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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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