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Çelik MH, Gagneur J, Lim RG, Wu J, Thompson LM, Xie X. Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers. HGG ADVANCES 2024; 5:100318. [PMID: 38872308 DOI: 10.1016/j.xhgg.2024.100318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
The high heritability of amyotrophic lateral sclerosis (ALS) contrasts with its low molecular diagnosis rate post-genetic testing, pointing to potential undiscovered genetic factors. To aid the exploration of these factors, we introduced EpiOut, an algorithm to identify chromatin accessibility outliers that are regions exhibiting divergent accessibility from the population baseline in a single or few samples. Annotation of accessible regions with histone chromatin immunoprecipitation sequencing and Hi-C indicates that outliers are concentrated in functional loci, especially among promoters interacting with active enhancers. Across different omics levels, outliers are robustly replicated, and chromatin accessibility outliers are reliable predictors of gene expression outliers and aberrant protein levels. When promoter accessibility does not align with gene expression, our results indicate that molecular aberrations are more likely to be linked to post-transcriptional regulation rather than transcriptional regulation. Our findings demonstrate that the outlier detection paradigm can uncover dysregulated regions in rare diseases. EpiOut is available at github.com/uci-cbcl/EpiOut.
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Affiliation(s)
- Muhammed Hasan Çelik
- Department of Computer Science, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany; Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Ryan G Lim
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Leslie M Thompson
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA; UCI MIND, University of California Irvine, Irvine, CA, USA; Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California Irvine, Irvine, CA, USA; Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Xiaohui Xie
- Department of Computer Science, University of California Irvine, Irvine, CA, USA.
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2
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Hernan-Godoy M, Rouaux C. From Environment to Gene Expression: Epigenetic Methylations and One-Carbon Metabolism in Amyotrophic Lateral Sclerosis. Cells 2024; 13:967. [PMID: 38891099 PMCID: PMC11171807 DOI: 10.3390/cells13110967] [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: 03/31/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The etiology of the neurodegenerative disease amyotrophic lateral sclerosis (ALS) is complex and considered multifactorial. The majority of ALS cases are sporadic, but familial cases also exist. Estimates of heritability range from 8% to 61%, indicating that additional factors beyond genetics likely contribute to ALS. Numerous environmental factors are considered, which may add up and synergize throughout an individual's lifetime building its unique exposome. One level of integration between genetic and environmental factors is epigenetics, which results in alterations in gene expression without modification of the genome sequence. Methylation reactions, targeting DNA or histones, represent a large proportion of epigenetic regulations and strongly depend on the availability of methyl donors provided by the ubiquitous one-carbon (1C) metabolism. Thus, understanding the interplay between exposome, 1C metabolism, and epigenetic modifications will likely contribute to elucidating the mechanisms underlying altered gene expression related to ALS and to developing targeted therapeutic interventions. Here, we review evidence for 1C metabolism alterations and epigenetic methylation dysregulations in ALS, with a focus on the impairments reported in neural tissues, and discuss these environmentally driven mechanisms as the consequences of cumulative exposome or late environmental hits, but also as the possible result of early developmental defects.
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Affiliation(s)
| | - Caroline Rouaux
- Inserm UMR_S 1329, Strasbourg Translational Neuroscience and Psychiatry, Université de Strasbourg, Centre de Recherche en Biomédecine de Strasbourg, 1 Rue Eugène Boeckel, 67 000 Strasbourg, France;
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3
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Van Es MA. Amyotrophic lateral sclerosis; clinical features, differential diagnosis and pathology. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:1-47. [PMID: 38802173 DOI: 10.1016/bs.irn.2024.04.011] [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 late-onset syndrome characterized by the progressive degeneration of both upper motor neurons (UMN) and lower motor neurons (LMN). ALS forms a clinical continuum with frontotemporal dementia (FTD), in which there are progressive language deficits or behavioral changes. The genetics and pathology underlying both ALS and FTD overlap as well, with cytoplasmatic misvocalization of TDP-43 as the hallmark. ALS is diagnosed by exclusion. Over the years several diagnostic criteria have been proposed, which in essence all require a history of slowly progressive motor symptoms, with UMN and LMN signs on neurological examination, clear spread of symptoms through the body, the exclusion of other disorder that cause similar symptoms and an EMG that it is compatible with LMN loss. ALS is heterogeneous disorder that may present in multitude ways, which makes the diagnosis challenging. Therefore, a systematic approach in the diagnostic process is required in line with the most common presentations. Subsequently, assessing whether there are cognitive and/or behavioral changes within the spectrum of FTD and lastly determining the cause is genetic. This chapter, an outline on how to navigate this 3 step process.
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Affiliation(s)
- Michael A Van Es
- Department of Neurology, Brain Center UMC Utrecht, Utrecht, The Netherlands.
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4
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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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5
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Al-Chalabi A, Andrews J, Farhan S. Recent advances in the genetics of familial and sporadic ALS. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:49-74. [PMID: 38802182 DOI: 10.1016/bs.irn.2024.04.007] [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
ALS shows complex genetic inheritance patterns. In about 5% to 10% of cases, there is a family history of ALS or a related condition such as frontotemporal dementia in a first or second degree relative, and for about 80% of such people a pathogenic gene variant can be identified. Such variants are also seen in people with no family history because of factor influencing the expression of genes, such as age. Genetic susceptibility factors also contribute to risk, and the heritability of ALS is between 40% and 60%. The genetic variants influencing ALS risk include single base changes, repeat expansions, copy number variants, and others. Here we review what is known of the genetic landscape and architecture of ALS.
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Affiliation(s)
- Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom.
| | - Jinsy Andrews
- Department of Neurology, Columbia University, New York, NY, United States
| | - Sali Farhan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montreal, QC, Canada; Department of Human Genetics, Montreal Neurological Institute-Hospital, Montreal, QC, Canada
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Nguyen L. Updates on Disease Mechanisms and Therapeutics for Amyotrophic Lateral Sclerosis. Cells 2024; 13:888. [PMID: 38891021 PMCID: PMC11172142 DOI: 10.3390/cells13110888] [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: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS), or Lou Gehrig's disease, is a motor neuron disease. In ALS, upper and lower motor neurons in the brain and spinal cord progressively degenerate during the course of the disease, leading to the loss of the voluntary movement of the arms and legs. Since its first description in 1869 by a French neurologist Jean-Martin Charcot, the scientific discoveries on ALS have increased our understanding of ALS genetics, pathology and mechanisms and provided novel therapeutic strategies. The goal of this review article is to provide a comprehensive summary of the recent findings on ALS mechanisms and related therapeutic strategies to the scientific audience. Several highlighted ALS research topics discussed in this article include the 2023 FDA approved drug for SOD1 ALS, the updated C9orf72 GGGGCC repeat-expansion-related mechanisms and therapeutic targets, TDP-43-mediated cryptic splicing and disease markers and diagnostic and therapeutic options offered by these recent discoveries.
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Affiliation(s)
- Lien Nguyen
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Otero G, Bolatto C, Isasi E, Cerri S, Rodríguez P, Boragno D, Marco M, Parada C, Stancov M, Cuitinho MN, Olivera-Bravo S. Adult aberrant astrocytes submitted to late passage cultivation lost differentiation markers and decreased their pro-inflammatory profile. Heliyon 2024; 10:e30360. [PMID: 38711658 PMCID: PMC11070869 DOI: 10.1016/j.heliyon.2024.e30360] [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: 08/15/2023] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
In amyotrophic lateral sclerosis (ALS), astrocytes are considered key players in some non-cell non-neuronal autonomous mechanisms that underlie motor neuron death. However, it is unknown how much of these deleterious features were permanently acquired. To assess this point, we evaluated if the most remarkable features of neurotoxic aberrant glial phenotypes (AbAs) isolated from paralytic rats of the ALS model G93A Cu/Zn superoxide dismutase 1 (SOD1) could remain upon long lasting cultivation. Real time PCR, immunolabelling and zymography analysis showed that upon many passages, AbAs preserved the cell proliferation capacity, mitochondrial function and response to different compounds that inhibit some key astrocyte functions but decreased the expression of parameters associated to cell lineage, homeostasis and inflammation. As these results are contrary to the sustained inflammatory status observed along disease progression in SOD1G93A rats, we propose that the most AbAs remarkable features related to homeostasis and neurotoxicity were not permanently acquired and might depend on the signaling coming from the injuring microenvironment present in the degenerating spinal cord of terminal rats.
