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Maggi P, Bulcke CV, Pedrini E, Bugli C, Sellimi A, Wynen M, Stölting A, Mullins WA, Kalaitzidis G, Lolli V, Perrotta G, El Sankari S, Duprez T, Li X, Calabresi PA, van Pesch V, Reich DS, Absinta M. B cell depletion therapy does not resolve chronic active multiple sclerosis lesions. EBioMedicine 2023; 94:104701. [PMID: 37437310 PMCID: PMC10436266 DOI: 10.1016/j.ebiom.2023.104701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Chronic active lesions (CAL) in multiple sclerosis (MS) have been observed even in patients taking high-efficacy disease-modifying therapy, including B-cell depletion. Given that CAL are a major determinant of clinical progression, including progression independent of relapse activity (PIRA), understanding the predicted activity and real-world effects of targeting specific lymphocyte populations is critical for designing next-generation treatments to mitigate chronic inflammation in MS. METHODS We analyzed published lymphocyte single-cell transcriptomes from MS lesions and bioinformatically predicted the effects of depleting lymphocyte subpopulations (including CD20 B-cells) from CAL via gene-regulatory-network machine-learning analysis. Motivated by the results, we performed in vivo MRI assessment of PRL changes in 72 adults with MS, 46 treated with anti-CD20 antibodies and 26 untreated, over ∼2 years. FINDINGS Although only 4.3% of lymphocytes in CAL were CD20 B-cells, their depletion is predicted to affect microglial genes involved in iron/heme metabolism, hypoxia, and antigen presentation. In vivo, tracking 202 PRL (150 treated) and 175 non-PRL (124 treated), none of the treated paramagnetic rims disappeared at follow-up, nor was there a treatment effect on PRL for lesion volume, magnetic susceptibility, or T1 time. PIRA occurred in 20% of treated patients, more frequently in those with ≥4 PRL (p = 0.027). INTERPRETATION Despite predicted effects on microglia-mediated inflammatory networks in CAL and iron metabolism, anti-CD20 therapies do not fully resolve PRL after 2-year MRI follow up. Limited tissue turnover of B-cells, inefficient passage of anti-CD20 antibodies across the blood-brain-barrier, and a paucity of B-cells in CAL could explain our findings. FUNDING Intramural Research Program of NINDS, NIH; NINDS grants R01NS082347 and R01NS082347; Dr. Miriam and Sheldon G. Adelson Medical Research Foundation; Cariplo Foundation (grant #1677), FRRB Early Career Award (grant #1750327); Fund for Scientific Research (FNRS).
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Affiliation(s)
- Pietro Maggi
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium; Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium; Centre Hospitalier Universitaire Vaudois, Université de Lausanne, Lausanne, Switzerland.
| | - Colin Vanden Bulcke
- Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium
| | - Edoardo Pedrini
- Institute of Experimental Neurology, Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Hospital, Milan, Italy
| | - Céline Bugli
- Plateforme Technologique de Support en Méthodologie et Calcul Statistique, Université Catholique de Louvain, Brussels, Belgium
| | - Amina Sellimi
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Maxence Wynen
- Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium
| | - Anna Stölting
- Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium
| | - William A Mullins
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Grigorios Kalaitzidis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valentina Lolli
- Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Gaetano Perrotta
- Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Souraya El Sankari
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Thierry Duprez
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Xu Li
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vincent van Pesch
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Martina Absinta
- Institute of Experimental Neurology, Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Hospital, Milan, Italy; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Vanden Bulcke C, Wynen M, Detobel J, La Rosa F, Absinta M, Dricot L, Macq B, Bach Cuadra M, Maggi P. BMAT: An open-source BIDS managing and analysis tool. Neuroimage Clin 2022; 36:103252. [PMID: 36451357 PMCID: PMC9723304 DOI: 10.1016/j.nicl.2022.103252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/16/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Magnetic Resonance Imaging (MRI) is an established technique to study in vivo neurological disorders such as Multiple Sclerosis (MS). To avoid errors on MRI data organization and automated processing, a standard called Brain Imaging Data Structure (BIDS) has been recently proposed. The BIDS standard eases data sharing and processing within or between centers by providing guidelines for their description and organization. However, the transformation from the complex unstructured non-open file data formats coming directly from the MRI scanner to a correct BIDS structure can be cumbersome and time consuming. This hinders a wider adoption of the BIDS format across different study centers. To solve this problem and ease the day-to-day use of BIDS for the neuroimaging scientific community, we present the BIDS Managing and Analysis Tool (BMAT). The BMAT software is a complete and easy-to-use local open-source neuroimaging analysis tool with a graphical user interface (GUI) that uses the BIDS format to organize and process brain MRI data for MS imaging research studies. BMAT provides the possibility to translate data from MRI scanners to the BIDS structure, create and manage BIDS datasets as well as develop and run automated processing pipelines, and is faster than its competitor. BMAT software propose the possibility to download useful analysis apps, especially applied to MS research with lesion segmentation and processing of imaging contrasts for novel disease biomarkers such as the central vein sign and the paramagnetic rim lesions.
