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Karagianni K, Dafou D, Xanthopoulos K, Sklaviadis T, Kanata E. RNA editing regulates glutamatergic synapses in the frontal cortex of a molecular subtype of Amyotrophic Lateral Sclerosis. Mol Med 2024; 30:101. [PMID: 38997636 PMCID: PMC11241978 DOI: 10.1186/s10020-024-00863-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/12/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Amyotrophic Lateral Sclerosis (ALS) is a highly heterogenous neurodegenerative disorder that primarily affects upper and lower motor neurons, affecting additional cell types and brain regions. Underlying molecular mechanisms are still elusive, in part due to disease heterogeneity. Molecular disease subtyping through integrative analyses including RNA editing profiling is a novel approach for identification of molecular networks involved in pathogenesis. METHODS We aimed to highlight the role of RNA editing in ALS, focusing on the frontal cortex and the prevalent molecular disease subtype (ALS-Ox), previously determined by transcriptomic profile stratification. We established global RNA editing (editome) and gene expression (transcriptome) profiles in control and ALS-Ox cases, utilizing publicly available RNA-seq data (GSE153960) and an in-house analysis pipeline. Functional annotation and pathway analyses identified molecular processes affected by RNA editing alterations. Pearson correlation analyses assessed RNA editing effects on expression. Similar analyses on additional ALS-Ox and control samples (GSE124439) were performed for verification. Targeted re-sequencing and qRT-PCR analysis targeting CACNA1C, were performed using frontal cortex tissue from ALS and control samples (n = 3 samples/group). RESULTS We identified reduced global RNA editing in the frontal cortex of ALS-Ox cases. Differentially edited transcripts are enriched in synapses, particularly in the glutamatergic synapse pathway. Bioinformatic analyses on additional ALS-Ox and control RNA-seq data verified these findings. We identified increased recoding at the Q621R site in the GRIK2 transcript and determined positive correlations between RNA editing and gene expression alterations in ionotropic receptor subunits GRIA2, GRIA3 and the CACNA1C transcript, which encodes the pore forming subunit of a post-synaptic L-type calcium channel. Experimental data verified RNA editing alterations and editing-expression correlation in CACNA1C, highlighting CACNA1C as a target for further study. CONCLUSIONS We provide evidence on the involvement of RNA editing in the frontal cortex of an ALS molecular subtype, highlighting a modulatory role mediated though recoding and gene expression regulation on glutamatergic synapse related transcripts. We report RNA editing effects in disease-related transcripts and validated editing alterations in CACNA1C. Our study provides targets for further functional studies that could shed light in underlying disease mechanisms enabling novel therapeutic approaches.
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Affiliation(s)
- Korina Karagianni
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Dimitra Dafou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Konstantinos Xanthopoulos
- Laboratory of Pharmacology, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001, Thermi, Greece
| | - Theodoros Sklaviadis
- Laboratory of Pharmacology, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Eirini Kanata
- Laboratory of Pharmacology, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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2
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Caldi Gomes L, Hänzelmann S, Hausmann F, Khatri R, Oller S, Parvaz M, Tzeplaeff L, Pasetto L, Gebelin M, Ebbing M, Holzapfel C, Columbro SF, Scozzari S, Knöferle J, Cordts I, Demleitner AF, Deschauer M, Dufke C, Sturm M, Zhou Q, Zelina P, Sudria-Lopez E, Haack TB, Streb S, Kuzma-Kozakiewicz M, Edbauer D, Pasterkamp RJ, Laczko E, Rehrauer H, Schlapbach R, Carapito C, Bonetto V, Bonn S, Lingor P. Multiomic ALS signatures highlight subclusters and sex differences suggesting the MAPK pathway as therapeutic target. Nat Commun 2024; 15:4893. [PMID: 38849340 PMCID: PMC11161513 DOI: 10.1038/s41467-024-49196-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating motor neuron disease and lacks effective disease-modifying treatments. This study utilizes a comprehensive multiomic approach to investigate the early and sex-specific molecular mechanisms underlying ALS. By analyzing the prefrontal cortex of 51 patients with sporadic ALS and 50 control subjects, alongside four transgenic mouse models (C9orf72-, SOD1-, TDP-43-, and FUS-ALS), we have uncovered significant molecular alterations associated with the disease. Here, we show that males exhibit more pronounced changes in molecular pathways compared to females. Our integrated analysis of transcriptomes, (phospho)proteomes, and miRNAomes also identified distinct ALS subclusters in humans, characterized by variations in immune response, extracellular matrix composition, mitochondrial function, and RNA processing. The molecular signatures of human subclusters were reflected in specific mouse models. Our study highlighted the mitogen-activated protein kinase (MAPK) pathway as an early disease mechanism. We further demonstrate that trametinib, a MAPK inhibitor, has potential therapeutic benefits in vitro and in vivo, particularly in females, suggesting a direction for developing targeted ALS treatments.
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Affiliation(s)
- Lucas Caldi Gomes
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Sonja Hänzelmann
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Hausmann
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robin Khatri
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sergio Oller
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mojan Parvaz
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Laura Tzeplaeff
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Laura Pasetto
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marie Gebelin
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, Infrastructure Nationale de Protéomique, Strasbourg, France
| | - Melanie Ebbing
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Constantin Holzapfel
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Serena Scozzari
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Johanna Knöferle
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Isabell Cordts
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Antonia F Demleitner
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Marcus Deschauer
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Qihui Zhou
- German Center for Neurodegenerative Diseases (DZNE), München, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Pavol Zelina
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emma Sudria-Lopez
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Sebastian Streb
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | | | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), München, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Endre Laczko
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, Infrastructure Nationale de Protéomique, Strasbourg, France
| | - Valentina Bonetto
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Stefan Bonn
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Paul Lingor
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), München, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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3
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Castelli L, Vasta R, Allen SP, Waller R, Chiò A, Traynor BJ, Kirby J. From use of omics to systems biology: Identifying therapeutic targets for amyotrophic lateral sclerosis. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:209-268. [PMID: 38802176 DOI: 10.1016/bs.irn.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a heterogeneous progressive neurodegenerative disorder with available treatments such as riluzole and edaravone extending survival by an average of 3-6 months. The lack of highly effective, widely available therapies reflects the complexity of ALS. Omics technologies, including genomics, transcriptomic and proteomics have contributed to the identification of biological pathways dysregulated and targeted by therapeutic strategies in preclinical and clinical trials. Integrating clinical, environmental and neuroimaging information with omics data and applying a systems biology approach can further improve our understanding of the disease with the potential to stratify patients and provide more personalised medicine. This chapter will review the omics technologies that contribute to a systems biology approach and how these components have assisted in identifying therapeutic targets. Current strategies, including the use of genetic screening and biosampling in clinical trials, as well as the future application of additional technological advances, will also be discussed.
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Affiliation(s)
- Lydia Castelli
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Rosario Vasta
- ALS Expert Center,'Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy; Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Scott P Allen
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Rachel Waller
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Adriano Chiò
- ALS Expert Center,'Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy; Neurology 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza of Turin, Turin, Italy
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States; RNA Therapeutics Laboratory, National Center for Advancing Translational Sciences, NIH, Rockville, MD, United States; National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States; Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, United States; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology,University College London, London, United Kingdom
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.
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Ortega JA, Soares de Aguiar GP, Chandravanshi P, Levy N, Engel E, Álvarez Z. Exploring the properties and potential of the neural extracellular matrix for next-generation regenerative therapies. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1962. [PMID: 38723788 DOI: 10.1002/wnan.1962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/24/2024]
Abstract
The extracellular matrix (ECM) is a dynamic and complex network of proteins and molecules that surrounds cells and tissues in the nervous system and orchestrates a myriad of biological functions. This review carefully examines the diverse interactions between cells and the ECM, as well as the transformative chemical and physical changes that the ECM undergoes during neural development, aging, and disease. These transformations play a pivotal role in shaping tissue morphogenesis and neural activity, thereby influencing the functionality of the central nervous system (CNS). In our comprehensive review, we describe the diverse behaviors of the CNS ECM in different physiological and pathological scenarios and explore the unique properties that make ECM-based strategies attractive for CNS repair and regeneration. Addressing the challenges of scalability, variability, and integration with host tissues, we review how advanced natural, synthetic, and combinatorial matrix approaches enhance biocompatibility, mechanical properties, and functional recovery. Overall, this review highlights the potential of decellularized ECM as a powerful tool for CNS modeling and regenerative purposes and sets the stage for future research in this exciting field. This article is categorized under: Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement Therapeutic Approaches and Drug Discovery > Nanomedicine for Neurological Disease Implantable Materials and Surgical Technologies > Nanomaterials and Implants.
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Affiliation(s)
- J Alberto Ortega
- Department of Pathology and Experimental Therapeutics, Institute of Neurosciences, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet del Llobregat, Spain
| | - Gisele P Soares de Aguiar
- Department of Pathology and Experimental Therapeutics, Institute of Neurosciences, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet del Llobregat, Spain
| | - Palash Chandravanshi
- Biomaterials for Neural Regeneration Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Natacha Levy
- Biomaterials for Neural Regeneration Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Elisabeth Engel
- IMEM-BRT Group, Department of Materials Science and Engineering, EEBE, Technical University of Catalonia (UPC), Barcelona, Spain
- Biomaterials for Regenerative Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- CIBER en Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain
| | - Zaida Álvarez
- Biomaterials for Neural Regeneration Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- CIBER en Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois, USA
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5
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Tzeplaeff L, Jürs AV, Wohnrade C, Demleitner AF. Unraveling the Heterogeneity of ALS-A Call to Redefine Patient Stratification for Better Outcomes in Clinical Trials. Cells 2024; 13:452. [PMID: 38474416 PMCID: PMC10930688 DOI: 10.3390/cells13050452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Despite tremendous efforts in basic research and a growing number of clinical trials aiming to find effective treatments, amyotrophic lateral sclerosis (ALS) remains an incurable disease. One possible reason for the lack of effective causative treatment options is that ALS may not be a single disease entity but rather may represent a clinical syndrome, with diverse genetic and molecular causes, histopathological alterations, and subsequent clinical presentations contributing to its complexity and variability among individuals. Defining a way to subcluster ALS patients is becoming a central endeavor in the field. Identifying specific clusters and applying them in clinical trials could enable the development of more effective treatments. This review aims to summarize the available data on heterogeneity in ALS with regard to various aspects, e.g., clinical, genetic, and molecular.