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Affiliation(s)
- Gabriel Otero
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Carmen Bolatto
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Department of Histology and Embryology, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Eugenia Isasi
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Department of Histology and Embryology, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Sofía Cerri
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Paola Rodríguez
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Daniela Boragno
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Marta Marco
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Department of Clinical Biochemistry, School of Chemistry (UdelaR), Montevideo, Uruguay
| | - Cristina Parada
- Department of Histology and Embryology, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Matías Stancov
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - María Noel Cuitinho
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Silvia Olivera-Bravo
- Department of Neurobiology and Neuropathology (NBNP), Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
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8
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Libonati L, Cambieri C, Colavito D, Moret F, D'Andrea E, Del Giudice E, Leon A, Inghilleri M, Ceccanti M. Genetics screening in an Italian cohort of patients with Amyotrophic Lateral Sclerosis: the importance of early testing and its implication. J Neurol 2024; 271:1921-1936. [PMID: 38112783 DOI: 10.1007/s00415-023-12142-x] [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: 09/06/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease with an elusive etiology. While environmental factors have been considered, familial ALS cases have raised the possibility of genetic involvement. This genetic connection is increasingly evident, even in patients with sporadic ALS. We allowed access to the genetic test to all patients attending our clinic to identify the prevalence and the role of genetic variants in the development of the disease and to identify patients with potentially treatable forms of the disease. MATERIALS AND METHODS 194 patients with probable or definite ALS, were enrolled. A comprehensive genetic testing was performed, including sequencing all exons of the SOD1 gene and testing for hexanucleotide intronic repeat expansions (G4C2) in the C9orf72 gene using fluorescent repeat-primed PCR (RP-PCR). Whole Exome NGS Sequencing (WES) was performed, followed by an in silico multigene panel targeting neuromuscular diseases, spastic paraplegia, and motor distal neuropathies. We conducted statistical analyses to compare different patient groups. RESULTS Clinically significant pathogenetic variants were detected in 14.43% of cases. The highest prevalence of pathogenetic variants was observed in fALS patients, but a substantial proportion of sALS patients also displayed at least one variant, either pathogenetic or of uncertain significance (VUS). The most observed pathogenetic variant was the expansion of the C9orf72 gene, which was associated with a shorter survival. SOD1 variants were found in 1.6% of fALS and 2.5% of sALS patients. DISCUSSION The study reveals a significant number of ALS patients carrying pathogenic or likely pathogenic variants, with a higher prevalence in familial ALS cases. The expansion of the C9orf72 gene emerges as the most common genetic cause of ALS, affecting familial and sporadic cases. Additionally, SOD1 variants are detected at an unexpectedly higher rate, even in patients without a familial history of ALS, underscoring the crucial role of genetic testing in treatment decisions and potential participation in clinical trials. We also investigated variants in genes such as TARDBP, FUS, NEK1, TBK1, and DNAJC7, shedding light on their potential involvement in ALS. These findings underscore the complexity of interpreting variants of uncertain significance (VUS) and their ethical implications in patient communication and genetic counseling for patients' relatives. CONCLUSION This study emphasizes the diverse genetic basis of ALS and advocates for integrating comprehensive genetic testing into diagnostic protocols. The evolving landscape of genetic therapies requires identifying all eligible patients transcending traditional familial boundaries. The presence of VUS highlights the multifaceted nature of ALS genetics, prompting further exploration of complex interactions among genetic variants, environmental factors, and disease development.
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Affiliation(s)
- Laura Libonati
- Department of Human Neurosciences, Rare Neuromuscular Diseases Centre, Sapienza University, Viale Dell'Università 30, 00185, Rome, Italy.
| | - Chiara Cambieri
- Department of Human Neurosciences, Rare Neuromuscular Diseases Centre, Sapienza University, Viale Dell'Università 30, 00185, Rome, Italy
| | - Davide Colavito
- R & I Genetics, C.So Stati Uniti 4int.F, 35127, Padua, Italy
| | - Federica Moret
- Department of Human Neurosciences, Rare Neuromuscular Diseases Centre, Sapienza University, Viale Dell'Università 30, 00185, Rome, Italy
| | - Edoardo D'Andrea
- Department of Human Neurosciences, Rare Neuromuscular Diseases Centre, Sapienza University, Viale Dell'Università 30, 00185, Rome, Italy
| | | | - Alberta Leon
- R & I Genetics, C.So Stati Uniti 4int.F, 35127, Padua, Italy
| | - Maurizio Inghilleri
- Department of Human Neurosciences, Rare Neuromuscular Diseases Centre, Sapienza University, Viale Dell'Università 30, 00185, Rome, Italy
| | - Marco Ceccanti
- Department of Human Neurosciences, Rare Neuromuscular Diseases Centre, Sapienza University, Viale Dell'Università 30, 00185, Rome, Italy
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Cox SN, Lo Giudice C, Lavecchia A, Poeta ML, Chiara M, Picardi E, Pesole G. Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue. Biomolecules 2024; 14:411. [PMID: 38672428 PMCID: PMC11048214 DOI: 10.3390/biom14040411] [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: 02/01/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive disease with prevalent mitochondrial dysfunctions affecting both upper and lower motor neurons in the motor cortex, brainstem, and spinal cord. Despite mitochondria having their own genome (mtDNA), in humans, most mitochondrial genes are encoded by the nuclear genome (nDNA). Our study aimed to simultaneously screen for nDNA and mtDNA genomes to assess for specific variant enrichment in ALS compared to control tissues. Here, we analysed whole exome (WES) and whole genome (WGS) sequencing data from spinal cord tissues, respectively, of 6 and 12 human donors. A total of 31,257 and 301,241 variants in nuclear-encoded mitochondrial genes were identified from WES and WGS, respectively, while mtDNA reads accounted for 73 and 332 variants. Despite technical differences, both datasets consistently revealed a specific enrichment of variants in the mitochondrial Control Region (CR) and in several of these genes directly associated with mitochondrial dynamics or with Sirtuin pathway genes within ALS tissues. Overall, our data support the hypothesis of a variant burden in specific genes, highlighting potential actionable targets for therapeutic interventions in ALS.
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Affiliation(s)
- Sharon Natasha Cox
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Claudio Lo Giudice
- Institute of Biomedical Technologies, National Research Council, 70126 Bari, Italy;
| | - Anna Lavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Maria Luana Poeta
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
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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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11
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Olsen CG, Busk ØL, Holla ØL, Tveten K, Holmøy T, Tysnes OB, Høyer H. Genetic overlap between ALS and other neurodegenerative or neuromuscular disorders. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:177-187. [PMID: 37849306 DOI: 10.1080/21678421.2023.2270705] [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: 08/09/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023]
Abstract
OBJECTIVE In Norway, 89% of patients with Amyotrophic lateral sclerosis (ALS) lacks a genetic diagnose. ALS genes and genes that cause other neuromuscular or neurodegenerative disorders extensively overlap. This population-based study examined whether patients with ALS have a family history of neurological disorders and explored the occurrence of rare genetic variants associated with other neurodegenerative or neuromuscular disorders. METHODS During a two-year period, blood samples and clinical data from patients with ALS were collected from all 17 neurological departments in Norway. Our genetic analysis involved exome sequencing and bioinformatics filtering of 510 genes associated with neurodegenerative and neuromuscular disorders. The variants were interpreted using genotype-phenotype correlations and bioinformatics tools. RESULTS A total of 279 patients from a Norwegian population-based ALS cohort participated in this study. Thirty-one percent of the patients had first- or second-degree relatives with other neurodegenerative disorders, most commonly dementia and Parkinson's disease. The genetic analysis identified 20 possible pathogenic variants, in ATL3, AFG3L2, ATP7A, BICD2, HARS1, KIF1A, LRRK2, MSTO1, NEK1, NEFH, and SORL1, in 25 patients. NEK1 risk variants were present in 2.5% of this ALS cohort. Only four of the 25 patients reported relatives with other neurodegenerative or neuromuscular disorders. CONCLUSION Gene variants known to cause other neurodegenerative or neuromuscular disorders, most frequently in NEK1, were identified in 9% of the patients with ALS. Most of these patients had no family history of other neurodegenerative or neuromuscular disorders. Our findings indicated that AFG3L2, ATP7A, BICD2, KIF1A, and MSTO1 should be further explored as potential ALS-causing genes.
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Affiliation(s)
- Cathrine Goberg Olsen
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
- Institute of Clinical Medicine, University of Oslo, Nordbyhagen, Norway
| | | | | | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Trygve Holmøy
- Institute of Clinical Medicine, University of Oslo, Nordbyhagen, Norway
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway, and
| | - Ole-Bjørn Tysnes
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Helle Høyer
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
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12
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Tang L, Tang X, Zhao Q, Li Y, Bu Y, Liu Z, Li J, Guo J, Shen L, Jiang H, Tang B, Xu R, Cao W, Yuan Y, Wang J. Mutation and clinical analysis of the CLCC1 gene in amyotrophic lateral sclerosis patients from Central South China. Ann Clin Transl Neurol 2024; 11:79-88. [PMID: 37916886 PMCID: PMC10791024 DOI: 10.1002/acn3.51934] [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: 08/14/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023] Open
Abstract
INTRODUCTION Recently, chloride channel CLIC-like 1 (CLCC1) was reported to be a novel ALS-related gene. We aimed to screen CLCC1 variants in our ALS cohort and further explore the genotype-phenotype correlation of CLCC1-related ALS. METHODS We screened rare damaging variants in CLCC1 from our cohorts of 1005 ALS patients and 1224 healthy controls with whole-exome sequencing in Central South China. Fisher's exact test was conducted for association analysis at the entire gene level and single variant level. RESULTS In total, four heterozygous missense variants in CLCC1 were identified from four unrelated sporadic ALS patients and predicted to be putative pathogenic by in silico tools and protein model prediction, accounting for 0.40% of all patients (4/1005). The four variants were c.A275C (p.Q92P), c.G1139A (p.R380K), c.C1244T (p.T415M), and c.G1328A (p.R443Q), respectively, which had not been reported in ALS patients previously. Three of four variants were located in exon 10. Patients harboring CLCC1 variants seemed to share a group of similar clinical features, including earlier age at onset, rapid progression, spinal onset, and vulnerable cognitive status. Statistically, we did not find CLCC1 to be associated with the risk of ALS at the entire gene level or single variant level. CONCLUSION Our findings further expanded the genetic and clinical spectrum of CLCC1-related ALS and provided more genetic evidence for anion channel involvement in the pathogenesis of ALS, but further investigations are needed to verify our findings.
