga D, García-Vellisca MA, Villa AEP, Buldú JM, García-Ojalvo J, Pons AJ. Synchronization-based computation through networks of coupled oscillators. Front Comput Neurosci 2015; 9:97. [PMID: 26300765 PMCID: PMC4523791 DOI: 10.3389/fncom.2015.00097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/14/2015] [Indexed: 11/13/2022] Open
Abstract
The mesoscopic activity of the brain is strongly dynamical, while at the same time exhibits remarkable computational capabilities. In order to examine how these two features coexist, here we show that the patterns of synchronized oscillations displayed by networks of neural mass models, representing cortical columns, can be used as substrates for Boolean-like computations. Our results reveal that the same neural mass network may process different combinations of dynamical inputs as different logical operations or combinations of them. This dynamical feature of the network allows it to process complex inputs in a very sophisticated manner. The results are reproduced experimentally with electronic circuits of coupled Chua oscillators, showing the robustness of this kind of computation to the intrinsic noise and parameter mismatch of the coupled oscillators. We also show that the information-processing capabilities of coupled oscillations go beyond the simple juxtaposition of logic gates.
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Affiliation(s)
- Daniel Malagarriga
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya Terrassa, Spain ; Neuroheuristic Research Group, HEC Lausanne, University of Lausanne Lausanne, Switzerland
| | - Mariano A García-Vellisca
- Laboratory of Biological Networks, Center for Biomedical Technology, Universidad Politécnica de Madrid Madrid, Spain
| | - Alessandro E P Villa
- Neuroheuristic Research Group, HEC Lausanne, University of Lausanne Lausanne, Switzerland
| | - Javier M Buldú
- Laboratory of Biological Networks, Center for Biomedical Technology, Universidad Politécnica de Madrid Madrid, Spain ; Complex Systems Group and GISC, Universidad Rey Juan Carlos Madrid, Spain
| | - Jordi García-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park Barcelona, Spain
| | - Antonio J Pons
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya Terrassa, Spain
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Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC SYSTEMS BIOLOGY 2013; 7:135. [PMID: 24321545 PMCID: PMC3892043 DOI: 10.1186/1752-0509-7-135] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/26/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. RESULTS We present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. CONCLUSIONS SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.
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Affiliation(s)
- Claudine Chaouiya
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Duncan Bérenguier
- Institut de Mathématiques de Luminy, Campus de Luminy, Case 907, 13288 Marseille Cedex 9, France
| | - Sarah M Keating
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aurélien Naldi
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Martijn P van Iersel
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicolas Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Andreas Dräger
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany
| | - Finja Büchel
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany
| | - Thomas Cokelaer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bryan Kowal
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Benjamin Wicks
- College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julien Dorier
- Swiss-Prot & Vital-IT group, SIB- Swiss Institute of Bioinformatics, Center for Integrative Genomics, University of Lausanne, Quartier Sorge - Batiment Genopode, CH-1015 Lausanne, Switzerland
| | - Michel Page
- INRIA Grenoble – Rhône-Alpes, 655 avenue de l’Europe, Montbonnot, 38334 Saint-Ismier Cedex, France
- IAE Grenoble, Université Pierre-Mendès-France, Domaine universitaire BP 47, 38040 Grenoble Cedex 9, France
| | - Pedro T Monteiro
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
- Instituto de Engenharia de Sistemas e Computadores - Investigação e Desenvolvimento (INESC-ID), Rua Alves Redol 9, 1000-029 Lisbon, Portugal
| | - Axel von Kamp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany
| | - Ioannis Xenarios
- Swiss-Prot & Vital-IT group, SIB- Swiss Institute of Bioinformatics, Center for Integrative Genomics, University of Lausanne, Quartier Sorge - Batiment Genopode, CH-1015 Lausanne, Switzerland
| | - Hidde de Jong
- INRIA Grenoble – Rhône-Alpes, 655 avenue de l’Europe, Montbonnot, 38334 Saint-Ismier Cedex, France
| | - Michael Hucka
- Computing and Mathematical sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany
| | - Denis Thieffry
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS) - UMR CNRS 8197 - INSERM 1024 46 rue d’Ulm, 75230 Paris Cedex 05, France
| | - Nicolas Le Novère
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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