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Affiliation(s)
- Colin Vanden Bulcke
- ICTEAM Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium,Louvain Neuroinflammation Imaging Lab (NIL), Institute of NeuroScience, Université catholique de Louvain, Brussels, Belgium,Corresponding authors at: Louvain Neuroinflammation Imaging Lab (NIL), Institute of NeuroScience, Université catholique de Louvain, Brussels, Belgium.
| | - Maxence Wynen
- ICTEAM Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium,Louvain Neuroinflammation Imaging Lab (NIL), Institute of NeuroScience, Université catholique de Louvain, Brussels, Belgium,CIBM Center for Biomedical Imaging, Lausanne, Switzerland,Radiology Department, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jules Detobel
- ICTEAM Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium,Louvain Neuroinflammation Imaging Lab (NIL), Institute of NeuroScience, Université catholique de Louvain, Brussels, Belgium
| | - Francesco La Rosa
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland,CIBM Center for Biomedical Imaging, Lausanne, Switzerland,Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martina Absinta
- Institute of Experimental Neurology, Division of Neuroscience, Vita-Salute San Raffaele University and Hospital, Milan, Italy
| | - Laurence Dricot
- Institute of NeuroScience, Université catholique de Louvain, Brussels, Belgium
| | - Benoît Macq
- ICTEAM Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Meritxell Bach Cuadra
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland,Radiology Department, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pietro Maggi
- Louvain Neuroinflammation Imaging Lab (NIL), Institute of NeuroScience, Université catholique de Louvain, Brussels, Belgium,Department of Neurology, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium,Department of Neurology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland,Corresponding authors at: Louvain Neuroinflammation Imaging Lab (NIL), Institute of NeuroScience, Université catholique de Louvain, Brussels, Belgium.
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La Rosa F, Wynen M, Al-Louzi O, Beck ES, Huelnhagen T, Maggi P, Thiran JP, Kober T, Shinohara RT, Sati P, Reich DS, Granziera C, Absinta M, Bach Cuadra M. Cortical lesions, central vein sign, and paramagnetic rim lesions in multiple sclerosis: Emerging machine learning techniques and future avenues. Neuroimage Clin 2022; 36:103205. [PMID: 36201950 PMCID: PMC9668629 DOI: 10.1016/j.nicl.2022.103205] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 12/14/2022]
Abstract
The current diagnostic criteria for multiple sclerosis (MS) lack specificity, and this may lead to misdiagnosis, which remains an issue in present-day clinical practice. In addition, conventional biomarkers only moderately correlate with MS disease progression. Recently, some MS lesional imaging biomarkers such as cortical lesions (CL), the central vein sign (CVS), and paramagnetic rim lesions (PRL), visible in specialized magnetic resonance imaging (MRI) sequences, have shown higher specificity in differential diagnosis. Moreover, studies have shown that CL and PRL are potential prognostic biomarkers, the former correlating with cognitive impairments and the latter with early disability progression. As machine learning-based methods have achieved extraordinary performance in the assessment of conventional imaging biomarkers, such as white matter lesion segmentation, several automated or semi-automated methods have been proposed as well for CL, PRL, and CVS. In the present review, we first introduce these MS biomarkers and their imaging methods. Subsequently, we describe the corresponding machine learning-based methods that were proposed to tackle these clinical questions, putting them into context with respect to the challenges they are facing, including non-standardized MRI protocols, limited datasets, and moderate inter-rater variability. We conclude by presenting the current limitations that prevent their broader deployment and suggesting future research directions.
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Key Words
- ms, multiple sclerosis
- mri, magnetic resonance imaging
- dl, deep learning
- ml, machine learning
- cl, cortical lesions
- prl, paramagnetic rim lesions
- cvs, central vein sign
- wml, white matter lesions
- flair, fluid-attenuated inversion recovery
- mprage, magnetization prepared rapid gradient-echo
- gm, gray matter
- wm, white matter
- psir, phase-sensitive inversion recovery
- dir, double inversion recovery
- mp2rage, magnetization-prepared 2 rapid gradient echoes
- sels, slowly evolving/expanding lesions
- cnn, convolutional neural network
- xai, explainable ai
- pv, partial volume
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Affiliation(s)
- Francesco La Rosa
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; CIBM Center for Biomedical Imaging, Switzerland; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Maxence Wynen
- CIBM Center for Biomedical Imaging, Switzerland; ICTeam, UCLouvain, Louvain-la-Neuve, Belgium; Louvain Inflammation Imaging Lab (NIL), Institute of Neuroscience (IoNS), UCLouvain, Brussels, Belgium; Radiology Department, Lausanne University and University Hospital, Switzerland
| | - Omar Al-Louzi
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Erin S Beck
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Till Huelnhagen
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Radiology Department, Lausanne University and University Hospital, Switzerland; Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland
| | - Pietro Maggi
- Louvain Inflammation Imaging Lab (NIL), Institute of Neuroscience (IoNS), UCLouvain, Brussels, Belgium; Department of Neurology, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium; Department of Neurology, CHUV, Lausanne, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; CIBM Center for Biomedical Imaging, Switzerland; Radiology Department, Lausanne University and University Hospital, Switzerland
| | - Tobias Kober
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Radiology Department, Lausanne University and University Hospital, Switzerland; Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland
| | - Russell T Shinohara
- Center for Biomedical Image Computing and Analysis (CBICA), Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA; Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, PA, USA; Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pascal Sati
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Cristina Granziera
- Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, Faculty of Medicine, University Hospital Basel and University of Basel, Switzerland; Neurologic Clinic and Policlinic, MS Center and Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel and University of Basel, Basel, Switzerland
| | - Martina Absinta
- IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Meritxell Bach Cuadra
- CIBM Center for Biomedical Imaging, Switzerland; Radiology Department, Lausanne University and University Hospital, Switzerland
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