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Affiliation(s)
- Laura Tzeplaeff
- Department of Neurology, Rechts der Isar Hospital, Technical University of Munich, 81675 München, Germany
| | - Alexandra V. Jürs
- Translational Neurodegeneration Section “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, 18057 Rostock, Germany
| | - Camilla Wohnrade
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany;
| | - Antonia F. Demleitner
- Department of Neurology, Rechts der Isar Hospital, Technical University of Munich, 81675 München, Germany
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6
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Marriott H, Kabiljo R, Hunt GP, Khleifat AA, Jones A, Troakes C, Pfaff AL, Quinn JP, Koks S, Dobson RJ, Schwab P, Al-Chalabi A, Iacoangeli A. Unsupervised machine learning identifies distinct ALS molecular subtypes in post-mortem motor cortex and blood expression data. Acta Neuropathol Commun 2023; 11:208. [PMID: 38129934 PMCID: PMC10734072 DOI: 10.1186/s40478-023-01686-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) displays considerable clinical and genetic heterogeneity. Machine learning approaches have previously been utilised for patient stratification in ALS as they can disentangle complex disease landscapes. However, lack of independent validation in different populations and tissue samples have greatly limited their use in clinical and research settings. We overcame these issues by performing hierarchical clustering on the 5000 most variably expressed autosomal genes from motor cortex expression data of people with sporadic ALS from the KCL BrainBank (N = 112). Three molecular phenotypes linked to ALS pathogenesis were identified: synaptic and neuropeptide signalling, oxidative stress and apoptosis, and neuroinflammation. Cluster validation was achieved by applying linear discriminant analysis models to cases from TargetALS US motor cortex (N = 93), as well as Italian (N = 15) and Dutch (N = 397) blood expression datasets, for which there was a high assignment probability (80-90%) for each molecular subtype. The ALS and motor cortex specificity of the expression signatures were tested by mapping KCL BrainBank controls (N = 59), and occipital cortex (N = 45) and cerebellum (N = 123) samples from TargetALS to each cluster, before constructing case-control and motor cortex-region logistic regression classifiers. We found that the signatures were not only able to distinguish people with ALS from controls (AUC 0.88 ± 0.10), but also reflect the motor cortex-based disease process, as there was perfect discrimination between motor cortex and the other brain regions. Cell types known to be involved in the biological processes of each molecular phenotype were found in higher proportions, reinforcing their biological interpretation. Phenotype analysis revealed distinct cluster-related outcomes in both motor cortex datasets, relating to disease onset and progression-related measures. Our results support the hypothesis that different mechanisms underpin ALS pathogenesis in subgroups of patients and demonstrate potential for the development of personalised treatment approaches. Our method is available for the scientific and clinical community at https://alsgeclustering.er.kcl.ac.uk .
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Affiliation(s)
- Heather Marriott
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Renata Kabiljo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Guy P Hunt
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, 6150, Australia
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
| | - Ashley Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, 6150, Australia
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, 6150, Australia
| | - Richard J Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre (BRC), South London and Maudsley NHS Foundation Trust and King's College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Patrick Schwab
- GlaxoSmithKline, Artificial Intelligence and Machine Learning, Durham, NC, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- King's College Hospital, London, SE5 9RS, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK.
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
- NIHR Maudsley Biomedical Research Centre (BRC), South London and Maudsley NHS Foundation Trust and King's College London, London, UK.
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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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8
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Mimic S, Aru B, Pehlivanoğlu C, Sleiman H, Andjus PR, Yanıkkaya Demirel G. Immunology of amyotrophic lateral sclerosis - role of the innate and adaptive immunity. Front Neurosci 2023; 17:1277399. [PMID: 38105925 PMCID: PMC10723830 DOI: 10.3389/fnins.2023.1277399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/07/2023] [Indexed: 12/19/2023] Open
Abstract
This review aims to summarize the latest evidence about the role of innate and adaptive immunity in Amyotrophic Lateral Sclerosis (ALS). ALS is a devastating neurodegenerative disease affecting upper and lower motor neurons, which involves essential cells of the immune system that play a basic role in innate or adaptive immunity, that can be neurotoxic or neuroprotective for neurons. However, distinguishing between the sole neurotoxic or neuroprotective function of certain cells such as astrocytes can be challenging due to intricate nature of these cells, the complexity of the microenvironment and the contextual factors. In this review, in regard to innate immunity we focus on the involvement of monocytes/macrophages, microglia, the complement, NK cells, neutrophils, mast cells, and astrocytes, while regarding adaptive immunity, in addition to humoral immunity the most important features and roles of T and B cells are highlighted, specifically different subsets of CD4+ as well as CD8+ T cells. The role of autoantibodies and cytokines is also discussed in distinct sections of this review.
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Affiliation(s)
- Stefan Mimic
- Centre for Laser Microscopy, Institute of Physiology and Biochemistry “Jean Giaja”, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Başak Aru
- Immunology Department, Faculty of Medicine, Yeditepe University, Istanbul, Türkiye
| | - Cemil Pehlivanoğlu
- Immunology Department, Faculty of Medicine, Yeditepe University, Istanbul, Türkiye
| | - Hadi Sleiman
- Faculty of Medicine, Yeditepe University, Istanbul, Türkiye
| | - Pavle R. Andjus
- Centre for Laser Microscopy, Institute of Physiology and Biochemistry “Jean Giaja”, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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9
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Xie M, Pallegar PN, Parusel S, Nguyen AT, Wu LJ. Regulation of cortical hyperexcitability in amyotrophic lateral sclerosis: focusing on glial mechanisms. Mol Neurodegener 2023; 18:75. [PMID: 37858176 PMCID: PMC10585818 DOI: 10.1186/s13024-023-00665-w] [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: 04/01/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterized by the loss of both upper and lower motor neurons, resulting in muscle weakness, atrophy, paralysis, and eventually death. Motor cortical hyperexcitability is a common phenomenon observed at the presymptomatic stage of ALS. Both cell-autonomous (the intrinsic properties of motor neurons) and non-cell-autonomous mechanisms (cells other than motor neurons) are believed to contribute to cortical hyperexcitability. Decoding the pathological relevance of these dynamic changes in motor neurons and glial cells has remained a major challenge. This review summarizes the evidence of cortical hyperexcitability from both clinical and preclinical research, as well as the underlying mechanisms. We discuss the potential role of glial cells, particularly microglia, in regulating abnormal neuronal activity during the disease progression. Identifying early changes such as neuronal hyperexcitability in the motor system may provide new insights for earlier diagnosis of ALS and reveal novel targets to halt the disease progression.
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Affiliation(s)
- Manling Xie
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Praveen N Pallegar
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, USA
| | - Sebastian Parusel
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Aivi T Nguyen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Long-Jun Wu
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
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10
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La Cognata V, D’Amico AG, Maugeri G, Morello G, Guarnaccia M, Magrì B, Aronica E, Alkon DL, D’Agata V, Cavallaro S. The ε-Isozyme of Protein Kinase C (PKCε) Is Impaired in ALS Motor Cortex and Its Pulse Activation by Bryostatin-1 Produces Long Term Survival in Degenerating SOD1-G93A Motor Neuron-like Cells. Int J Mol Sci 2023; 24:12825. [PMID: 37629005 PMCID: PMC10454105 DOI: 10.3390/ijms241612825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and ultimately fatal neurodegenerative disease, characterized by a progressive depletion of upper and lower motor neurons (MNs) in the brain and spinal cord. The aberrant regulation of several PKC-mediated signal transduction pathways in ALS has been characterized so far, describing either impaired expression or altered activity of single PKC isozymes (α, β, ζ and δ). Here, we detailed the distribution and cellular localization of the ε-isozyme of protein kinase C (PKCε) in human postmortem motor cortex specimens and reported a significant decrease in both PKCε mRNA (PRKCE) and protein immunoreactivity in a subset of sporadic ALS patients. We furthermore investigated the steady-state levels of both pan and phosphorylated PKCε in doxycycline-activated NSC-34 cell lines carrying the human wild-type (WT) or mutant G93A SOD1 and the biological long-term effect of its transient agonism by Bryostatin-1. The G93A-SOD1 cells showed a significant reduction of the phosphoPKCε/panPKCε ratio compared to the WT. Moreover, a brief pulse activation of PKCε by Bryostatin-1 produced long-term survival in activated G93A-SOD1 degenerating cells in two different cell death paradigms (serum starvation and chemokines-induced toxicity). Altogether, the data support the implication of PKCε in ALS pathophysiology and suggests its pharmacological modulation as a potential neuroprotective strategy, at least in a subgroup of sporadic ALS patients.
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Affiliation(s)
- Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Agata Grazia D’Amico
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Grazia Maugeri
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Benedetta Magrì
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 Amsterdam, The Netherlands
| | | | - Velia D’Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
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11
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Morello G, La Cognata V, Guarnaccia M, La Bella V, Conforti FL, Cavallaro S. A Diagnostic Gene-Expression Signature in Fibroblasts of Amyotrophic Lateral Sclerosis. Cells 2023; 12:1884. [PMID: 37508548 PMCID: PMC10378077 DOI: 10.3390/cells12141884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease with limited treatment options. Diagnosis can be difficult due to the heterogeneity and non-specific nature of the initial symptoms, resulting in delays that compromise prompt access to effective therapeutic strategies. Transcriptome profiling of patient-derived peripheral cells represents a valuable benchmark in overcoming such challenges, providing the opportunity to identify molecular diagnostic signatures. In this study, we characterized transcriptome changes in skin fibroblasts of sporadic ALS patients (sALS) and controls and evaluated their utility as a molecular classifier for ALS diagnosis. Our analysis identified 277 differentially expressed transcripts predominantly involved in transcriptional regulation, synaptic transmission, and the inflammatory response. A support vector machine classifier based on this 277-gene signature was developed to discriminate patients with sALS from controls, showing significant predictive power in both the discovery dataset and in six independent publicly available gene expression datasets obtained from different sALS tissue/cell samples. Taken together, our findings support the utility of transcriptional signatures in peripheral cells as valuable biomarkers for the diagnosis of ALS.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Center and Neurochemistry Laboratory, BiND, University of Palermo, 90133 Palermo, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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12
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La Cognata V, D’Amico AG, Maugeri G, Morello G, Guarnaccia M, Magrì B, Aronica E, D’Agata V, Cavallaro S. CXCR2 Is Deregulated in ALS Spinal Cord and Its Activation Triggers Apoptosis in Motor Neuron-Like Cells Overexpressing hSOD1-G93A. Cells 2023; 12:1813. [PMID: 37508478 PMCID: PMC10377984 DOI: 10.3390/cells12141813] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/08/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a multifactorial neurodegenerative disease characterized by progressive depletion of motor neurons (MNs). Recent evidence suggests a role in ALS pathology for the C-X-C motif chemokine receptor 2 (CXCR2), whose expression was found increased at both mRNA and protein level in cortical neurons of sporadic ALS patients. Previous findings also showed that the receptor inhibition is able to prevent iPSC-derived MNs degeneration in vitro and improve neuromuscular function in SOD1-G93A mice. Here, by performing transcriptional analysis and immunofluorescence studies, we detailed the increased expression and localization of CXCR2 and its main ligand CXCL8 in the human lumbar spinal cord of sporadic ALS patients. We further investigated the functional role of CXCR2/ligands axis in NSC-34 motor neuron-like cells expressing human wild-type (WT) or mutant (G93A) SOD1. A significant expression of CXCR2 was found in doxycycline-induced G93A-SOD1-expressing cells, but not in WT cells. In vitro assays showed CXCR2 activation by GROα and MIP2α, two murine endogenous ligands and functional homologs of CXCL8, reduces cellular viability and triggers apoptosis in a dose dependent manner, while treatment with reparixin, a non-competitive allosteric CXCR2 inhibitor, effectively counteracts GROα and MIP2α toxicity, significantly inhibiting the chemokine-induced cell death. Altogether, data further support a role of CXCR2 axis in ALS etiopathogenesis and confirm its pharmacological modulation as a candidate therapeutic strategy.
