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Niarakis A, Laubenbacher R, An G, Ilan Y, Fisher J, Flobak Å, Reiche K, Rodríguez Martínez M, Geris L, Ladeira L, Veschini L, Blinov ML, Messina F, Fonseca LL, Ferreira S, Montagud A, Noël V, Marku M, Tsirvouli E, Torres MM, Harris LA, Sego TJ, Cockrell C, Shick AE, Balci H, Salazar A, Rian K, Hemedan AA, Esteban-Medina M, Staumont B, Hernandez-Vargas E, Martis B S, Madrid-Valiente A, Karampelesis P, Sordo Vieira L, Harlapur P, Kulesza A, Nikaein N, Garira W, Malik Sheriff RS, Thakar J, Tran VDT, Carbonell-Caballero J, Safaei S, Valencia A, Zinovyev A, Glazier JA. Immune digital twins for complex human pathologies: applications, limitations, and challenges. NPJ Syst Biol Appl 2024; 10:141. [PMID: 39616158 PMCID: PMC11608242 DOI: 10.1038/s41540-024-00450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 09/27/2024] [Indexed: 12/06/2024] Open
Abstract
Digital twins represent a key technology for precision health. Medical digital twins consist of computational models that represent the health state of individual patients over time, enabling optimal therapeutics and forecasting patient prognosis. Many health conditions involve the immune system, so it is crucial to include its key features when designing medical digital twins. The immune response is complex and varies across diseases and patients, and its modelling requires the collective expertise of the clinical, immunology, and computational modelling communities. This review outlines the initial progress on immune digital twins and the various initiatives to facilitate communication between interdisciplinary communities. We also outline the crucial aspects of an immune digital twin design and the prerequisites for its implementation in the clinic. We propose some initial use cases that could serve as "proof of concept" regarding the utility of immune digital technology, focusing on diseases with a very different immune response across spatial and temporal scales (minutes, days, months, years). Lastly, we discuss the use of digital twins in drug discovery and point out emerging challenges that the scientific community needs to collectively overcome to make immune digital twins a reality.
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Affiliation(s)
- Anna Niarakis
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France.
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France.
| | | | - Gary An
- Department of Surgery, University of Vermont Larner College of Medicine, Vermont, USA
| | - Yaron Ilan
- Faculty of Medicine Hebrew University, Hadassah Medical Center, Jerusalem, Israel
| | - Jasmin Fisher
- UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Åsmund Flobak
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- The Cancer Clinic, St Olav's University Hospital, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute of Clinical Immunology, Medical Faculty, University Hospital, University of Leipzig, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden/Leipzig, Germany
| | - María Rodríguez Martínez
- Department of Biomedical Informatics & Data Science, Yale School of Medicine, New Haven, CT, USA
| | - Liesbet Geris
- Prometheus Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Biomechanics Research Unit, GIGA Molecular and Computational Biology, University of Liège, Liège, Belgium
| | - Luiz Ladeira
- Biomechanics Research Unit, GIGA Molecular and Computational Biology, University of Liège, Liège, Belgium
| | - Lorenzo Veschini
- Faculty of Dentistry Oral & Craniofacial Sciences, King's College London, London, UK
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, 47408, USA
| | - Michael L Blinov
- Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, 06030, USA
| | - Francesco Messina
- Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases 'Lazzaro Spallanzani' - I.R.C.C.S., Rome, Italy
| | - Luis L Fonseca
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Sandra Ferreira
- Mathematics Department and Center of Mathematics, University of Beira Interior, Covilhã, Portugal
| | - Arnau Montagud
- Barcelona Supercomputing Center (BSC), Barcelone, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Valencia, Spain
| | - Vincent Noël
- Institut Curie, Université PSL, F-75005, Paris, France
- INSERM, U900, F-75005, Paris, France
- Mines ParisTech, Université PSL, F-75005, Paris, France
| | - Malvina Marku
- Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Eirini Tsirvouli
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marcella M Torres
- Department of Mathematics and Statistics, University of Richmond, Richmond, VA, USA
| | - Leonard A Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
- Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - T J Sego
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Chase Cockrell
- Department of Surgery, University of Vermont Larner College of Medicine, Vermont, USA
| | - Amanda E Shick
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, USA
| | - Hasan Balci
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Albin Salazar
- INRIA Paris/CNRS/École Normale Supérieure/PSL Research University, Paris, France
| | - Kinza Rian
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
| | - Ahmed Abdelmonem Hemedan
- Bioinformatics Core Unit, Luxembourg Centre of Systems Biomedicine LCSB, Luxembourg University, Esch-sur-Alzette, Luxembourg
| | - Marina Esteban-Medina
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
| | - Bernard Staumont
- Biomechanics Research Unit, GIGA Molecular and Computational Biology, University of Liège, Liège, Belgium
| | - Esteban Hernandez-Vargas
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, 83844-1103, USA
| | | | | | | | | | - Pradyumna Harlapur
- Department of Bioengineering, Indian Institute of Science, Bengaluru, India
| | | | - Niloofar Nikaein
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-70182, Örebro, Sweden
- X-HiDE - Exploring Inflammation in Health and Disease Consortium, Örebro University, Örebro, Sweden
| | - Winston Garira
- Multiscale Mathematical Modelling of Living Systems program (M3-LSP), Kimberley, South Africa
- Department of Mathematical Sciences, Sol Plaatje University, Kimberley, South Africa
- Private Bag X5008, Kimberley, 8300, South Africa
| | - Rahuman S Malik Sheriff
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, Cambridge, UK
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Juilee Thakar
- Department of Microbiology & Immunology and Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Van Du T Tran
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Soroush Safaei
- Institute of Biomedical Engineering and Technology, Ghent University, Gent, Belgium
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Barcelone, Spain
- ICREA, 23 Passeig Lluís Companys, 08010, Barcelona, Spain
| | | | - James A Glazier
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, 47408, USA
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