1
|
Omrani M, Rita Chiarelli R, Acquaviva M, Bassani C, Dalla Costa G, Montini F, Preziosa P, Pagani L, Grassivaro F, Guerrieri S, Romeo M, Sangalli F, Colombo B, Moiola L, Zaffaroni M, Pietroboni A, Protti A, Puthenparampil M, Bergamaschi R, Comi G, Rocca MA, Martinelli V, Filippi M, Farina C. Machine learning-driven diagnosis of multiple sclerosis from whole blood transcriptomics. Brain Behav Immun 2024; 121:S0889-1591(24)00520-8. [PMID: 39097200 DOI: 10.1016/j.bbi.2024.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/23/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024] Open
Abstract
Multiple sclerosis (MS) is a neurological disorder characterized by immune dysregulation. It begins with a first clinical manifestation, a clinically isolated syndrome (CIS), which evolves to definite MS in case of further clinical and/or neuroradiological episodes. Here we evaluated the diagnostic value of transcriptional alterations in MS and CIS blood by machine learning (ML). Deep sequencing of more than 200 blood RNA samples comprising CIS, MS and healthy subjects, generated transcriptomes that were analyzed by the binary classification workflow to distinguish MS from healthy subjects and the Time-To-Event pipeline to predict CIS conversion to MS along time. To identify optimal classifiers, we performed algorithm benchmarking by nested cross-validation with the train set in both pipelines and then tested models generated with the train set on an independent dataset for final validation. The binary classification model identified a blood transcriptional signature classifying definite MS from healthy subjects with 97% accuracy, indicating that MS is associated with a clear predictive transcriptional signature in blood cells. When analyzing CIS data with ML survival models, prediction power of CIS conversion to MS was about 72% when using paraclinical data and 74.3% when using blood transcriptomes, indicating that blood-based classifiers obtained at the first clinical event can efficiently predict risk of developing MS. Coupling blood transcriptomics with ML approaches enables retrieval of predictive signatures of CIS conversion and MS state, thus introducing early non-invasive approaches to MS diagnosis.
Collapse
Affiliation(s)
- Maryam Omrani
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rosaria Rita Chiarelli
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Acquaviva
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Bassani
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gloria Dalla Costa
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Federico Montini
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Paolo Preziosa
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | | | - Francesca Grassivaro
- Dipartimento di Neuroscienze, Azienda Ospedale - Università di Padova, Padova, Italy
| | - Simone Guerrieri
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marzia Romeo
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Sangalli
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bruno Colombo
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lucia Moiola
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mauro Zaffaroni
- Centro Sclerosi Multipla, ASST della Valle Olona, Ospedale di Gallarate, Gallarate, Italy
| | - Anna Pietroboni
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Marco Puthenparampil
- Dipartimento di Neuroscienze, Azienda Ospedale - Università di Padova, Padova, Italy
| | | | - Giancarlo Comi
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Maria A Rocca
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Vittorio Martinelli
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Filippi
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Cinthia Farina
- Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| |
Collapse
|
2
|
Khan Z, Mehan S, Gupta GD, Narula AS. Immune System Dysregulation in the Progression of Multiple Sclerosis: Molecular Insights and Therapeutic Implications. Neuroscience 2024; 548:9-26. [PMID: 38692349 DOI: 10.1016/j.neuroscience.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 05/03/2024]
Abstract
Multiple sclerosis (MS), a prevalent neurological disorder, predominantly affects young adults and is characterized by chronic autoimmune activity. The study explores the immune system dysregulation in MS, highlighting the crucial roles of immune and non-neuronal cells in the disease's progression. This review examines the dual role of cytokines, with some like IL-6, TNF-α, and interferon-gamma (IFN-γ) promoting inflammation and CNS tissue injury, and others such as IL-4, IL-10, IL-37, and TGF-β fostering remyelination and protecting against MS. Elevated chemokine levels in the cerebrospinal fluid (CSF), including CCL2, CCL5, CXCL10, CXCL13, and fractalkine, are analyzed for their role in facilitating immune cell migration across the blood-brain barrier (BBB), worsening inflammation and neurodegeneration. The study also delves into the impact of auto-antibodies targeting myelin components like MOG and AQP4, which activate complement cascades leading to further myelin destruction. The article discusses how compromised BBB integrity allows immune cells and inflammatory mediators to infiltrate the CNS, intensifying MS symptoms. It also examines the involvement of astrocytes, microglia, and oligodendrocytes in the disease's progression. Additionally, the effectiveness of immunomodulatory drugs such as IFN-β and CD20-targeting monoclonal antibodies (e.g., rituximab) in modulating immune responses is reviewed, highlighting their potential to reduce relapse rates and delaying MS progression. These insights emphasize the importance of immune system dysfunction in MS development and progression, guiding the development of new therapeutic strategies. The study underscores recent advancements in understanding MS's molecular pathways, opening avenues for more targeted and effective treatments.