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Affiliation(s)
- Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Agata Grazia D’Amico
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Grazia Maugeri
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Benedetta Magrì
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 Amsterdam, The Netherlands
| | - Velia D’Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
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13
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Swanson MEV, Mrkela M, Murray HC, Cao MC, Turner C, Curtis MA, Faull RLM, Walker AK, Scotter EL. Microglial CD68 and L-ferritin upregulation in response to phosphorylated-TDP-43 pathology in the amyotrophic lateral sclerosis brain. Acta Neuropathol Commun 2023; 11:69. [PMID: 37118836 PMCID: PMC10142752 DOI: 10.1186/s40478-023-01561-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/29/2023] [Indexed: 04/30/2023] Open
Abstract
Microglia, the innate immune cells of the brain, are activated by damage or disease. In mouse models of amyotrophic lateral sclerosis (ALS), microglia shift from neurotrophic to neurotoxic states with disease progression. It remains unclear how human microglia change relative to the TAR DNA-binding protein 43 (TDP-43) aggregation that occurs in 97% of ALS cases. Here we examine spatial relationships between microglial activation and TDP-43 pathology in brain tissue from people with ALS and from a TDP-43-driven ALS mouse model. Post-mortem human brain tissue from the Neurological Foundation Human Brain Bank was obtained from 10 control and 10 ALS cases in parallel with brain tissue from a bigenic NEFH-tTA/tetO-hTDP-43∆NLS (rNLS) mouse model of ALS at disease onset, early disease, and late disease stages. The spatiotemporal relationship between microglial activation and ALS pathology was determined by investigating microglial functional marker expression in brain regions with low and high TDP-43 burden at end-stage human disease: hippocampus and motor cortex, respectively. Sections were immunohistochemically labelled with a two-round multiplexed antibody panel against; microglial functional markers (L-ferritin, HLA-DR, CD74, CD68, and Iba1), a neuronal marker, an astrocyte marker, and pathological phosphorylated TDP-43 (pTDP-43). Single-cell levels of microglial functional markers were quantified using custom analysis pipelines and mapped to anatomical regions and ALS pathology. We identified a significant increase in microglial Iba1 and CD68 expression in the human ALS motor cortex, with microglial CD68 being significantly correlated with pTDP-43 pathology load. We also identified two subpopulations of microglia enriched in the ALS motor cortex that were defined by high L-ferritin expression. A similar pattern of microglial changes was observed in the rNLS mouse, with an increase first in CD68 and then in L-ferritin expression, with both occurring only after pTDP-43 inclusions were detectable. Our data strongly suggest that microglia are phagocytic at early-stage ALS but transition to a dysfunctional state at end-stage disease, and that these functional states are driven by pTDP-43 aggregation. Overall, these findings enhance our understanding of microglial phenotypes and function in ALS.
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Affiliation(s)
- Molly E V Swanson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Miran Mrkela
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Helen C Murray
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Maize C Cao
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- Department of Anatomical Pathology, Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Maurice A Curtis
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Adam K Walker
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Emma L Scotter
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
- Centre for Brain Research, University of Auckland, Auckland, New Zealand.
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14
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Teruel-Peña B, Gómez-Urquiza JL, Suleiman-Martos N, Prieto I, García-Cózar FJ, Ramírez-Sánchez M, Fernández-Martos C, Domínguez-Vías G. Systematic Review and Meta-Analyses of Aminopeptidases as Prognostic Biomarkers in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2023; 24:ijms24087169. [PMID: 37108335 PMCID: PMC10138961 DOI: 10.3390/ijms24087169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons in the spinal cord, brain stem, and cerebral cortex. Biomarkers for ALS are essential for disease detection and to provide information on potential therapeutic targets. Aminopeptidases catalyze the cleavage of amino acids from the amino terminus of protein or substrates such as neuropeptides. Since certain aminopeptidases are known to increase the risk of neurodegeneration, such mechanisms may reveal new targets to determine their association with ALS risk and their interest as a diagnostic biomarker. The authors performed a systematic review and meta-analyses of genome-wide association studies (GWASs) to identify reported aminopeptidases genetic loci associated with the risk of ALS. PubMed, Scopus, CINAHL, ISI Web of Science, ProQuest, LILACS, and Cochrane databases were searched to retrieve eligible studies in English or Spanish, published up to 27 January 2023. A total of 16 studies were included in this systematic review, where a series of aminopeptidases could be related to ALS and could be promising biomarkers (DPP1, DPP2, DPP4, LeuAP, pGluAP, and PSA/NPEPPS). The literature reported the association of single-nucleotide polymorphisms (SNPs: rs10260404 and rs17174381) with the risk of ALS. The genetic variation rs10260404 in the DPP6 gene was identified to be highly associated with ALS susceptibility, but meta-analyses of genotypes in five studies in a matched cohort of different ancestry (1873 cases and 1861 control subjects) showed no ALS risk association. Meta-analyses of eight studies for minor allele frequency (MAF) also found no ALS association for the "C" allele. The systematic review identified aminopeptidases as possible biomarkers. However, the meta-analyses for rs1060404 of DPP6 do not show a risk associated with ALS.
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Affiliation(s)
- Bárbara Teruel-Peña
- Department of Health Sciences, University of Jaén, 23071 Jaén, Spain
- Department of Physiology, Faculty of Health Sciences, Ceuta University of Granada, 51001 Ceuta, Spain
| | - José Luís Gómez-Urquiza
- Nursing Department, Faculty of Health Sciences, Ceuta University of Granada, 51001 Ceuta, Spain
| | - Nora Suleiman-Martos
- Nursing Department, Faculty of Health Sciences, University of Granada, 18071 Granada, Spain
| | - Isabel Prieto
- Department of Health Sciences, University of Jaén, 23071 Jaén, Spain
| | | | | | | | - Germán Domínguez-Vías
- Department of Physiology, Faculty of Health Sciences, Ceuta University of Granada, 51001 Ceuta, Spain
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15
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Founta K, Dafou D, Kanata E, Sklaviadis T, Zanos TP, Gounaris A, Xanthopoulos K. Gene targeting in amyotrophic lateral sclerosis using causality-based feature selection and machine learning. Mol Med 2023; 29:12. [PMID: 36694130 PMCID: PMC9872307 DOI: 10.1186/s10020-023-00603-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a rare progressive neurodegenerative disease that affects upper and lower motor neurons. As the molecular basis of the disease is still elusive, the development of high-throughput sequencing technologies, combined with data mining techniques and machine learning methods, could provide remarkable results in identifying pathogenetic mechanisms. High dimensionality is a major problem when applying machine learning techniques in biomedical data analysis, since a huge number of features is available for a limited number of samples. The aim of this study was to develop a methodology for training interpretable machine learning models in the classification of ALS and ALS-subtypes samples, using gene expression datasets. METHODS We performed dimensionality reduction in gene expression data using a semi-automated preprocessing systematic gene selection procedure using Statistically Equivalent Signature (SES), a causality-based feature selection algorithm, followed by Boosted Regression Trees (XGBoost) and Random Forest to train the machine learning classifiers. The SHapley Additive exPlanations (SHAP values) were used for interpretation of the machine learning classifiers. The methodology was developed and tested using two distinct publicly available ALS RNA-seq datasets. We evaluated the performance of SES as a dimensionality reduction method against: (a) Least Absolute Shrinkage and Selection Operator (LASSO), and (b) Local Outlier Factor (LOF). RESULTS The proposed methodology achieved 85.18% accuracy for the classification of cerebellum or frontal cortex samples as C9orf72-related familial ALS, sporadic ALS or healthy samples. Importantly, the genes identified as the most determinative have also been reported as disease-associated in ALS literature. When tested in the evaluation dataset, the methodology achieved 88.89% accuracy for the classification of sporadic ALS motor neuron samples. When LASSO was used as feature selection method instead of SES, the accuracy of the machine learning classifiers ranged from 74.07 to 96.30%, depending on tissue assessed, while LOF underperformed significantly (77.78% accuracy for the classification of pooled cerebellum and frontal cortex samples). CONCLUSIONS Using SES, we addressed the challenge of high dimensionality in gene expression data analysis, and we trained accurate machine learning ALS classifiers, specific for the gene expression patterns of different disease subtypes and tissue samples, while identifying disease-associated genes.
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Affiliation(s)
- Kyriaki Founta
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitra Dafou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Eirini Kanata
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros Sklaviadis
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros P Zanos
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Feinstein Institutes for Medical Research, Institute of Health Systems Science, Northwell Health, Manhasset, NY, 11030, USA
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
| | - Anastasios Gounaris
- School of Informatics, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Konstantinos Xanthopoulos
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001, Thermi, Greece.
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16
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Molecular subtypes of ALS are associated with differences in patient prognosis. Nat Commun 2023; 14:95. [PMID: 36609402 PMCID: PMC9822908 DOI: 10.1038/s41467-022-35494-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/06/2022] [Indexed: 01/09/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease with poorly understood clinical heterogeneity, underscored by significant differences in patient age at onset, symptom progression, therapeutic response, disease duration, and comorbidity presentation. We perform a patient stratification analysis to better understand the variability in ALS pathology, utilizing postmortem frontal and motor cortex transcriptomes derived from 208 patients. Building on the emerging role of transposable element (TE) expression in ALS, we consider locus-specific TEs as distinct molecular features during stratification. Here, we identify three unique molecular subtypes in this ALS cohort, with significant differences in patient survival. These results suggest independent disease mechanisms drive some of the clinical heterogeneity in ALS.