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Affiliation(s)
- Linxin Tang
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
| | - Xuxiong Tang
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
| | - Qianqian Zhao
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
| | - Yongchao Li
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
| | - Yue Bu
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
| | - Zhen Liu
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Diseases, Xiangya HospitalCentral South UniversityChangshaP. R. China
- Center for Medical Genetics, School of Life SciencesCentral South UniversityChangshaP. R. China
- Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaP. R. China
| | - Jifeng Guo
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
- National Clinical Research Center for Geriatric Diseases, Xiangya HospitalCentral South UniversityChangshaP. R. China
- Center for Medical Genetics, School of Life SciencesCentral South UniversityChangshaP. R. China
- Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaP. R. China
- Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaP. R. China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaP. R. China
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative DiseasesChangshaP. R. China
| | - Lu Shen
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
- National Clinical Research Center for Geriatric Diseases, Xiangya HospitalCentral South UniversityChangshaP. R. China
- Center for Medical Genetics, School of Life SciencesCentral South UniversityChangshaP. R. China
- Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaP. R. China
- Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaP. R. China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaP. R. China
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative DiseasesChangshaP. R. China
| | - Hong Jiang
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
- National Clinical Research Center for Geriatric Diseases, Xiangya HospitalCentral South UniversityChangshaP. R. China
- Center for Medical Genetics, School of Life SciencesCentral South UniversityChangshaP. R. China
- Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaP. R. China
- Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaP. R. China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaP. R. China
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative DiseasesChangshaP. R. China
| | - Beisha Tang
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
- National Clinical Research Center for Geriatric Diseases, Xiangya HospitalCentral South UniversityChangshaP. R. China
- Center for Medical Genetics, School of Life SciencesCentral South UniversityChangshaP. R. China
- Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaP. R. China
- Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaP. R. China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaP. R. China
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative DiseasesChangshaP. R. China
| | - Renshi Xu
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Jiangxi Provincial People's Hospital, Clinical College of Nanchang Medical CollegeFirst Affiliated Hospital of Nanchang Medical CollegeNanchangP. R. China
| | - Wenfeng Cao
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Jiangxi Provincial People's Hospital, Clinical College of Nanchang Medical CollegeFirst Affiliated Hospital of Nanchang Medical CollegeNanchangP. R. China
| | - Yanchun Yuan
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
| | - Junling Wang
- Department of Neurology, Xiangya HospitalCentral South University, Jiangxi Hospital, National Regional Center for Neurological DiseasesNanchangP. R. China
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaP. R. China
- National Clinical Research Center for Geriatric Diseases, Xiangya HospitalCentral South UniversityChangshaP. R. China
- Center for Medical Genetics, School of Life SciencesCentral South UniversityChangshaP. R. China
- Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaP. R. China
- Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaP. R. China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaP. R. China
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative DiseasesChangshaP. R. China
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13
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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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14
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Reis J, Buguet A, Román GC, Spencer PS. Environmental neurology: Concepts and short history of an interdisciplinary approach to etiology, treatment and prevention. J Neurol Sci 2023; 454:120861. [PMID: 37924592 DOI: 10.1016/j.jns.2023.120861] [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: 04/18/2023] [Revised: 08/09/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Environmental Neurology (EN), a sub-discipline of Neurology and Neurological Sciences, favors an interdisciplinary collaboration allowing a holistic approach to understanding the impact of environmental factors on the nervous system and their relationship with neurological diseases. Several examples of diseases and conditions show the large scope of subjects addressed by EN. The EN sub-discipline focuses on both individual and population issues thus joining patient care and public health, respectively. Neuropathogenesis is addressed by several major questions: How do the environment and nervous system interact? Which exogenous factors can trigger neurological disease? When, where and how do they act? What are the therapeutic implications, and how can these disorders be controlled or prevented. To answer such questions, we address the incentive for, philosophy of and methods developed by EN, which seeks to safeguard Brain Health and, thus, the quality of life.
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Affiliation(s)
- Jacques Reis
- Department of Neurology, Centre Hospitalier Universitaire, 1 Avenue Molière, 67200 Strasbourg, France; Association RISE, 67205 Oberhausbergen, France.
| | - Alain Buguet
- Malaria Research Unit, UMR 5246 CNRS, Claude-Bernard Lyon-1 University, 69622 Villeurbanne, France
| | - Gustavo C Román
- Department of Neurology, Neurological Institute, Houston Methodist Hospital, 6560 Fannin Street, Suite 802, Houston, TX 77030, USA
| | - Peter S Spencer
- Department of Neurology, School of Medicine, Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA.
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15
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Dilliott AA, Kwon S, Rouleau GA, Iqbal S, Farhan SMK. Characterizing proteomic and transcriptomic features of missense variants in amyotrophic lateral sclerosis genes. Brain 2023; 146:4608-4621. [PMID: 37394881 PMCID: PMC10629772 DOI: 10.1093/brain/awad224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/28/2023] [Accepted: 06/11/2023] [Indexed: 07/04/2023] Open
Abstract
Within recent years, there has been a growing number of genes associated with amyotrophic lateral sclerosis (ALS), resulting in an increasing number of novel variants, particularly missense variants, many of which are of unknown clinical significance. Here, we leverage the sequencing efforts of the ALS Knowledge Portal (3864 individuals with ALS and 7839 controls) and Project MinE ALS Sequencing Consortium (4366 individuals with ALS and 1832 controls) to perform proteomic and transcriptomic characterization of missense variants in 24 ALS-associated genes. The two sequencing datasets were interrogated for missense variants in the 24 genes, and variants were annotated with gnomAD minor allele frequencies, ClinVar pathogenicity classifications, protein sequence features including Uniprot functional site annotations, and PhosphoSitePlus post-translational modification site annotations, structural features from AlphaFold predicted monomeric 3D structures, and transcriptomic expression levels from Genotype-Tissue Expression. We then applied missense variant enrichment and gene-burden testing following binning of variation based on the selected proteomic and transcriptomic features to identify those most relevant to pathogenicity in ALS-associated genes. Using predicted human protein structures from AlphaFold, we determined that missense variants carried by individuals with ALS were significantly enriched in β-sheets and α-helices, as well as in core, buried or moderately buried regions. At the same time, we identified that hydrophobic amino acid residues, compositionally biased protein regions and regions of interest are predominantly enriched in missense variants carried by individuals with ALS. Assessment of expression level based on transcriptomics also revealed enrichment of variants of high and medium expression across all tissues and within the brain. We further explored enriched features of interest using burden analyses and identified individual genes were indeed driving certain enrichment signals. A case study is presented for SOD1 to demonstrate proof-of-concept of how enriched features may aid in defining variant pathogenicity. Our results present proteomic and transcriptomic features that are important indicators of missense variant pathogenicity in ALS and are distinct from features associated with neurodevelopmental disorders.
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Affiliation(s)
- Allison A Dilliott
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 0G4, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Seulki Kwon
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guy A Rouleau
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 0G4, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Sumaiya Iqbal
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sali M K Farhan
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 0G4, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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16
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Roggenbuck J, Eubank BHF, Wright J, Harms MB, Kolb SJ. Evidence-based consensus guidelines for ALS genetic testing and counseling. Ann Clin Transl Neurol 2023; 10:2074-2091. [PMID: 37691292 PMCID: PMC10646996 DOI: 10.1002/acn3.51895] [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: 07/22/2023] [Accepted: 08/12/2023] [Indexed: 09/12/2023] Open
Abstract
OBJECTIVE Advances in amyotrophic lateral sclerosis (ALS) gene discovery, ongoing gene therapy trials, and patient demand have driven increased use of ALS genetic testing. Despite this progress, the offer of genetic testing to persons with ALS is not yet "standard of care." Our primary goal is to develop clinical ALS genetic counseling and testing guidelines to improve and standardize genetic counseling and testing practice among neurologists, genetic counselors or any provider caring for persons with ALS. METHODS Core clinical questions were identified and a rapid review performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) 2015 method. Guideline recommendations were drafted and the strength of evidence for each recommendation was assessed by combining two systems: the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) System and the Evaluation of Genomic Applications in Practice and Prevention (EGAPP). A modified Delphi approach was used to reach consensus among a group of content experts for each guideline statement. RESULTS A total of 35 guideline statements were developed. In summary, all persons with ALS should be offered single-step genetic testing, consisting of a C9orf72 assay, along with sequencing of SOD1, FUS, and TARDBP, at a minimum. The key education and genetic risk assessments that should be provided before and after testing are delineated. Specific guidance regarding testing methods and reporting for C9orf72 and other genes is provided for commercial laboratories. INTERPRETATION These evidence-based, consensus guidelines will support all stakeholders in the ALS community in navigating benefits and challenges of genetic testing.