Collapse
Affiliation(s)
- Zuber Khan
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy (Affiliated to IK Gujral Punjab Technical University, Jalandhar, Punjab 144603, India), Moga 142001, Punjab, India
| | - Sidharth Mehan
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy (Affiliated to IK Gujral Punjab Technical University, Jalandhar, Punjab 144603, India), Moga 142001, Punjab, India.
| | - Ghanshyam Das Gupta
- Department of Pharmaceutics, ISF College of Pharmacy (Affiliated to IK Gujral Punjab Technical University, Jalandhar, Punjab 144603, India), Moga, Punjab, India
| | - Acharan S Narula
- Narula Research, LLC, 107 Boulder Bluff, Chapel Hill, NC 27516, USA
| |
Collapse
|
3
|
Grel H, Woznica D, Ratajczak K, Kalwarczyk E, Anchimowicz J, Switlik W, Olejnik P, Zielonka P, Stobiecka M, Jakiela S. Mitochondrial Dynamics in Neurodegenerative Diseases: Unraveling the Role of Fusion and Fission Processes. Int J Mol Sci 2023; 24:13033. [PMID: 37685840 PMCID: PMC10487704 DOI: 10.3390/ijms241713033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
Neurodegenerative diseases (NDs) are a diverse group of disorders characterized by the progressive degeneration and death of neurons, leading to a range of neurological symptoms. Despite the heterogeneity of these conditions, a common denominator is the implication of mitochondrial dysfunction in their pathogenesis. Mitochondria play a crucial role in creating biomolecules, providing energy through adenosine triphosphate (ATP) generated by oxidative phosphorylation (OXPHOS), and producing reactive oxygen species (ROS). When they're not functioning correctly, becoming fragmented and losing their membrane potential, they contribute to these diseases. In this review, we explore how mitochondria fuse and undergo fission, especially in the context of NDs. We discuss the genetic and protein mutations linked to these diseases and how they impact mitochondrial dynamics. We also look at the key regulatory proteins in fusion (MFN1, MFN2, and OPA1) and fission (DRP1 and FIS1), including their post-translational modifications. Furthermore, we highlight potential drugs that can influence mitochondrial dynamics. By unpacking these complex processes, we aim to direct research towards treatments that can improve life quality for people with these challenging conditions.
Collapse
Affiliation(s)
- Hubert Grel
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Damian Woznica
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Katarzyna Ratajczak
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Ewelina Kalwarczyk
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Julia Anchimowicz
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Weronika Switlik
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Piotr Olejnik
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Piotr Zielonka
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Magdalena Stobiecka
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Slawomir Jakiela
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| |
Collapse
|
4
|
Potentially toxic elements in the brains of people with multiple sclerosis. Sci Rep 2023; 13:655. [PMID: 36635465 PMCID: PMC9837144 DOI: 10.1038/s41598-022-27169-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/26/2022] [Indexed: 01/14/2023] Open
Abstract
Potentially toxic elements such as lead and aluminium have been proposed to play a role in the pathogenesis of multiple sclerosis (MS), since their neurotoxic mechanisms mimic many of the pathogenetic processes in MS. We therefore examined the distribution of several potentially toxic elements in the autopsied brains of people with and without MS, using two methods of elemental bio-imaging. Toxicants detected in the locus ceruleus were used as indicators of past exposures. Autometallography of paraffin sections from multiple brain regions of 21 MS patients and 109 controls detected inorganic mercury, silver, or bismuth in many locus ceruleus neurons of both groups, and in widespread blood vessels, oligodendrocytes, astrocytes, and neurons of four MS patients and one control. Laser ablation-inductively coupled plasma-mass spectrometry imaging of pons paraffin sections from all MS patients and 12 controls showed that combinations of iron, silver, lead, aluminium, mercury, nickel, and bismuth were present more often in the locus ceruleus of MS patients and were located predominantly in white matter tracts. Based on these results, we propose that metal toxicants in locus ceruleus neurons weaken the blood-brain barrier, enabling multiple interacting toxicants to pass through blood vessels and enter astrocytes and oligodendroglia, leading to demyelination.
Collapse
|