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17
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Ghaffari LT, Trotti D, Haeusler AR, Jensen BK. Breakdown of the central synapses in C9orf72-linked ALS/FTD. Front Mol Neurosci 2022; 15:1005112. [PMID: 36187344 PMCID: PMC9523884 DOI: 10.3389/fnmol.2022.1005112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/29/2022] [Indexed: 01/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, fatal neurodegenerative disease that leads to the death of motor and cortical neurons. The clinical manifestations of ALS are heterogenous, and efficacious treatments to significantly slow the progression of the disease are lacking. Cortical hyper-excitability is observed pre-symptomatically across disease-causative genetic variants, as well as in the early stages of sporadic ALS, and typically precedes motor neuron involvement and overt neurodegeneration. The causes of cortical hyper-excitability are not yet fully understood but is mainly agreed to be an early event. The identification of the nucleotide repeat expansion (GGGGCC)n in the C9ORF72 gene has provided evidence that ALS and another neurodegenerative disease, frontotemporal dementia (FTD), are part of a disease spectrum with common genetic origins. ALS and FTD are diseases in which synaptic dysfunction is reported throughout disease onset and stages of progression. It has become apparent that ALS/FTD-causative genes, such as C9ORF72, may have roles in maintaining the normal physiology of the synapse, as mutations in these genes often manifest in synaptic dysfunction. Here we review the dysfunctions of the central nervous system synapses associated with the nucleotide repeat expansion in C9ORF72 observed in patients, organismal, and cellular models of ALS and FTD.
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18
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Sai Swaroop R, Akhil PS, Sai Sanwid P, Bandana P, Raksha RK, Meghana M, Bibha C, Sivaramakrishnan V. Integrated multi-omic data analysis and validation with yeast model show oxidative phosphorylation modulates protein aggregation in amyotrophic lateral sclerosis. J Biomol Struct Dyn 2022:1-20. [PMID: 35749136 DOI: 10.1080/07391102.2022.2090441] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amyotrophic Lateral Sclerosis is a progressive, incurable amyloid aggregating neurodegenerative disease involving the motor neurons. Identifying potential biomarkers and therapeutic targets can assist in the better management of the disease. We used an integrative approach encompassing analysis of transcriptomic datasets of human and mice from the GEO database. Our analysis of ALS patient datasets showed deregulation in Non-alcoholic fatty acid liver disease and oxidative phosphorylation. Transgenic mice datasets of SOD1, FUS and TDP-43 showed deregulation in oxidative phosphorylation and ribosome-associated pathways. Commonality analysis between the human and mice datasets showed oxidative phosphorylation as a major deregulated pathway. Further, protein-protein and protein-drug interaction network analysis of mitochondrial electron transport chain showed enrichment of proteins and inhibitors of mitochondrial Complex III and IV. The results were further validated using the yeast model system. Inhibitor studies using metformin (Complex-I inhibitor) and malonate (Complex-II inhibitor) did not show any effect in mitigating the amyloids, while antimycin (Complex-III inhibitor) and azide (Complex-IV inhibitor) reduced amyloidogenesis. Knock-out of QCR8 (Complex-III) or COX8 (Complex-IV) cleared the amyloids. Taken together, our results show a critical role for mitochondrial oxidative phosphorylation in amyloidogenesis and as a potential therapeutic target in ALS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R Sai Swaroop
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - P S Akhil
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India.,Scientist B, Central Water and Power Research Station, Khadakwasla, Pune
| | - Pradhan Sai Sanwid
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | | | - Rao K Raksha
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Manjunath Meghana
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Choudhary Bibha
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
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19
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Fels JA, Casalena G, Konrad C, Holmes HE, Dellinger RW, Manfredi G. Gene expression profiles in sporadic ALS fibroblasts define disease subtypes and the metabolic effects of the investigational drug EH301. Hum Mol Genet 2022; 31:3458-3477. [PMID: 35652455 DOI: 10.1093/hmg/ddac118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/04/2022] [Accepted: 05/17/2022] [Indexed: 01/18/2023] Open
Abstract
Metabolic alterations shared between the nervous system and skin fibroblasts have emerged in ALS. Recently, we found that a subgroup of sporadic ALS (sALS) fibroblasts (sALS1) is characterized by metabolic profiles distinct from other sALS cases (sALS2) and controls, suggesting that metabolic therapies could be effective in sALS. The metabolic modulators nicotinamide riboside and pterostilbene (EH301) are under clinical development for the treatment of ALS. Here, we studied the transcriptome and metabolome of sALS cells to understand the molecular bases of sALS metabotypes and the impact of EH301. Metabolomics and transcriptomics were investigated at baseline and after EH301 treatment. Moreover, weighted gene co-expression network analysis (WGCNA) was used to investigate the association of metabolic and clinical features. We found that the sALS1 transcriptome is distinct from sALS2 and that EH301 modifies gene expression differently in sALS1, sALS2, and controls. Furthermore, EH301 had strong protective effects against metabolic stress, an effect linked to anti-inflammatory and antioxidant pathways. WGCNA revealed that ALS functional rating scale and metabotypes are associated with gene modules enriched for cell cycle, immunity, autophagy, and metabolism genes, which are modified by EH301. Meta-analysis of publicly available transcriptomics data from induced motor neurons by Answer ALS confirmed functional associations of genes correlated with disease traits. A subset of genes differentially expressed in sALS fibroblasts was used in a machine learning model to predict disease progression. In conclusion, multi-omics analyses highlighted differential metabolic and transcriptomic profiles in patient-derived fibroblast sALS, which translate into differential responses to the investigational drug EH301.
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Affiliation(s)
- Jasmine A Fels
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY 10065.,Neuroscience Graduate Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Ave, New York, NY 10065
| | - Gabriella Casalena
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY 10065
| | - Csaba Konrad
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY 10065
| | | | | | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY 10065
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20
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Cortical Hyperexcitability in the Driver’s Seat in ALS. CLINICAL AND TRANSLATIONAL NEUROSCIENCE 2022. [DOI: 10.3390/ctn6010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by the degeneration of cortical and spinal motor neurons. With no effective treatment available to date, patients face progressive paralysis and eventually succumb to the disease due to respiratory failure within only a few years. Recent research has revealed the multifaceted nature of the mechanisms and cell types involved in motor neuron degeneration, thereby opening up new therapeutic avenues. Intriguingly, two key features present in both ALS patients and rodent models of the disease are cortical hyperexcitability and hyperconnectivity, the mechanisms of which are still not fully understood. We here recapitulate current findings arguing for cell autonomous and non-cell autonomous mechanisms causing cortical excitation and inhibition imbalance, which is involved in the degeneration of motor neurons in ALS. Moreover, we will highlight recent evidence that strongly indicates a cardinal role for the motor cortex as a main driver and source of the disease, thus arguing for a corticofugal trajectory of the pathology.
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21
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Li C, Yang T, Ou R, Shang H. Overlapping Genetic Architecture Between Schizophrenia and Neurodegenerative Disorders. Front Cell Dev Biol 2022; 9:797072. [PMID: 35004692 PMCID: PMC8740133 DOI: 10.3389/fcell.2021.797072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/06/2021] [Indexed: 02/05/2023] Open
Abstract
Epidemiological and clinical studies have suggested comorbidity between schizophrenia and several neurodegenerative disorders. However, little is known whether there exists shared genetic architecture. To explore their relationship from a genetic and transcriptomic perspective, we applied polygenic and linkage disequilibrium-informed methods to examine the genetic correlation between schizophrenia and amyotrophic lateral sclerosis (ALS), Parkinson’s disease, Alzheimer’s disease and frontotemporal dementia. We further combined genome-wide association summary statistics with large-scale transcriptomic datasets, to identify putative shared genes and explore related pathological tissues. We identified positive and significant correlation between schizophrenia and ALS at genetic (correlation 0.22; 95% CI: 0.16–0.28; p = 4.00E-04) and transcriptomic (correlation 0.08; 95% CI: 0.04–0.11; p = 0.034) levels. We further demonstrated that schizophrenia- and ALS-inferred gene expression overlap significantly in four tissues including skin, small intestine, brain cortex and lung, and highlighted three genes, namely GLB1L3, ZNHIT3 and TMEM194A as potential mediators of the correlation between schizophrenia and ALS. Our findings revealed overlapped gene expression profiles in specific tissues between schizophrenia and ALS, and identified novel potential shared genes. These results provided a better understanding for the pleiotropy of schizophrenia, and paved way for future studies to further elucidate the molecular drivers of schizophrenia.
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Affiliation(s)
- Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Tianmi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Ruwei Ou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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22
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Ruffo P, Strafella C, Cascella R, Caputo V, Conforti FL, Andò S, Giardina E. Deregulation of ncRNA in Neurodegenerative Disease: Focus on circRNA, lncRNA and miRNA in Amyotrophic Lateral Sclerosis. Front Genet 2021; 12:784996. [PMID: 34925464 PMCID: PMC8674781 DOI: 10.3389/fgene.2021.784996] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 01/17/2023] Open
Abstract
Parallel and massive sequencing of total RNA samples derived from different samples are possible thanks to the use of NGS (Next Generation Sequencing) technologies. This allowed characterizing the transcriptomic profile of both cell and tissue populations, increasing the knowledge of the molecular pathological processes of complex diseases, such as neurodegenerative diseases (NDs). Among the NDs, Amyotrophic Lateral Sclerosis (ALS) is caused by the progressive loss of motor neurons (MNs), and, to date, the diagnosis is often made by exclusion because there is no specific symptomatologic picture. For this reason, it is important to search for biomarkers that are clinically useful for carrying out a fast and accurate diagnosis of ALS. Thanks to various studies, it has been possible to propose several molecular mechanisms associated with the disease, some of which include the action of non-coding RNA, including circRNAs, miRNAs, and lncRNAs which will be discussed in the present review. The evidence analyzed in this review highlights the importance of conducting studies to better characterize the different ncRNAs in the disease to use them as possible diagnostic, prognostic, and/or predictive biomarkers of ALS and other NDs.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Sebastiano Andò
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
- Centro Sanitario, University of Calabria, Arcavacata di Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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23
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Gentile G, Perrone B, Morello G, Simone IL, Andò S, Cavallaro S, Conforti FL. Individual Oligogenic Background in p.D91A- SOD1 Amyotrophic Lateral Sclerosis Patients. Genes (Basel) 2021; 12:genes12121843. [PMID: 34946792 PMCID: PMC8701978 DOI: 10.3390/genes12121843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/20/2021] [Indexed: 01/02/2023] Open
Abstract
The p.D91A is one of the most common ALS-causing SOD1 mutations and is known to be either recessive or dominant. The homozygous phenotype is characterized by prolonged survival and slow progression of disease, whereas the affected heterozygous phenotypes can vary. To date, no genetic protective factors located close to SOD1 have been associated with the mild progressive homozygous phenotype. Using Next Generation Sequencing (NGS), we characterized a small cohort of sporadic and familial p.D91A-SOD1 heterozygous (n = 2) or homozygous (n = 5) ALS patients, to reveal any additional contributing variant in 39 ALS-related genes. We detected unique sets of non-synonymous variants, four of which were of uncertain significance and several in untranslated regions of ALS-related genes. Our results supported an individual oligogenic background underlying both sporadic and familial p.D91A cases irrespective of their p.D91A mutant alleles. We suggest that a comprehensive genomic view of p.D91A-SOD1 ALS patients may be useful in identifying emerging variants and improving disease diagnosis as well as guiding precision medicine.