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Affiliation(s)
- Jennifer Roggenbuck
- Division of Human Genetics, Department of Internal MedicineThe Ohio State University Wexner Medical CenterColumbusOhioUSA
- Department of NeurologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
| | - Breda H. F. Eubank
- Health & Physical Education Department, Faculty of Health, Community, & EducationMount Royal University4825 Mount Royal Gate SWCalgaryAlbertaCanada
| | - Joshua Wright
- Department of NeurologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
| | - Matthew B. Harms
- Department of NeurologyColumbia University Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Stephen J. Kolb
- Department of NeurologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
- Department of Biological Chemistry & PharmacologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
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17
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Goutman SA, Savelieff MG, Jang DG, Hur J, Feldman EL. The amyotrophic lateral sclerosis exposome: recent advances and future directions. Nat Rev Neurol 2023; 19:617-634. [PMID: 37709948 PMCID: PMC11027963 DOI: 10.1038/s41582-023-00867-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease of motor neuron degeneration with typical survival of only 2-5 years from diagnosis. The causes of ALS are multifactorial: known genetic mutations account for only around 70% of cases of familial ALS and 15% of sporadic cases, and heritability estimates range from 8% to 61%, indicating additional causes beyond genetics. Consequently, interest has grown in environmental contributions to ALS risk and progression. The gene-time-environment hypothesis posits that ALS onset occurs through an interaction of genes with environmental exposures during ageing. An alternative hypothesis, the multistep model of ALS, suggests that several hits, at least some of which could be environmental, are required to trigger disease onset, even in the presence of highly penetrant ALS-associated mutations. Studies have sought to characterize the ALS exposome - the lifetime accumulation of environmental exposures that increase disease risk and affect progression. Identifying the full scope of environmental toxicants that enhance ALS risk raises the prospect of preventing disease by eliminating or mitigating exposures. In this Review, we summarize the evidence for an ALS exposome, discussing the strengths and limitations of epidemiological studies that have identified contributions from various sources. We also consider potential mechanisms of exposure-mediated toxicity and suggest future directions for ALS exposome research.
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Affiliation(s)
- Stephen A Goutman
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI, USA
| | - Masha G Savelieff
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Dae-Gyu Jang
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Eva L Feldman
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI, USA.
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18
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Van Daele SH, Moisse M, van Vugt JJFA, Zwamborn RAJ, van der Spek R, van Rheenen W, Van Eijk K, Kenna K, Corcia P, Vourc'h P, Couratier P, Hardiman O, McLaughin R, Gotkine M, Drory V, Ticozzi N, Silani V, Ratti A, de Carvalho M, Mora Pardina JS, Povedano M, Andersen PM, Weber M, Başak NA, Shaw C, Shaw PJ, Morrison KE, Landers JE, Glass JD, van Es MA, van den Berg LH, Al-Chalabi A, Veldink J, Van Damme P. Genetic variability in sporadic amyotrophic lateral sclerosis. Brain 2023; 146:3760-3769. [PMID: 37043475 PMCID: PMC10473563 DOI: 10.1093/brain/awad120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/13/2023] Open
Abstract
With the advent of gene therapies for amyotrophic lateral sclerosis (ALS), there is a surge in gene testing for this disease. Although there is ample experience with gene testing for C9orf72, SOD1, FUS and TARDBP in familial ALS, large studies exploring genetic variation in all ALS-associated genes in sporadic ALS (sALS) are still scarce. Gene testing in a diagnostic setting is challenging, given the complex genetic architecture of sALS, for which there are genetic variants with large and small effect sizes. Guidelines for the interpretation of genetic variants in gene panels and for counselling of patients are lacking. We aimed to provide a thorough characterization of genetic variability in ALS genes by applying the American College of Medical Genetics and Genomics (ACMG) criteria on whole genome sequencing data from a large cohort of 6013 sporadic ALS patients and 2411 matched controls from Project MinE. We studied genetic variation in 90 ALS-associated genes and applied customized ACMG-criteria to identify pathogenic and likely pathogenic variants. Variants of unknown significance were collected as well. In addition, we determined the length of repeat expansions in C9orf72, ATXN1, ATXN2 and NIPA1 using the ExpansionHunter tool. We found C9orf72 repeat expansions in 5.21% of sALS patients. In 50 ALS-associated genes, we did not identify any pathogenic or likely pathogenic variants. In 5.89%, a pathogenic or likely pathogenic variant was found, most commonly in SOD1, TARDBP, FUS, NEK1, OPTN or TBK1. Significantly more cases carried at least one pathogenic or likely pathogenic variant compared to controls (odds ratio 1.75; P-value 1.64 × 10-5). Isolated risk factors in ATXN1, ATXN2, NIPA1 and/or UNC13A were detected in 17.33% of cases. In 71.83%, we did not find any genetic clues. A combination of variants was found in 2.88%. This study provides an inventory of pathogenic and likely pathogenic genetic variation in a large cohort of sALS patients. Overall, we identified pathogenic and likely pathogenic variants in 11.13% of ALS patients in 38 known ALS genes. In line with the oligogenic hypothesis, we found significantly more combinations of variants in cases compared to controls. Many variants of unknown significance may contribute to ALS risk, but diagnostic algorithms to reliably identify and weigh them are lacking. This work can serve as a resource for counselling and for the assembly of gene panels for ALS. Further characterization of the genetic architecture of sALS is necessary given the growing interest in gene testing in ALS.
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Affiliation(s)
- Sien Hilde Van Daele
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, and Leuven Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
- Department of Human genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, and Leuven Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Joke J F A van Vugt
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Ramona A J Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Rick van der Spek
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Kristel Van Eijk
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Kevin Kenna
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Philippe Corcia
- Centre SLA, CHRU de Tours, 37044 Tours, France
- UMR 1253, iBrain, Université de Tours, Inserm, 37032 Tours, France
| | - Patrick Vourc'h
- UMR 1253, iBrain, Université de Tours, Inserm, 37032 Tours, France
| | | | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin D02 PN40, Republic of Ireland
| | - Russell McLaughin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Republic of Ireland
| | - Marc Gotkine
- The Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Vivian Drory
- Department of Neurology, Tel-Aviv Sourasky Medical Centre, 64239 Tel Aviv, Israel
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milano, Italy
- Department of Pathophysiology and Transplantation, ‘Dino Ferrari’ Center, Università degli Studi di Milano, 20122 Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milano, Italy
- Department of Pathophysiology and Transplantation, ‘Dino Ferrari’ Center, Università degli Studi di Milano, 20122 Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milano, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20133 Milano, Italy
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | | | | | - Peter M Andersen
- Department of Clinical Science, Neurosciences, Umeå University, 901 87 Umeå, Sweden
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Nazli A Başak
- Koç University, School of Medicine, KUTTAM-NDAL, 34010 Istanbul, Turkey
| | - Chris Shaw
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London SE5 9RT, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Karen E Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jonathan D Glass
- Department Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael A van Es
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London SE5 9RT, UK
| | - Jan Veldink
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, and Leuven Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
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19
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Akçimen F, Lopez ER, Landers JE, Nath A, Chiò A, Chia R, Traynor BJ. Amyotrophic lateral sclerosis: translating genetic discoveries into therapies. Nat Rev Genet 2023; 24:642-658. [PMID: 37024676 PMCID: PMC10611979 DOI: 10.1038/s41576-023-00592-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 04/08/2023]
Abstract
Recent advances in sequencing technologies and collaborative efforts have led to substantial progress in identifying the genetic causes of amyotrophic lateral sclerosis (ALS). This momentum has, in turn, fostered the development of putative molecular therapies. In this Review, we outline the current genetic knowledge, emphasizing recent discoveries and emerging concepts such as the implication of distinct types of mutation, variability in mutated genes in diverse genetic ancestries and gene-environment interactions. We also propose a high-level model to synthesize the interdependent effects of genetics, environmental and lifestyle factors, and ageing into a unified theory of ALS. Furthermore, we summarize the current status of therapies developed on the basis of genetic knowledge established for ALS over the past 30 years, and we discuss how developing treatments for ALS will advance our understanding of targeting other neurological diseases.
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Affiliation(s)
- Fulya Akçimen
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Elia R Lopez
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute for Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Institute of Cognitive Sciences and Technologies, C.N.R, Rome, Italy
- Azienda Ospedaliero Universitaria Citta' della Salute e della Scienza, Turin, Italy
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
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20
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Cheng J, Ho WK, Wu BT, Liu HP, Lin WY. miRNA profiling as a complementary diagnostic tool for amyotrophic lateral sclerosis. Sci Rep 2023; 13:13805. [PMID: 37612427 PMCID: PMC10447559 DOI: 10.1038/s41598-023-40879-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: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS), the most prevalent motor neuron disease characterized by its complex genetic structure, lacks a single diagnostic test capable of providing a conclusive diagnosis. In order to demonstrate the potential for genetic diagnosis and shed light on the pathogenic role of miRNAs in ALS, we developed an ALS diagnostic rule by training the model using 80% of a miRNA profiling dataset consisting of 253 ALS samples and 103 control samples. Subsequently, we validated the diagnostic rule using the remaining 20% of unseen samples. The diagnostic rule we developed includes miR-205-5p, miR-206, miR-376a-5p, miR-412-5p, miR-3927-3p, miR-4701-3p, miR-6763-5p, and miR-6801-3p. Remarkably, the rule achieved an 82% true positive rate and a 73% true negative rate when predicting the unseen samples. Furthermore, the identified miRNAs target 21 genes in the PI3K-Akt pathway and 27 genes in the ALS pathway, including notable genes such as BCL2, NEFH, and OPTN. We propose that miRNA profiling may serve as a complementary diagnostic tool to supplement the clinical presentation and aid in the early recognition of ALS.
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Affiliation(s)
- Jack Cheng
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Wen-Kuang Ho
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Bor-Tsang Wu
- Department of Senior Citizen Service Management, National Taichung University of Science and Technology, Taichung City, 40343, Taiwan
| | - Hsin-Ping Liu
- Graduate Institute of Acupuncture Science, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan.
| | - Wei-Yong Lin
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan.
- Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan.
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21
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De Oliveira HM, Soma A, Baker MR, Turner MR, Talbot K, Williams TL. A survey of current practice in genetic testing in amyotrophic lateral sclerosis in the UK and Republic of Ireland: implications for future planning. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:405-413. [PMID: 36458618 DOI: 10.1080/21678421.2022.2150556] [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: 07/19/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Objective: To determine the current practice in genetic testing for patients with apparently sporadic motor neurone disease/amyotrophic lateral sclerosis (MND/ALS) and asymptomatic at-risk relatives of familial MND/ALS patients seen in specialized care centers in the UK. Methods: An online survey with 10 questions distributed to specialist healthcare professionals with a role in requesting genetic testing working at MND/ALS care centers. Results: Considerable variation in practice was found. Almost 30% of respondents reported some discomfort in discussing genetic testing with MND/ALS patients and a majority (77%) did not think that all patients with apparently sporadic disease should be routinely offered genetic testing at present. Particular concerns were identified in relation to testing asymptomatic at-risk individuals and the majority view was that clinical genetics services should have a role in supporting genetic testing in MND/ALS, especially in asymptomatic individuals at-risk of carrying pathogenic variants. Conclusions: Variation in practice in genetic testing among MND/ALS clinics may be driven by differences in experience and perceived competence, compounded by the increasing complexity of the genetic underpinnings of MND/ALS. Clear and accessible guidelines for referral pathways between MND/ALS clinics and clinical genetics may be the best way to standardize and improve current practice, ensuring that patients and relatives receive optimal and geographically equitable support.
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Affiliation(s)
- Hugo M De Oliveira
- Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Arunachalam Soma
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Mark R Baker
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Clinical Neurophysiology, Royal Victoria Infirmary, Newcastle upon Tyne, UK, and
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences. Level 6, John Radcliffe Hospital, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences. Level 6, John Radcliffe Hospital, Oxford, UK
| | - Timothy L Williams
- Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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22
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Scaber J, Thompson AG, Farrimond L, Feneberg E, Proudfoot M, Ossher L, Turner MR, Talbot K. Advantages of routine next-generation sequencing over standard genetic testing in the amyotrophic lateral sclerosis clinic. Eur J Neurol 2023; 30:2240-2249. [PMID: 37159497 PMCID: PMC10947345 DOI: 10.1111/ene.15855] [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: 09/12/2022] [Revised: 04/17/2023] [Accepted: 05/04/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND Next-generation sequencing has enhanced our understanding of amyotrophic lateral sclerosis (ALS) and its genetic epidemiology. Outside the research setting, testing is often restricted to those who report a family history. The aim of this study was to explore the added benefit of offering routine genetic testing to all patients in a regional ALS centre. METHODS C9ORF72 expansion testing and exome sequencing was offered to consecutive patients (150 with ALS and 12 with primary lateral sclerosis [PLS]) attending the Oxford Motor Neuron Disease Clinic within a defined time period. RESULTS A total of 17 (11.3%) highly penetrant pathogenic variants in C9ORF72, SOD1, TARDBP, FUS and TBK1 were detected, of which 10 were also found through standard clinical genetic testing pathways. The systematic approach resulted in five additional diagnoses of a C9ORF72 expansion (number needed to test [NNT] = 28), and two further missense variants in TARDBP and SOD1 (NNT = 69). Additionally, 3 patients were found to carry pathogenic risk variants in NEK1, and 13 patients harboured common missense variants in CFAP410 and KIF5A, also associated with an increased risk of ALS. We report two novel non-coding loss-of-function splice variants in TBK1 and OPTN. No relevant variants were found in the PLS patients. Patients were offered double-blinded participation, but >80% requested disclosure of the results. CONCLUSIONS This study provides evidence that expanding genetic testing to all patients with a clinical diagnosis of ALS enhances the potential for recruitment to clinical trials, but will have direct resource implications for genetic counselling.
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Affiliation(s)
- Jakub Scaber
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | - Alexander G. Thompson
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
| | - Lucy Farrimond
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | - Emily Feneberg
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
| | - Malcolm Proudfoot
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
| | - Lynn Ossher
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
| | - Martin R. Turner
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
| | - Kevin Talbot
- Nuffield Department of Clinical NeurosciencesUniversity of Oxford, John Radcliffe HospitalOxfordUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordUK
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23
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Calafatti M, Cocozza G, Limatola C, Garofalo S. Microglial crosstalk with astrocytes and immune cells in amyotrophic lateral sclerosis. Front Immunol 2023; 14:1223096. [PMID: 37564648 PMCID: PMC10410456 DOI: 10.3389/fimmu.2023.1223096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023] Open
Abstract
In recent years, biomedical research efforts aimed to unravel the mechanisms involved in motor neuron death that occurs in amyotrophic lateral sclerosis (ALS). While the main causes of disease progression were first sought in the motor neurons, more recent studies highlight the gliocentric theory demonstrating the pivotal role of microglia and astrocyte, but also of infiltrating immune cells, in the pathological processes that take place in the central nervous system microenvironment. From this point of view, microglia-astrocytes-lymphocytes crosstalk is fundamental to shape the microenvironment toward a pro-inflammatory one, enhancing neuronal damage. In this review, we dissect the current state-of-the-art knowledge of the microglial dialogue with other cell populations as one of the principal hallmarks of ALS progression. Particularly, we deeply investigate the microglia crosstalk with astrocytes and immune cells reporting in vitro and in vivo studies related to ALS mouse models and human patients. At last, we highlight the current experimental therapeutic approaches that aim to modulate microglial phenotype to revert the microenvironment, thus counteracting ALS progression.
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Affiliation(s)
- Matteo Calafatti
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Germana Cocozza
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Cristina Limatola
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
- Department of Physiology and Pharmacology, Sapienza University, Laboratory Affiliated to Istituto Pasteur, Rome, Italy
| | - Stefano Garofalo
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
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24
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Henden L, Fearnley LG, Grima N, McCann EP, Dobson-Stone C, Fitzpatrick L, Friend K, Hobson L, Chan Moi Fat S, Rowe DB, D'Silva S, Kwok JB, Halliday GM, Kiernan MC, Mazumder S, Timmins HC, Zoing M, Pamphlett R, Adams L, Bahlo M, Blair IP, Williams KL. Short tandem repeat expansions in sporadic amyotrophic lateral sclerosis and frontotemporal dementia. SCIENCE ADVANCES 2023; 9:eade2044. [PMID: 37146135 PMCID: PMC10162670 DOI: 10.1126/sciadv.ade2044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pathogenic short tandem repeat (STR) expansions cause over 20 neurodegenerative diseases. To determine the contribution of STRs in sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), we used ExpansionHunter, REviewer, and polymerase chain reaction validation to assess 21 neurodegenerative disease-associated STRs in whole-genome sequencing data from 608 patients with sporadic ALS, 68 patients with sporadic FTD, and 4703 matched controls. We also propose a data-derived outlier detection method for defining allele thresholds in rare STRs. Excluding C9orf72 repeat expansions, 17.6% of clinically diagnosed ALS and FTD cases had at least one expanded STR allele reported to be pathogenic or intermediate for another neurodegenerative disease. We identified and validated 162 disease-relevant STR expansions in C9orf72 (ALS/FTD), ATXN1 [spinal cerebellar ataxia type 1 (SCA1)], ATXN2 (SCA2), ATXN8 (SCA8), TBP (SCA17), HTT (Huntington's disease), DMPK [myotonic dystrophy type 1 (DM1)], CNBP (DM2), and FMR1 (fragile-X disorders). Our findings suggest clinical and pathological pleiotropy of neurodegenerative disease genes and highlight their importance in ALS and FTD.