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Affiliation(s)
- Giulia Gentile
- Institute for Biomedical Research and Innovation, Department of Biomedical Sciences, National Research Council (CNR), 95126 Catania, Italy; (G.G.); (G.M.); (S.C.)
| | - Benedetta Perrone
- Medical Genetics Laboratory, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (B.P.); (S.A.)
| | - Giovanna Morello
- Institute for Biomedical Research and Innovation, Department of Biomedical Sciences, National Research Council (CNR), 95126 Catania, Italy; (G.G.); (G.M.); (S.C.)
| | - Isabella Laura Simone
- Neurology Unit, Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, 70121 Bari, Italy;
| | - Sebastiano Andò
- Medical Genetics Laboratory, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (B.P.); (S.A.)
- Centro Sanitario, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, Department of Biomedical Sciences, National Research Council (CNR), 95126 Catania, Italy; (G.G.); (G.M.); (S.C.)
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (B.P.); (S.A.)
- Correspondence:
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24
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La Cognata V, Golini E, Iemmolo R, Balletta S, Morello G, De Rosa C, Villari A, Marinelli S, Vacca V, Bonaventura G, Dell'Albani P, Aronica E, Mammano F, Mandillo S, Cavallaro S. CXCR2 increases in ALS cortical neurons and its inhibition prevents motor neuron degeneration in vitro and improves neuromuscular function in SOD1G93A mice. Neurobiol Dis 2021; 160:105538. [PMID: 34743985 DOI: 10.1016/j.nbd.2021.105538] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/13/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease characterized by depletion of motor neurons (MNs), for which effective medical treatments are still required. Previous transcriptomic analysis revealed the up-regulation of C-X-C motif chemokine receptor 2 (CXCR2)-mRNA in a subset of sporadic ALS patients and SOD1G93A mice. Here, we confirmed the increase of CXCR2 in human ALS cortex, and showed that CXCR2 is mainly localized in cell bodies and axons of cortical neurons. We also investigated the effects of reparixin, an allosteric inhibitor of CXCR2, in degenerating human iPSC-derived MNs and SOD1G93A mice. In vitro, reparixin rescued MNs from apoptotic cell death, preserving neuronal morphology, mitochondrial membrane potential and cytoplasmic membrane integrity, whereas in vivo it improved neuromuscular function of SOD1G93A mice. Altogether, these data suggest a role for CXCR2 in ALS pathology and support its pharmacological inhibition as a candidate therapeutic strategy against ALS at least in a specific subgroup of patients.
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Affiliation(s)
- Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Elisabetta Golini
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Rosario Iemmolo
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Sara Balletta
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Carla De Rosa
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Ambra Villari
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Sara Marinelli
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Valentina Vacca
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Gabriele Bonaventura
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Paola Dell'Albani
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 Amsterdam, the Netherlands.
| | - Fabio Mammano
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy; Department of Physics and Astronomy "G. Galilei", University of Padua, Padova, Italy.
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
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25
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Molecular Classification and Interpretation of Amyotrophic Lateral Sclerosis Using Deep Convolution Neural Networks and Shapley Values. Genes (Basel) 2021; 12:genes12111754. [PMID: 34828360 PMCID: PMC8626003 DOI: 10.3390/genes12111754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a prototypical neurodegenerative disease characterized by progressive degeneration of motor neurons to severely effect the functionality to control voluntary muscle movement. Most of the non-additive genetic aberrations responsible for ALS make its molecular classification very challenging along with limited sample size, curse of dimensionality, class imbalance and noise in the data. Deep learning methods have been successful in many other related areas but have low minority class accuracy and suffer from the lack of explainability when used directly with RNA expression features for ALS molecular classification. In this paper, we propose a deep-learning-based molecular ALS classification and interpretation framework. Our framework is based on training a convolution neural network (CNN) on images obtained from converting RNA expression values into pixels based on DeepInsight similarity technique. Then, we employed Shapley additive explanations (SHAP) to extract pixels with higher relevance to ALS classifications. These pixels were mapped back to the genes which made them up. This enabled us to classify ALS samples with high accuracy for a minority class along with identifying genes that might be playing an important role in ALS molecular classifications. Taken together with RNA expression images classified with CNN, our preliminary analysis of the genes identified by SHAP interpretation demonstrate the value of utilizing Machine Learning to perform molecular classification of ALS and uncover disease-associated genes.
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26
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Jiménez-Villegas J, Ferraiuolo L, Mead RJ, Shaw PJ, Cuadrado A, Rojo AI. NRF2 as a therapeutic opportunity to impact in the molecular roadmap of ALS. Free Radic Biol Med 2021; 173:125-141. [PMID: 34314817 DOI: 10.1016/j.freeradbiomed.2021.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/12/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a devastating heterogeneous disease with still no convincing therapy. To identify the most strategically significant hallmarks for therapeutic intervention, we have performed a comprehensive transcriptomics analysis of dysregulated pathways, comparing datasets from ALS patients and healthy donors. We have identified crucial alterations in RNA metabolism, intracellular transport, vascular system, redox homeostasis, proteostasis and inflammatory responses. Interestingly, the transcription factor NRF2 (nuclear factor (erythroid-derived 2)-like 2) has significant effects in modulating these pathways. NRF2 has been classically considered as the master regulator of the antioxidant cellular response, although it is currently considered as a key component of the transduction machinery to maintain coordinated control of protein quality, inflammation, and redox homeostasis. Herein, we will summarize the data from NRF2 activators in ALS pre-clinical models as well as those that are being studied in clinical trials. As we will discuss, NRF2 is a promising target to build a coordinated transcriptional response to motor neuron injury, highlighting its therapeutic potential to combat ALS.
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Affiliation(s)
- J Jiménez-Villegas
- Department of Biochemistry, Medical College, Autonomous University of Madrid (UAM), Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain; Instituto de Investigación Sanitaria La Paz (IdiPaz), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - L Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - R J Mead
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - P J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - A Cuadrado
- Department of Biochemistry, Medical College, Autonomous University of Madrid (UAM), Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain; Instituto de Investigación Sanitaria La Paz (IdiPaz), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - A I Rojo
- Department of Biochemistry, Medical College, Autonomous University of Madrid (UAM), Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain; Instituto de Investigación Sanitaria La Paz (IdiPaz), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
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27
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Shan L, Martens GJM, Swaab DF. Histamine-4 Receptor: Emerging Target for the Treatment of Neurological Diseases. Curr Top Behav Neurosci 2021; 59:131-145. [PMID: 34432256 DOI: 10.1007/7854_2021_237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A major challenge in the field of the biogenic amine histamine is the search for new-generation histamine receptor specific drugs. Daniel Bovet and Sir James Black received their Nobel Prizes for Medicine for their work on histamine-1 receptor (H1R) and H2R antagonists to treat allergies and gastrointestinal disorders. The first H3R-targeting drug to reach the market was approved for the treatment of the neurological disorder narcolepsy in 2018. The antagonists for the most recently identified histamine receptor, H4R, are currently under clinical evaluation for their potential therapeutic effects on inflammatory diseases such as atopic dermatitis and pruritus. In this chapter, we propose that H4R antagonists are endowed with prominent anti-inflammatory and immune effects, including in the brain. To substantiate this proposition, we combine data from transcriptional analyses of postmortem human neurodegenerative disease brain samples, human genome-wide association studies (GWAS), and translational animal model studies. The results prompt us to suggest the potential involvement of the H4R in various neurodegenerative diseases and how manipulating the H4R may create new therapeutic opportunities in central nervous system diseases.
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Affiliation(s)
- Ling Shan
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, An Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Faculty of Science, Donders Institute for Brain, Cognition and Behaviour, Donders Centre for Neuroscience, Nijmegen, GA, The Netherlands
| | - Dick F Swaab
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, An Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
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28
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De Marchi F, Munitic I, Amedei A, Berry JD, Feldman EL, Aronica E, Nardo G, Van Weehaeghe D, Niccolai E, Prtenjaca N, Sakowski SA, Bendotti C, Mazzini L. Interplay between immunity and amyotrophic lateral sclerosis: Clinical impact. Neurosci Biobehav Rev 2021; 127:958-978. [PMID: 34153344 PMCID: PMC8428677 DOI: 10.1016/j.neubiorev.2021.06.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/07/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating and rapidly fatal neurodegenerative disease. Despite decades of research and many new insights into disease biology over the 150 years since the disease was first described, causative pathogenic mechanisms in ALS remain poorly understood, especially in sporadic cases. Our understanding of the role of the immune system in ALS pathophysiology, however, is rapidly expanding. The aim of this manuscript is to summarize the recent advances regarding the immune system involvement in ALS, with particular attention to clinical translation. We focus on the potential pathophysiologic mechanism of the immune system in ALS, discussing local and systemic factors (blood, cerebrospinal fluid, and microbiota) that influence ALS onset and progression in animal models and people. We also explore the potential of Positron Emission Tomography to detect neuroinflammation in vivo, and discuss ongoing clinical trials of therapies targeting the immune system. With validation in human patients, new evidence in this emerging field will serve to identify novel therapeutic targets and provide realistic hope for personalized treatment strategies.
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Affiliation(s)
- Fabiola De Marchi
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, Novara, 28100, Italy
| | - Ivana Munitic
- Laboratory for Molecular Immunology, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000, Rijeka, Croatia
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - James D Berry
- Sean M. Healey & AMG Center for ALS, Department of Neurology, Massachusetts General Hospital, 165 Cambridge Street, Suite 600, Boston, MA, 02114, USA
| | - Eva L Feldman
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Department of (Neuro) Pathology, Amsterdam Neuroscience, Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Giovanni Nardo
- Laboratory of Molecular Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milanm, 20156, Italy
| | - Donatienne Van Weehaeghe
- Division of Nuclear Medicine, Department of Imaging and Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Elena Niccolai
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Nikolina Prtenjaca
- Laboratory for Molecular Immunology, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000, Rijeka, Croatia
| | - Stacey A Sakowski
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Caterina Bendotti
- Laboratory of Molecular Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milanm, 20156, Italy
| | - Letizia Mazzini
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, Novara, 28100, Italy.
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29
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Two distinct skeletal muscle microRNA signatures revealing the complex mechanism of sporadic ALS. Acta Neurol Belg 2021; 122:1499-1509. [PMID: 34241798 DOI: 10.1007/s13760-021-01743-w] [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: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Skeletal muscle pathology is thought to have an important role in the onset and/or progression of amyotrophic lateral sclerosis (ALS), which is a neurodegenerative disorder characterized by progressive muscle weakness. Since miRNAs are recognized as important regulatory factors of essential biological processes, we aimed to identify differentially expressed miRNAs in the skeletal muscle of sporadic ALS patients through the combination of molecular-omic technologies and bioinformatic tools. We analyzed the miRnome profiles of skeletal muscle biopsies acquired from ten sALS patients and five controls with Affymetrix GeneChip miRNA 4.0 Array. To find out differentially expressed miRNAs in patients, data were analyzed by The Institute for Genomic Research-Multi Experiment Viewer (MeV) and miRNAs whose expression difference were statistically significant were identified as candidates. The potential target genes of these miRNAs were predicted by miRWalk 2.0 and were functionally enriched by gene ontology (GO) analysis. The expression level of priority candidates was validated by quantitative real-time PCR (qRT-PCR) analysis. We identified ten differentially expressed miRNAs in patients with a fold change threshold ≥ 2.0, FDR = 0. We identified ten differentially expressed miRNAs in patients with a fold change threshold ≥ 2.0, FDR = 0. Nine out of the ten miRNAs were found to be related to top three enriched ALS-related terms. Based on the qRT-PCR validation of candidate miRNAs, patients were separated into two groups: those with upregulated miR-4429 and miR-1825 expression and those with downregulated miR-638 expression. The different muscle-specific miRNA profiles in sALS patients may indicate the involvement of etiologic heterogeneity, which may allow the development of novel therapeutic strategies.
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La Cognata V, Morello G, Cavallaro S. Omics Data and Their Integrative Analysis to Support Stratified Medicine in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22094820. [PMID: 34062930 PMCID: PMC8125201 DOI: 10.3390/ijms22094820] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/23/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Molecular and clinical heterogeneity is increasingly recognized as a common characteristic of neurodegenerative diseases (NDs), such as Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. This heterogeneity makes difficult the development of early diagnosis and effective treatment approaches, as well as the design and testing of new drugs. As such, the stratification of patients into meaningful disease subgroups, with clinical and biological relevance, may improve disease management and the development of effective treatments. To this end, omics technologies-such as genomics, transcriptomics, proteomics and metabolomics-are contributing to offer a more comprehensive view of molecular pathways underlying the development of NDs, helping to differentiate subtypes of patients based on their specific molecular signatures. In this article, we discuss how omics technologies and their integration have provided new insights into the molecular heterogeneity underlying the most prevalent NDs, aiding to define early diagnosis and progression markers as well as therapeutic targets that can translate into stratified treatment approaches, bringing us closer to the goal of personalized medicine in neurology.
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31
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iPSCs: A Preclinical Drug Research Tool for Neurological Disorders. Int J Mol Sci 2021; 22:ijms22094596. [PMID: 33925625 PMCID: PMC8123805 DOI: 10.3390/ijms22094596] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/24/2021] [Accepted: 04/24/2021] [Indexed: 02/07/2023] Open
Abstract
The development and commercialization of new drugs is an articulated, lengthy, and very expensive process that proceeds through several steps, starting from target identification, screening new leading compounds for testing in preclinical studies, and subsequently in clinical trials to reach the final approval for therapeutic use. Preclinical studies are usually performed using both cell cultures and animal models, although they do not completely resume the complexity of human diseases, in particular neurodegenerative conditions. To this regard, stem cells represent a powerful tool in all steps of drug discovery. The recent advancement in induced Pluripotent Stem Cells (iPSCs) technology has opened the possibility to obtain patient-specific disease models for drug screening and development. Here, we report the use of iPSCs as a disease model for drug development in the contest of neurological disorders, including Alzheimer’s (AD) and Parkinson’s disease (PD), Amyotrophic lateral Sclerosis (ALS), and Fragile X syndrome (FRAX).
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32
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Morello G, Salomone S, D’Agata V, Conforti FL, Cavallaro S. From Multi-Omics Approaches to Precision Medicine in Amyotrophic Lateral Sclerosis. Front Neurosci 2020; 14:577755. [PMID: 33192262 PMCID: PMC7661549 DOI: 10.3389/fnins.2020.577755] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and fatal neurodegenerative disorder, caused by the degeneration of upper and lower motor neurons for which there is no truly effective cure. The lack of successful treatments can be well explained by the complex and heterogeneous nature of ALS, with patients displaying widely distinct clinical features and progression patterns, and distinct molecular mechanisms underlying the phenotypic heterogeneity. Thus, stratifying ALS patients into consistent and clinically relevant subgroups can be of great value for the development of new precision diagnostics and targeted therapeutics for ALS patients. In the last years, the use and integration of high-throughput "omics" approaches have dramatically changed our thinking about ALS, improving our understanding of the complex molecular architecture of ALS, distinguishing distinct patient subtypes and providing a rational foundation for the discovery of biomarkers and new individualized treatments. In this review, we discuss the most significant contributions of omics technologies in unraveling the biological heterogeneity of ALS, highlighting how these approaches are revealing diagnostic, prognostic and therapeutic targets for future personalized interventions.
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Affiliation(s)
- Giovanna Morello
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Salvatore Salomone
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Velia D’Agata
- Human Anatomy and Histology, University of Catania, Catania, Italy
| | | | - Sebastiano Cavallaro
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
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33
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Volonté C, Morello G, Spampinato AG, Amadio S, Apolloni S, D’Agata V, Cavallaro S. Omics-based exploration and functional validation of neurotrophic factors and histamine as therapeutic targets in ALS. Ageing Res Rev 2020; 62:101121. [PMID: 32653439 DOI: 10.1016/j.arr.2020.101121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/27/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
A plethora of genetic and molecular mechanisms have been implicated in the pathophysiology of the heterogeneous and multifactorial amyotrophic lateral sclerosis (ALS) disease, and hence the conventional "one target-one drug" paradigm has failed so far to provide effective therapeutic solutions, precisely because of the complex nature of ALS. This review intends to highlight how the integration of emerging "omics" approaches may provide a rational foundation for the comprehensive exploration of molecular pathways and dynamic interactions involved in ALS, for the identification of candidate targets and biomarkers that will assist in the rapid diagnosis and prognosis, lastly for the stratification of patients into different subgroups with the aim of personalized therapeutic strategies. To this purpose, particular emphasis will be placed on some potential therapeutic targets, including neurotrophic factors and histamine signaling that both have emerged as dysregulated at different omics levels in specific subgroups of ALS patients, and have already shown promising results in in vitro and in vivo models of ALS. To conclude, we will discuss about the utility of using integrated omics coupled with network-based approaches to provide additional guidance for personalization of medicine applications in ALS.
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34
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Maugeri G, D'Amico AG, Morello G, Reglodi D, Cavallaro S, D'Agata V. Differential Vulnerability of Oculomotor Versus Hypoglossal Nucleus During ALS: Involvement of PACAP. Front Neurosci 2020; 14:805. [PMID: 32848572 PMCID: PMC7432287 DOI: 10.3389/fnins.2020.00805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive multifactorial disease characterized by the loss of motor neurons (MNs). Not all MNs undergo degeneration: neurons of the oculomotor nucleus, which regulate eye movements, are less vulnerable compared to hypoglossal nucleus MNs. Several molecular studies have been performed to understand the different vulnerability of these MNs. By analyzing postmortem samples from ALS patients to other unrelated decedents, the differential genomic pattern between the two nuclei has been profiled. Among identified genes, adenylate cyclase activating polypeptide 1 (ADCYAP1) gene, encoding for pituitary adenylate cyclase-activating polypeptide (PACAP), was found significantly up-regulated in the oculomotor versus hypoglossal nucleus suggesting that it could play a trophic effect on MNs in ALS. In the present review, some aspects regarding the different vulnerability of oculomotor and hypoglossal nucleus to degeneration will be summarized. The distribution and potential role of PACAP on these MNs as studied largely in an animal model of ALS compared to controls, will be discussed.
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Affiliation(s)
- Grazia Maugeri
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Sciences, University of Catania, Catania, Italy
| | | | - Giovanna Morello
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Catania, Italy
| | - Dora Reglodi
- Department of Anatomy, MTA-PTE PACAP Research Team, University of Pécs Medical School, Pécs, Hungary
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Catania, Italy
| | - Velia D'Agata
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Sciences, University of Catania, Catania, Italy
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35
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Calió ML, Henriques E, Siena A, Bertoncini CRA, Gil-Mohapel J, Rosenstock TR. Mitochondrial Dysfunction, Neurogenesis, and Epigenetics: Putative Implications for Amyotrophic Lateral Sclerosis Neurodegeneration and Treatment. Front Neurosci 2020; 14:679. [PMID: 32760239 PMCID: PMC7373761 DOI: 10.3389/fnins.2020.00679] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and devastating multifactorial neurodegenerative disorder. Although the pathogenesis of ALS is still not completely understood, numerous studies suggest that mitochondrial deregulation may be implicated in its onset and progression. Interestingly, mitochondrial deregulation has also been associated with changes in neural stem cells (NSC) proliferation, differentiation, and migration. In this review, we highlight the importance of mitochondrial function for neurogenesis, and how both processes are correlated and may contribute to the pathogenesis of ALS; we have focused primarily on preclinical data from animal models of ALS, since to date no studies have evaluated this link using human samples. As there is currently no cure and no effective therapy to counteract ALS, we have also discussed how improving neurogenic function by epigenetic modulation could benefit ALS. In support of this hypothesis, changes in histone deacetylation can alter mitochondrial function, which in turn might ameliorate cellular proliferation as well as neuronal differentiation and migration. We propose that modulation of epigenetics, mitochondrial function, and neurogenesis might provide new hope for ALS patients, and studies exploring these new territories are warranted in the near future.