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Affiliation(s)
- Lyndal Henden
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Liam G Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Natalie Grima
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Carol Dobson-Stone
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Lauren Fitzpatrick
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Kathryn Friend
- SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Lynne Hobson
- SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Sandrine Chan Moi Fat
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Dominic B Rowe
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Susan D'Silva
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - John B Kwok
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Glenda M Halliday
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Srestha Mazumder
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Hannah C Timmins
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Margaret Zoing
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Roger Pamphlett
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Discipline of Pathology, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Lorel Adams
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ian P Blair
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Kelly L Williams
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
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25
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Ziff OJ, Neeves J, Mitchell J, Tyzack G, Martinez-Ruiz C, Luisier R, Chakrabarti AM, McGranahan N, Litchfield K, Boulton SJ, Al-Chalabi A, Kelly G, Humphrey J, Patani R. Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology. Nat Commun 2023; 14:2176. [PMID: 37080969 PMCID: PMC10119258 DOI: 10.1038/s41467-023-37630-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) causes motor neuron degeneration, with 97% of cases exhibiting TDP-43 proteinopathy. Elucidating pathomechanisms has been hampered by disease heterogeneity and difficulties accessing motor neurons. Human induced pluripotent stem cell-derived motor neurons (iPSMNs) offer a solution; however, studies have typically been limited to underpowered cohorts. Here, we present a comprehensive compendium of 429 iPSMNs from 15 datasets, and 271 post-mortem spinal cord samples. Using reproducible bioinformatic workflows, we identify robust upregulation of p53 signalling in ALS in both iPSMNs and post-mortem spinal cord. p53 activation is greatest with C9orf72 repeat expansions but is weakest with SOD1 and FUS mutations. TDP-43 depletion potentiates p53 activation in both post-mortem neuronal nuclei and cell culture, thereby functionally linking p53 activation with TDP-43 depletion. ALS iPSMNs and post-mortem tissue display enrichment of splicing alterations, somatic mutations, and gene fusions, possibly contributing to the DNA damage response.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK.
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jamie Mitchell
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Giulia Tyzack
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Carlos Martinez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Raphaelle Luisier
- Genomics and Health Informatics Group, Idiap Research Institute, Martigny, Switzerland
| | | | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK.
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26
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Antonioni A, Govoni V, Brancaleoni L, Donà A, Granieri E, Bergamini M, Gerdol R, Pugliatti M. Amyotrophic Lateral Sclerosis and Air Pollutants in the Province of Ferrara, Northern Italy: An Ecological Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085591. [PMID: 37107873 PMCID: PMC10138704 DOI: 10.3390/ijerph20085591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/18/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023]
Abstract
The etiopathogenesis of amyotrophic lateral sclerosis (ALS) is still largely unknown, but likely depends on gene-environment interactions. Among the putative sources of environmental exposure are air pollutants and especially heavy metals. We aimed to investigate the relationship between ALS density and the concentration of air pollution heavy metals in Ferrara, northern Italy. An ecological study was designed to correlate the map of ALS distribution and that of air pollutants. All ALS cases diagnosed between 2000 and 2017 (Ferrara University Hospital administrative data) were plotted by residency in 100 sub-areas, and grouped in 4 sectors: urban, rural, northwestern and along the motorway. The concentrations of silver, aluminium, cadmium, chrome, copper, iron, manganese, lead, and selenium in moss and lichens were measured and monitored in 2006 and 2011. Based on 62 ALS patients, a strong and direct correlation of ALS density was observed only with copper concentrations in all sectors and in both sexes (Pearson coefficient (ρ) = 0.758; p = 0.000002). The correlation was higher in the urban sector (ρ = 0.767; p = 0.000128), in women for the overall population (ρ = 0.782, p = 0.000028) and in the urban (ρ = 0.872, p = 0.000047) population, and for the older cohort of diagnosed patients (2000-2009) the assessment correlated with the first assessment of air pollutants in 2006 (ρ = 0.724, p = 0.008). Our data is, in part, consistent with a hypothesis linking copper pollution to ALS.
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Affiliation(s)
- Annibale Antonioni
- Unit of Clinical Neurology, Department of Neurosciences and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy; (A.A.); (E.G.)
- Doctoral Program in Translational Neurosciences and Neurotechnologies, University of Ferrara, 44121 Ferrara, Italy
| | - Vittorio Govoni
- Unit of Clinical Neurology, Department of Neurosciences and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy; (A.A.); (E.G.)
| | - Lisa Brancaleoni
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Alessandro Donà
- Unit of Clinical Neurology, Department of Neurosciences and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy; (A.A.); (E.G.)
| | - Enrico Granieri
- Unit of Clinical Neurology, Department of Neurosciences and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy; (A.A.); (E.G.)
| | - Mauro Bergamini
- Preventive Medicine and Risk Assessment, University of Ferrara, 44121 Ferrara, Italy
| | - Renato Gerdol
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Maura Pugliatti
- Unit of Clinical Neurology, Department of Neurosciences and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy; (A.A.); (E.G.)
- Correspondence: ; Tel.: +39-0532-239309
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27
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Dong S, Yin X, Wang K, Yang W, Li J, Wang Y, Zhou Y, Liu X, Wang J, Chen X. Presence of Rare Variants is Associated with Poorer Survival in Chinese Patients with Amyotrophic Lateral Sclerosis. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:167-181. [PMID: 37197644 PMCID: PMC10110782 DOI: 10.1007/s43657-022-00093-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 05/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder with phenotypic and genetic heterogeneity. Recent studies have suggested an oligogenic basis of ALS, in which the co-occurrence of two or more genetic variants has additive or synergistic deleterious effects. To assess the contribution of possible oligogenic inheritance, we profiled a panel of 43 relevant genes in 57 sporadic ALS (sALS) patients and eight familial ALS (fALS) patients from five pedigrees in east China. We filtered rare variants using the combination of the Exome Aggregation Consortium, the 1000 Genomes and the HuaBiao Project. We analyzed patients with multiple rare variants in 43 known ALS causative genes and the genotype-phenotype correlation. Overall, we detected 30 rare variants in 16 different genes and found that 16 of the sALS patients and all the fALS patients examined harbored at least one variant in the investigated genes, among which two sALS and four fALS patients harbored two or more variants. Of note, the sALS patients with one or more variants in ALS genes had worse survival than the patients with no variants. Typically, in one fALS pedigree with three variants, the family member with three variants (Superoxide dismutase 1 (SOD1) p.V48A, Optineurin (OPTN) p.A433V and TANK binding kinase 1 (TBK1) p.R573H) exhibited much more severe disease phenotype than the member carrying one variant (TBK1 p.R573H). Our findings suggest that rare variants could exert a negative prognostic effect, thereby supporting the oligogenic inheritance of ALS.
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Affiliation(s)
- Siqi Dong
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Xianhong Yin
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
| | - Kun Wang
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Wenbo Yang
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Jiatong Li
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Yi Wang
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
| | - Yanni Zhou
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Xiaoni Liu
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Jiucun Wang
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
| | - Xiangjun Chen
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
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Piol D, Robberechts T, Da Cruz S. Lost in local translation: TDP-43 and FUS in axonal/neuromuscular junction maintenance and dysregulation in amyotrophic lateral sclerosis. Neuron 2023; 111:1355-1380. [PMID: 36963381 DOI: 10.1016/j.neuron.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/26/2023]
Abstract
Key early features of amyotrophic lateral sclerosis (ALS) are denervation of neuromuscular junctions and axonal degeneration. Motor neuron homeostasis relies on local translation through controlled regulation of axonal mRNA localization, transport, and stability. Yet the composition of the local transcriptome, translatome (mRNAs locally translated), and proteome during health and disease remains largely unexplored. This review covers recent discoveries on axonal translation as a critical mechanism for neuronal maintenance/survival. We focus on two RNA binding proteins, transactive response DNA binding protein-43 (TDP-43) and fused in sarcoma (FUS), whose mutations cause ALS and frontotemporal dementia (FTD). Emerging evidence points to their essential role in the maintenance of axons and synapses, including mRNA localization, transport, and local translation, and whose dysfunction may contribute to ALS. Finally, we describe recent advances in omics-based approaches mapping compartment-specific local RNA and protein compositions, which will be invaluable to elucidate fundamental local processes and identify key targets for therapy development.
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Affiliation(s)
- Diana Piol
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Tessa Robberechts
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Sandrine Da Cruz
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium.