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Affiliation(s)
| | - Elisandra Henriques
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Science, São Paulo, Brazil
| | - Amanda Siena
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Science, São Paulo, Brazil
| | - Clélia Rejane Antonio Bertoncini
- CEDEME, Center of Development of Experimental Models for Medicine and Biology, Federal University of São Paulo, São Paulo, Brazil
| | - Joana Gil-Mohapel
- Division of Medical Sciences, Faculty of Medicine, University of Victoria and Island Medical Program, University of British Columbia, Victoria, BC, Canada
| | - Tatiana Rosado Rosenstock
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Science, São Paulo, Brazil
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36
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Gunes ZI, Kan VWY, Ye X, Liebscher S. Exciting Complexity: The Role of Motor Circuit Elements in ALS Pathophysiology. Front Neurosci 2020; 14:573. [PMID: 32625051 PMCID: PMC7311855 DOI: 10.3389/fnins.2020.00573] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease, characterized by the degeneration of both upper and lower motor neurons. Despite decades of research, we still to date lack a cure or disease modifying treatment, emphasizing the need for a much-improved insight into disease mechanisms and cell type vulnerability. Altered neuronal excitability is a common phenomenon reported in ALS patients, as well as in animal models of the disease, but the cellular and circuit processes involved, as well as the causal relevance of those observations to molecular alterations and final cell death, remain poorly understood. Here, we review evidence from clinical studies, cell type-specific electrophysiology, genetic manipulations and molecular characterizations in animal models and culture experiments, which argue for a causal involvement of complex alterations of structure, function and connectivity of different neuronal subtypes within the cortical and spinal cord motor circuitries. We also summarize the current knowledge regarding the detrimental role of astrocytes and reassess the frequently proposed hypothesis of glutamate-mediated excitotoxicity with respect to changes in neuronal excitability. Together, these findings suggest multifaceted cell type-, brain area- and disease stage- specific disturbances of the excitation/inhibition balance as a cardinal aspect of ALS pathophysiology.
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Affiliation(s)
- Zeynep I Gunes
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig Maximilians University Munich, Munich, Germany.,Graduate School of Systemic Neurosciences, Ludwig Maximilians University Munich, Munich, Germany.,Biomedical Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Vanessa W Y Kan
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig Maximilians University Munich, Munich, Germany.,Graduate School of Systemic Neurosciences, Ludwig Maximilians University Munich, Munich, Germany.,Biomedical Center, Ludwig Maximilians University Munich, Munich, Germany
| | - XiaoQian Ye
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig Maximilians University Munich, Munich, Germany.,Biomedical Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Sabine Liebscher
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig Maximilians University Munich, Munich, Germany.,Biomedical Center, Ludwig Maximilians University Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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37
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Srinivasan E, Rajasekaran R. A Systematic and Comprehensive Review on Disease-Causing Genes in Amyotrophic Lateral Sclerosis. J Mol Neurosci 2020; 70:1742-1770. [PMID: 32415434 DOI: 10.1007/s12031-020-01569-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and is characterized by degeneration and axon loss from the upper motor neuron, that descends from the lower motor neuron in the brain. Over the period, assorted outcomes from medical findings, molecular pathogenesis, and structural and biophysical studies have abetted in providing thoughtful insights underlying the importance of disease-causing genes in ALS. Consequently, numerous mechanisms were proposed for the pathogenesis of ALS, considering protein mutations, aggregation, and misfolding. Besides, the answers to the majority of ALS cases that happen to be sporadic still remain obscure. The application in discovering susceptibility factors in ALS contemplating the genetic factors is to be further dissevered in the future years with innovation in research studies. Hence, this review targets in revisiting the breakthroughs on the disease-causing genes related with ALS.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (deemed to be university), Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (deemed to be university), Vellore, Tamil Nadu, 632014, India.
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38
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Brunet A, Stuart-Lopez G, Burg T, Scekic-Zahirovic J, Rouaux C. Cortical Circuit Dysfunction as a Potential Driver of Amyotrophic Lateral Sclerosis. Front Neurosci 2020; 14:363. [PMID: 32410944 PMCID: PMC7201269 DOI: 10.3389/fnins.2020.00363] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that affects selected cortical and spinal neuronal populations, leading to progressive paralysis and death. A growing body of evidences suggests that the disease may originate in the cerebral cortex and propagate in a corticofugal manner. In particular, transcranial magnetic stimulation studies revealed that ALS patients present with early cortical hyperexcitability arising from a combination of increased excitability and decreased inhibition. Here, we discuss the possibility that initial cortical circuit dysfunction might act as the main driver of ALS onset and progression, and review recent functional, imaging and transcriptomic studies conducted on ALS patients, along with electrophysiological, pathological and transcriptomic studies on animal and cellular models of the disease, in order to evaluate the potential cellular and molecular origins of cortical hyperexcitability in ALS.
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Affiliation(s)
| | | | | | | | - Caroline Rouaux
- INSERM UMR_S 1118, Mécanismes Centraux et Périphériques de la Neurodégénérescence, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
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39
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Splicing Players Are Differently Expressed in Sporadic Amyotrophic Lateral Sclerosis Molecular Clusters and Brain Regions. Cells 2020; 9:cells9010159. [PMID: 31936368 PMCID: PMC7017305 DOI: 10.3390/cells9010159] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/23/2019] [Accepted: 01/04/2020] [Indexed: 12/12/2022] Open
Abstract
Splicing is a tightly orchestrated process by which the brain produces protein diversity over time and space. While this process specializes and diversifies neurons, its deregulation may be responsible for their selective degeneration. In amyotrophic lateral sclerosis (ALS), splicing defects have been investigated at the singular gene level without considering the higher-order level, involving the entire splicing machinery. In this study, we analyzed the complete spectrum (396) of genes encoding splicing factors in the motor cortex (41) and spinal cord (40) samples from control and sporadic ALS (SALS) patients. A substantial number of genes (184) displayed significant expression changes in tissue types or disease states, were implicated in distinct splicing complexes and showed different topological hierarchical roles based on protein–protein interactions. The deregulation of one of these splicing factors has a central topological role, i.e., the transcription factor YBX1, which might also have an impact on stress granule formation, a pathological marker associated with ALS.
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40
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Krokidis MG. Transcriptomics and Metabolomics in Amyotrophic Lateral Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1195:205-212. [PMID: 32468479 DOI: 10.1007/978-3-030-32633-3_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving progressive and selective loss of motor neurons, muscle weakness, paralysis and death. The pathogenesis of ALS is not clearly understood, while reliable prognostic markers have not been identified to detect symptoms at earlier time points. The rapid development of microarray technology offers great potential for simultaneous analysis of the transcriptional expression of thousands of genes, aiming to determine novel candidate targets for efficient treatment. Additionally, metabolomics, as a high-throughput approach, is gaining significant attention in ALS research providing an opportunity to develop predictive biomarkers that may be utilized as indicators of clinical symptoms of ALS. In this review, recent evidences from gene expression profiling studies in ALS are illustrated in order to examine molecular signatures related to the disease's pathogenesis and potential discovery of therapeutic targets. Moreover, potent challenges are presented regarding the utilization of the metabolomics approach as a diagnostic tool in context with distinctive biomarkers' identification.
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Affiliation(s)
- Marios G Krokidis
- National Center for Scientific Research "Demokritos", Institute of Nanoscience and Nanotechnology, Patriarchou Grigoriou & Neapoleos, Athens, Greece.
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41
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Mejzini R, Flynn LL, Pitout IL, Fletcher S, Wilton SD, Akkari PA. ALS Genetics, Mechanisms, and Therapeutics: Where Are We Now? Front Neurosci 2019; 13:1310. [PMID: 31866818 PMCID: PMC6909825 DOI: 10.3389/fnins.2019.01310] [Citation(s) in RCA: 454] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022] Open
Abstract
The scientific landscape surrounding amyotrophic lateral sclerosis (ALS) continues to shift as the number of genes associated with the disease risk and pathogenesis, and the cellular processes involved, continues to grow. Despite decades of intense research and over 50 potentially causative or disease-modifying genes identified, etiology remains unexplained and treatment options remain limited for the majority of ALS patients. Various factors have contributed to the slow progress in understanding and developing therapeutics for this disease. Here, we review the genetic basis of ALS, highlighting factors that have contributed to the elusiveness of genetic heritability. The most commonly mutated ALS-linked genes are reviewed with an emphasis on disease-causing mechanisms. The cellular processes involved in ALS pathogenesis are discussed, with evidence implicating their involvement in ALS summarized. Past and present therapeutic strategies and the benefits and limitations of the model systems available to ALS researchers are discussed with future directions for research that may lead to effective treatment strategies outlined.
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Affiliation(s)
- Rita Mejzini
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- The Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Loren L. Flynn
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- The Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Ianthe L. Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- The Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- The Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- The Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - P. Anthony Akkari
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- The Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
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42
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Apolloni S, Amadio S, Fabbrizio P, Morello G, Spampinato AG, Latagliata EC, Salvatori I, Proietti D, Ferri A, Madaro L, Puglisi-Allegra S, Cavallaro S, Volonté C. Histaminergic transmission slows progression of amyotrophic lateral sclerosis. J Cachexia Sarcopenia Muscle 2019; 10:872-893. [PMID: 31020811 PMCID: PMC6711424 DOI: 10.1002/jcsm.12422] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Histamine is an immune modulator, neuroprotective, and remyelinating agent, beneficially acting on skeletal muscles and promoting anti-inflammatory features in amyotrophic lateral sclerosis (ALS) microglia. Drugs potentiating the endogenous release of histamine are in trial for neurological diseases, with a role not systematically investigated in ALS. Here, we examine histamine pathway associations in ALS patients and the efficacy of a histamine-mediated therapeutic strategy in ALS mice. METHODS We adopted an integrative multi-omics approach combining gene expression profiles, copy number variants, and single nucleotide polymorphisms of ALS patients. We treated superoxide dismutase 1 (SOD1)-G93A mice that recapitulate key ALS features, with the brain-permeable histamine precursor histidine in the symptomatic phase of the disease and analysed the rescue from disease pathological signs. We examined the action of histamine in cultured SOD1-G93A motor neuron-like cells. RESULTS We identified 13 histamine-related genes deregulated in the spinal cord of two ALS patient subgroups, among which genes involved in histamine metabolism, receptors, transport, and secretion. Some histamine-related genes overlapped with genomic regions disrupted by DNA copy number and with ALS-linked pathogenic variants. Histidine treatment in SOD1-G93A mice proved broad efficacy in ameliorating ALS features, among which most importantly lifespan, motor performance, microgliosis, muscle atrophy, and motor neurons survival in vivo and in vitro. CONCLUSIONS Our gene set/pathway enrichment analyses and preclinical studies started at the onset of symptoms establish that histamine-related genes are modifiers in ALS, supporting their role as candidate biomarkers and therapeutic targets. We disclose a novel important role for histamine in the characterization of the multi-gene network responsible for ALS and, furthermore, in the drug development process.
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Affiliation(s)
| | | | - Paola Fabbrizio
- IRCCS Fondazione Santa Lucia, Rome, Italy.,National Research Council, Institute of Cell Biology and Neurobiology, Rome, Italy
| | - Giovanna Morello
- National Research Council, Institute of Neurological Sciences, Catania, Italy
| | | | | | | | | | - Alberto Ferri
- IRCCS Fondazione Santa Lucia, Rome, Italy.,National Research Council, Institute of Translational Pharmacology, Rome, Italy
| | | | | | | | - Cinzia Volonté
- IRCCS Fondazione Santa Lucia, Rome, Italy.,National Research Council, Institute of Cell Biology and Neurobiology, Rome, Italy
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43
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Integrative multi-omic analysis identifies new drivers and pathways in molecularly distinct subtypes of ALS. Sci Rep 2019; 9:9968. [PMID: 31292500 PMCID: PMC6620285 DOI: 10.1038/s41598-019-46355-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/04/2019] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable and fatal neurodegenerative disease. Increasing the chances of success for future clinical strategies requires more in-depth knowledge of the molecular basis underlying disease heterogeneity. We recently laid the foundation for a molecular taxonomy of ALS by whole-genome expression profiling of motor cortex from sporadic ALS (SALS) patients. Here, we analyzed copy number variants (CNVs) occurring in the same patients, by using a customized exon-centered comparative genomic hybridization array (aCGH) covering a large panel of ALS-related genes. A large number of novel and known disease-associated CNVs were detected in SALS samples, including several subgroup-specific loci, suggestive of a great divergence of two subgroups at the molecular level. Integrative analysis of copy number profiles with their associated transcriptomic data revealed subtype-specific genomic perturbations and candidate driver genes positively correlated with transcriptional signatures, suggesting a strong interaction between genomic and transcriptomic events in ALS pathogenesis. The functional analysis confirmed our previous pathway-based characterization of SALS subtypes and identified 24 potential candidates for genomic-based patient stratification. To our knowledge, this is the first comprehensive "omics" analysis of molecular events characterizing SALS pathology, providing a road map to facilitate genome-guided personalized diagnosis and treatments for this devastating disease.
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Volonté C, Apolloni S, Sabatelli M. Histamine beyond its effects on allergy: Potential therapeutic benefits for the treatment of Amyotrophic Lateral Sclerosis (ALS). Pharmacol Ther 2019; 202:120-131. [PMID: 31233766 DOI: 10.1016/j.pharmthera.2019.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023]
Abstract
ALS currently remains a challenge despite many efforts in performing successful clinical trials and formulating therapeutic solutions. By learning from current failures and striving for success, scientists and clinicians are checking every possibility to search for missing hints and efficacious treatments. Because the disease is very complex and heterogeneous and, moreover, targeting not only motor neurons but also several different cell types including muscle, glial, and immune cells, the right answer to ALS is conceivably a multidrug strategy or the use of broad-spectrum molecules. The aim of the present work is to gather evidence about novel perspectives on ALS pathogenesis and to present recent and innovative paradigms for therapy. In particular, we describe how an old molecule possessing immunomodulatory and neuroprotective functions beyond its recognized effects on allergy, histamine, might have a renewed and far-reaching momentum in ALS.
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Affiliation(s)
- Cinzia Volonté
- CNR-Institute of Cell Biology and Neurobiology/UCSC, Largo Francesco Vito 1, 00168 Rome, Italy; Fondazione Santa Lucia IRCCS, Preclinical Neuroscience, Via Del Fosso di Fiorano 65, 00143 Rome, Italy.
| | - Savina Apolloni
- Fondazione Santa Lucia IRCCS, Preclinical Neuroscience, Via Del Fosso di Fiorano 65, 00143 Rome, Italy
| | - Mario Sabatelli
- Institute of Neurology-Catholic University of Sacro Cuore, Clinic Center NEMO- Fondazione Pol. A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168 Rome, Italy
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Zhang F, Liu M, Li Q, Song FX. Exploration of attractor modules for sporadic amyotrophic lateral sclerosis via systemic module inference and attract method. Exp Ther Med 2019; 17:2575-2580. [PMID: 30906448 PMCID: PMC6425136 DOI: 10.3892/etm.2019.7264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 02/01/2019] [Indexed: 12/01/2022] Open
Abstract
Sporadic amyotrophic lateral sclerosis (SALS) is a devastating neurodegenerative disorder. However, the understanding of SALS is still poor. This research aimed to excavate attractor modules for SALS by integrating the systemic module inference and attract method. To achieve this, gene expression data and protein-protein data were recruited and preprocessed. Then, based on the Spearman's correlation coefficient (SCC) of the interactions under these two conditions, two PPI networks separately with 870 nodes (979 interactions) in normal control group and 601 nodes (777 interactions) in SALS group were built. Systemic module inference method was performed to identify the modules, and attract method was used to identify attractor modules. Finally, pathway enrichment analysis was performed to disclose the functional enrichment of these attractor modules. In total 44 and 118 modules were identified for normal control and SALS groups, respectively. Among them, 6 modules were with similar gene composition between the two groups, and all 6 modules were considered as the attractor module via attract method. These attractor modules might be potential biomarkers for early diagnosis and therapy of SALS, which could provide insight into the disease biology and suggest possible directions for drug screening programs.
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Affiliation(s)
- Fang Zhang
- Department of Rehabilitation, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Mei Liu
- Department of Rehabilitation, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Qun Li
- Department of Rehabilitation, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Fei-Xue Song
- Department of Oncology, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
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Ungaro C, Citrigno L, Trojsi F, Sprovieri T, Gentile G, Muglia M, Monsurrò MR, Tedeschi G, Cavallaro S, Conforti FL. ALS and CHARGE syndrome: a clinical and genetic study. Acta Neurol Belg 2018; 118:629-635. [PMID: 30317490 PMCID: PMC6244742 DOI: 10.1007/s13760-018-1029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/06/2018] [Indexed: 12/30/2022]
Abstract
Amyotrophic Lateral Sclerosis and CHARGE syndrome are complex neurological disorders, which never occurred together in the same family and, to date, no putative correlation between them has been described on PubMed Central. Due to our aim was to evaluate the presence of different genetic variants involved in these pathologies, we reported a clinical and genetic description of two sisters affected by these two different disorders. In the CHARGE patient, molecular analysis of the CHD7 gene revealed the c.8016G >A de novo variant in exon 37. The ALS patient had been screened negative for mutations in SOD1, TARDBP, FUS/TLS, C9orf72 and KIF5A genes. Anyway, targeted next generation sequencing analysis identified known and unknown genetic variations in 39 ALS-related genes: a total of 380 variants were reported, of which 194 in the ALS patient and 186 in the CHARGE patient. To date, although the results suggest that the occurrence of the two syndromes in the same family is co-incidental rather than based on a causative genetic variant, we could hypothesize that other factors might act as modulators in the pathogenesis of these different phenotypes.
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Affiliation(s)
- Carmine Ungaro
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Luigi Citrigno
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Francesca Trojsi
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Teresa Sprovieri
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Giulia Gentile
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Maria Muglia
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Maria Rosaria Monsurrò
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Gioacchino Tedeschi
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Francesca Luisa Conforti
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy.
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Protein-protein interactions reveal key canonical pathways, upstream regulators, interactome domains, and novel targets in ALS. Sci Rep 2018; 8:14732. [PMID: 30283000 PMCID: PMC6170493 DOI: 10.1038/s41598-018-32902-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/18/2018] [Indexed: 02/08/2023] Open
Abstract
Developing effective treatment strategies for neurodegenerative diseases require an understanding of the underlying cellular pathways that lead to neuronal vulnerability and progressive degeneration. To date, numerous mutations in 147 distinct genes are identified to be "associated" with, "modifier" or "causative" of amyotrophic lateral sclerosis (ALS). Protein products of these genes and their interactions helped determine the protein landscape of ALS, and revealed upstream modulators, key canonical pathways, interactome domains and novel therapeutic targets. Our analysis originates from known human mutations and circles back to human, revealing increased PPARG and PPARGC1A expression in the Betz cells of sALS patients and patients with TDP43 pathology, and emphasizes the importance of lipid homeostasis. Downregulation of YWHAZ, a 14-3-3 protein, and cytoplasmic accumulation of ZFYVE27 especially in diseased Betz cells of ALS patients reinforce the idea that perturbed protein communications, interactome defects, and altered converging pathways will reveal novel therapeutic targets in ALS.
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48
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Morello G, Spampinato AG, Conforti FL, Cavallaro S. Taxonomy Meets Neurology, the Case of Amyotrophic Lateral Sclerosis. Front Neurosci 2018; 12:673. [PMID: 30319346 PMCID: PMC6168652 DOI: 10.3389/fnins.2018.00673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/07/2018] [Indexed: 12/13/2022] Open
Abstract
Recent landmark publications from our research group outline a transformative approach to defining, studying and treating amyotrophic lateral sclerosis (ALS). Rather than approaching ALS as a single entity, we advocate targeting therapies to distinct "clusters" of patients based on their specific genomic and molecular features. Our findings point to the existence of a molecular taxonomy for ALS, bringing us a step closer to the establishment of a precision medicine approach in neurology practice.
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Affiliation(s)
- Giovanna Morello
- Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
| | | | | | - Sebastiano Cavallaro
- Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
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Maugeri G, D'Amico AG, Rasà DM, Federico C, Saccone S, Morello G, La Cognata V, Cavallaro S, D'Agata V. Molecular mechanisms involved in the protective effect of pituitary adenylate cyclase-activating polypeptide in an in vitro model of amyotrophic lateral sclerosis. J Cell Physiol 2018; 234:5203-5214. [PMID: 30238989 DOI: 10.1002/jcp.27328] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the loss of upper and lower motor neurons. Based on transcriptional profiles of motor cortex samples, in a previous work, we were able to classify two subgroups of sporadic ALS (SALS) patients, named SALS1 and SALS2. A further meta-analysis study has revealed sixteen drug targets commonly deregulated in SALS2 and superoxide dismutase 1 (SOD1) G93A mice. The identified candidate drug targets included pituitary adenylate cyclase-activating polypeptide (PACAP), epidermal growth factor receptor (EGFR) and matrix metallopeptidase-2 (MMP-2). By using a motor neuron-like hybrid cell line (NSC-34) expressing human SOD1 G93A as an in vitro model of ALS, here we investigated the functional correlation among these three genes. Our results have shown that PACAP increases cell viability following serum deprivation. This effect is induced through EGFR transactivation mediated by protein kinase A stimulation. Furthermore, EGFR phosphorylation activates mitogen-activated protein kinases/extracellular signal-regulated kinases 1 and 2 survival signaling pathway and increases MMP-2 expression, significantly reduced by serum starvation. These results suggest that a deeper characterization of mechanisms involved in PACAP/EGFR/MMP-2 axis activation in G93A SOD1 mutated neurons may allow identifying new targets for ALS therapy.
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Affiliation(s)
- Grazia Maugeri
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania, Catania, Italy
| | - Agata G D'Amico
- Department of Human Science and Promotion of Quality of Life, San Raffaele Open University of Rome, Rome, Italy
| | - Daniela M Rasà
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania, Catania, Italy
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology, University of Catania, Catania, Italy
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology, University of Catania, Catania, Italy
| | - Giovanna Morello
- Institute of Neurological Sciences, National Research Council, Catania, Italy
| | | | | | - Velia D'Agata
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania, Catania, Italy
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La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
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