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Adey BN, Cooper-Knock J, Al Khleifat A, Fogh I, van Damme P, Corcia P, Couratier P, Hardiman O, McLaughlin R, Gotkine M, Drory V, Silani V, Ticozzi N, Veldink JH, van den Berg LH, de Carvalho M, Pinto S, Mora Pardina JS, Povedano Panades M, Andersen PM, Weber M, Başak NA, Shaw CE, Shaw PJ, Morrison KE, Landers JE, Glass JD, Vourc’h P, Dobson RJB, Breen G, Al-Chalabi A, Jones AR, Iacoangeli A. Large-scale analyses of CAV1 and CAV2 suggest their expression is higher in post-mortem ALS brain tissue and affects survival. Front Cell Neurosci 2023; 17:1112405. [PMID: 36937187 PMCID: PMC10017967 DOI: 10.3389/fncel.2023.1112405] [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: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction: Caveolin-1 and Caveolin-2 (CAV1 and CAV2) are proteins associated with intercellular neurotrophic signalling. There is converging evidence that CAV1 and CAV2 (CAV1/2) genes have a role in amyotrophic lateral sclerosis (ALS). Disease-associated variants have been identified within CAV1/2 enhancers, which reduce gene expression and lead to disruption of membrane lipid rafts. Methods: Using large ALS whole-genome sequencing and post-mortem RNA sequencing datasets (5,987 and 365 tissue samples, respectively), and iPSC-derived motor neurons from 55 individuals, we investigated the role of CAV1/2 expression and enhancer variants in the ALS phenotype. Results: We report a differential expression analysis between ALS cases and controls for CAV1 and CAV2 genes across various post-mortem brain tissues and three independent datasets. CAV1 and CAV2 expression was consistently higher in ALS patients compared to controls, with significant results across the primary motor cortex, lateral motor cortex, and cerebellum. We also identify increased survival among carriers of CAV1/2 enhancer mutations compared to non-carriers within Project MinE and slower progression as measured by the ALSFRS. Carriers showed a median increase in survival of 345 days. Discussion: These results add to an increasing body of evidence linking CAV1 and CAV2 genes to ALS. We propose that carriers of CAV1/2 enhancer mutations may be conceptualised as an ALS subtype who present a less severe ALS phenotype with a longer survival duration and slower progression. Upregulation of CAV1/2 genes in ALS cases may indicate a causal pathway or a compensatory mechanism. Given prior research supporting the beneficial role of CAV1/2 expression in ALS patients, we consider a compensatory mechanism to better fit the available evidence, although further investigation into the biological pathways associated with CAV1/2 is needed to support this conclusion.
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Affiliation(s)
- Brett N. Adey
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - 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, United Kingdom
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Philip van Damme
- Department of Neurosciences, KU Leuven-University of Leuven, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
- VIB, Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours, France
- Centre de référence sur la SLA, CHU de Tours, Tours, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges, France
- UMR 1094, Université de Limoges, Inserm, Limoges, France
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Russell McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem, Israel
| | - Vivian Drory
- Department of Neurology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Mónica Povedano Panades
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L’Hospitalet de Llobregat, Barcelona, Spain
| | | | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, St. Gallen, Switzerland
| | - Nazli A. Başak
- Koc University School of Medicine, Translational Medicine Research Center, NDAL, Istanbul, Turkey
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Karen E. Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Jonathan D. Glass
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Patrick Vourc’h
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
- Service de Biochimie et Biologie molécularie, CHU de Tours, Tours, France
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
- NIHR Biomedical Research Centre at University College London Hospitals, NHS Foundation Trust, London, United Kingdom
| | - Gerome Breen
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - 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, United Kingdom
- King’s College Hospital, London, United Kingdom
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
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Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-022-00604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
AbstractDiseases that have a complex genetic architecture tend to suffer from considerable amounts of genetic variants that, although playing a role in the disease, have not yet been revealed as such. Two major causes for this phenomenon are genetic variants that do not stack up effects, but interact in complex ways; in addition, as recently suggested, the omnigenic model postulates that variants interact in a holistic manner to establish disease phenotypes. Here we present DiseaseCapsule, as a capsule-network-based approach that explicitly addresses to capture the hierarchical structure of the underlying genome data, and has the potential to fully capture the non-linear relationships between variants and disease. DiseaseCapsule is the first such approach to operate in a whole-genome manner when predicting disease occurrence from individual genotype profiles. In experiments, we evaluated DiseaseCapsule on amyotrophic lateral sclerosis (ALS) and Parkinson’s disease, with a particular emphasis on ALS, which is known to have a complex genetic architecture and is affected by 40% missing heritability. On ALS, DiseaseCapsule achieves 86.9% accuracy on hold-out test data in predicting disease occurrence, thereby outperforming all other approaches by large margins. Also, DiseaseCapsule required sufficiently less training data for reaching optimal performance. Last but not least, the systematic exploitation of the network architecture yielded 922 genes of particular interest, and 644 ‘non-additive’ genes that are crucial factors in DiseaseCapsule, but remain masked within linear schemes.
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Spencer PS, Palmer VS, Kisby GE, Lagrange E, Horowitz BZ, Valdes Angues R, Reis J, Vernoux JP, Raoul C, Camu W. Early-onset, conjugal, twin-discordant, and clusters of sporadic ALS: Pathway to discovery of etiology via lifetime exposome research. Front Neurosci 2023; 17:1005096. [PMID: 36860617 PMCID: PMC9969898 DOI: 10.3389/fnins.2023.1005096] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023] Open
Abstract
The identity and role of environmental factors in the etiology of sporadic amyotrophic lateral sclerosis (sALS) is poorly understood outside of three former high-incidence foci of Western Pacific ALS and a hotspot of sALS in the French Alps. In both instances, there is a strong association with exposure to DNA-damaging (genotoxic) chemicals years or decades prior to clinical onset of motor neuron disease. In light of this recent understanding, we discuss published geographic clusters of ALS, conjugal cases, single-affected twins, and young-onset cases in relation to their demographic, geographic and environmental associations but also whether, in theory, there was the possibility of exposure to genotoxic chemicals of natural or synthetic origin. Special opportunities to test for such exposures in sALS exist in southeast France, northwest Italy, Finland, the U.S. East North Central States, and in the U.S. Air Force and Space Force. Given the degree and timing of exposure to an environmental trigger of ALS may be related to the age at which the disease is expressed, research should focus on the lifetime exposome (from conception to clinical onset) of young sALS cases. Multidisciplinary research of this type may lead to the identification of ALS causation, mechanism, and primary prevention, as well as to early detection of impending ALS and pre-clinical treatment to slow development of this fatal neurological disease.
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Affiliation(s)
- Peter S. Spencer
- Department of Neurology, School of Medicine, Oregon Health and Science University, Portland, OR, United States,Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR, United States,*Correspondence: Peter S. Spencer,
| | - Valerie S. Palmer
- Department of Neurology, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Glen E. Kisby
- College of Osteopathic Medicine of the Pacific Northwest, Western University of Health Sciences, Lebanon, OR, United States
| | - Emmeline Lagrange
- Department of Neurology, Reference Center of Neuromuscular Disease and ALS Consultations, Grenoble University Hospital, Grenoble, France
| | - B. Zane Horowitz
- Department of Emergency Medicine, Oregon-Alaska Poison Center, Oregon Health and Science University, Portland, OR, United States
| | - Raquel Valdes Angues
- Department of Neurology, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Jacques Reis
- University of Strasbourg, Faculté de Médecine, Strasbourg, France
| | - Jean-Paul Vernoux
- Normandie Université, UNICAEN, Unité de Recherche Aliments Bioprocédés Toxicologie Environnements, Caen, France
| | - Cédric Raoul
- INM, University of Montpellier, INSERM, Montpellier, France
| | - William Camu
- ALS Reference Center, Montpellier University Hospital and University of Montpellier, INSERM, Montpellier, France
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Wang TW, Wuu J, Cooley A, Yeh TS, Benatar M, Weisskopf M. Occupational lead exposure and survival with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:100-107. [PMID: 35400246 PMCID: PMC9547984 DOI: 10.1080/21678421.2022.2059379] [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: 08/31/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 01/26/2023]
Abstract
Objective: Lead exposure has been hypothesized to increase the risk of ALS, but only two studies have examined the association with ALS survival, and with inconsistent results. The use of occupational history to assess lead exposure can avoid reverse causation that may occur in epidemiologic analyses that use biomarkers of lead exposure collected after ALS onset.Methods: We evaluated the relationship of occupational lead exposure to ALS survival among 135 cases from an international ALS cohort that included deep phenotyping, careful follow-up, and questionnaires to quantify participants' occupation history. ALS patients were recruited in 2015-2019. We determined occupational lead exposure using a job-exposure matrix. We estimated hazard ratios (HR) and 95% confidence intervals (CI) for survival using Cox proportional hazard analysis with adjustment for covariates.Results: A total of 135 ALS patients completed the environmental questionnaires, among whom 38 reached a survival endpoint (death or permanent assisted ventilation). The median survival was 48.3 months (25th-75th percentile, 30.9-74.1). Older patients and those with initial symptom other than limb onset had shorter survival time. There were 36 ALS cases with occupational lead exposure. After adjusting for age, sex, site of onset, smoking, and military service, lead exposure was associated with an HR of 3.26 (95%CI 1.28-8.28). Results with adjustment for subsets of these covariates were similar.Conclusions: These results suggest that lead exposure prior to onset of ALS is associated with shorter survival following onset of ALS, and this association is independent of other prognostic factors.
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Affiliation(s)
- Te-Wei Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Joanne Wuu
- Department of Neurology, Miller Schoof of Medicine, University of Miami, Miami, FL, USA
| | - Anne Cooley
- Department of Neurology, Miller Schoof of Medicine, University of Miami, Miami, FL, USA
| | - Tian-Shin Yeh
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Michael Benatar
- Department of Neurology, Miller Schoof of Medicine, University of Miami, Miami, FL, USA
| | - Marc Weisskopf
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
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Tazelaar GHP, Hop PJ, Seelen M, van Vugt JJFA, van Rheenen W, Kool L, van Eijk KR, Gijzen M, Dooijes D, Moisse M, Calvo A, Moglia C, Brunetti M, Canosa A, Nordin A, Pardina JSM, Ravits J, Al-Chalabi A, Chio A, McLaughlin RL, Hardiman O, Van Damme P, de Carvalho M, Neuwirth C, Weber M, Andersen PM, van den Berg LH, Veldink JH, van Es MA. Whole genome sequencing analysis reveals post-zygotic mutation variability in monozygotic twins discordant for amyotrophic lateral sclerosis. Neurobiol Aging 2023; 122:76-87. [PMID: 36521271 DOI: 10.1016/j.neurobiolaging.2022.11.010] [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: 05/11/2022] [Revised: 10/23/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Amyotrophic lateral sclerosis is a heterogeneous, fatal neurodegenerative disease, characterized by motor neuron loss and in 50% of cases also by cognitive and/or behavioral changes. Mendelian forms of ALS comprise approximately 10-15% of cases. The majority is however considered sporadic, but also with a high contribution of genetic risk factors. To explore the contribution of somatic mutations and/or epigenetic changes to disease risk, we performed whole genome sequencing and methylation analyses using samples from multiple tissues on a cohort of 26 monozygotic twins discordant for ALS, followed by in-depth validation and replication experiments. The results of these analyses implicate several mechanisms in ALS pathophysiology, which include a role for de novo mutations, defects in DNA damage repair and accelerated aging.
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Affiliation(s)
- Gijs H P Tazelaar
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paul J Hop
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Meinie Seelen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joke J F A van Vugt
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lindy Kool
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marleen Gijzen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dennis Dooijes
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Matthieu Moisse
- Neurology Department University Hospitals Leuven, Department of Neurosciences and Leuven Brain Institute (LBI) KU Leuven-University of Leuven, Leuven, Belgium; VIB, Center for Brain & Disease Research, Leuven, Belgium
| | - Andrea Calvo
- ALS Centre, "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy; Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, SC Neurologia 1U, Turin, Italy; Neuroscience Institute of Turin (NIT), Turin, Italy
| | - Cristina Moglia
- ALS Centre, "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy; Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, SC Neurologia 1U, Turin, Italy; Neuroscience Institute of Turin (NIT), Turin, Italy
| | - Maura Brunetti
- ALS Centre, "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy; Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, SC Neurologia 1U, Turin, Italy; Neuroscience Institute of Turin (NIT), Turin, Italy
| | - Antonio Canosa
- ALS Centre, "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy; Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, SC Neurologia 1U, Turin, Italy; Neuroscience Institute of Turin (NIT), Turin, Italy
| | - Angelica Nordin
- Department of Clinical Science, Neurosciences, Umeå University Umeå, Sweden
| | | | - John Ravits
- Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute, King's College London, London, UK; Department of Neurology, King's College Hospital, London, UK
| | - Adriano Chio
- ALS Centre, "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy; Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, SC Neurologia 1U, Turin, Italy; Neuroscience Institute of Turin (NIT), Turin, Italy
| | - Russell L McLaughlin
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Republic of Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Republic of Ireland; Department of Neurology, Beaumont Hospital, Dublin, Republic of Ireland
| | - Philip Van Damme
- Neurology Department University Hospitals Leuven, Department of Neurosciences and Leuven Brain Institute (LBI) KU Leuven-University of Leuven, Leuven, Belgium; VIB, Center for Brain & Disease Research, Leuven, Belgium
| | - Mamede de Carvalho
- Department of Neurosciences, Hospital de Santa Maria-CHLN, Lisbon, Portugal; Institute of Physiology, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Christoph Neuwirth
- Neuromuscular Diseases Unit / ALS Clinic, Kantonsspital St.Gallen, St.Gallen, Switzerland
| | - Markus Weber
- Neuromuscular Diseases Unit / ALS Clinic, Kantonsspital St.Gallen, St.Gallen, Switzerland
| | - Peter M Andersen
- Department of Clinical Science, Neurosciences, Umeå University Umeå, Sweden
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Michael A van Es
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands.
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Pain O, Jones A, Al Khleifat A, Agarwal D, Hramyka D, Karoui H, Kubica J, Llewellyn DJ, Ranson JM, Yao Z, Iacoangeli A, Al-Chalabi A. Harnessing Transcriptomic Signals for Amyotrophic Lateral Sclerosis to Identify Novel Drugs and Enhance Risk Prediction. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.18.23284589. [PMID: 36747854 PMCID: PMC9901068 DOI: 10.1101/2023.01.18.23284589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Introduction Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. This study integrates the latest ALS genome-wide association study (GWAS) summary statistics with functional genomic annotations with the aim of providing mechanistic insights into ALS risk loci, inferring drug repurposing opportunities, and enhancing prediction of ALS risk and clinical characteristics. Methods Genes associated with ALS were identified using GWAS summary statistic methodology including SuSiE SNP-based fine-mapping, and transcriptome- and proteome-wide association study (TWAS/PWAS) analyses. Using several approaches, gene associations were integrated with the DrugTargetor drug-gene interaction database to identify drugs that could be repurposed for the treatment of ALS. Furthermore, ALS gene associations from TWAS were combined with observed blood expression in two external ALS case-control datasets to calculate polytranscriptomic scores and evaluate their utility for prediction of ALS risk and clinical characteristics, including site of onset, age at onset, and survival. Results SNP-based fine-mapping, TWAS and PWAS identified 117 genes associated with ALS, with TWAS and PWAS providing novel mechanistic insights. Drug repurposing analyses identified five drugs significantly enriched for interactions with ALS associated genes, with directional analyses highlighting α-glucosidase inhibitors may exacerbate ALS pathology. Additionally, drug class enrichment analysis showed calcium channel blockers may reduce ALS risk. Across the two observed expression target samples, ALS polytranscriptomic scores significantly predicted ALS risk (R2 = 4%; p-value = 2.1×10-21). Conclusions Functionally-informed analyses of ALS GWAS summary statistics identified novel mechanistic insights into ALS aetiology, highlighted several therapeutic research avenues, and enabled statistically significant prediction of ALS risk.
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Affiliation(s)
- Oliver Pain
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Ashley Jones
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Devika Agarwal
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, United Kingdom
| | - Dzmitry Hramyka
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Hajer Karoui
- Multiple Sclerosis and Parkinson’s Tissue Bank, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Jędrzej Kubica
- Laboratory of Structural Bioinformatics, Institute of Evolutionary Biology, University of Warsaw, Poland
- Laboratory of Theory of Biopolimers, Faculty of Chemistry, University of Warsaw, Poland
| | - David J. Llewellyn
- University of Exeter Medical School, Exeter, United Kingdom
- Alan Turing Institute, London, United Kingdom
| | | | - Zhi Yao
- LifeArc, Stevenage, United Kingdom
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
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Megat S, Mora N, Sanogo J, Roman O, Catanese A, Alami NO, Freischmidt A, Mingaj X, De Calbiac H, Muratet F, Dirrig-Grosch S, Dieterle S, Van Bakel N, Müller K, Sieverding K, Weishaupt J, Andersen PM, Weber M, Neuwirth C, Margelisch M, Sommacal A, Van Eijk KR, Veldink JH, Lautrette G, Couratier P, Camuzat A, Le Ber I, Grassano M, Chio A, Boeckers T, Ludolph AC, Roselli F, Yilmazer-Hanke D, Millecamps S, Kabashi E, Storkebaum E, Sellier C, Dupuis L. Integrative genetic analysis illuminates ALS heritability and identifies risk genes. Nat Commun 2023; 14:342. [PMID: 36670122 PMCID: PMC9860017 DOI: 10.1038/s41467-022-35724-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/21/2022] [Indexed: 01/22/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) has substantial heritability, in part shared with fronto-temporal dementia (FTD). We show that ALS heritability is enriched in splicing variants and in binding sites of 6 RNA-binding proteins including TDP-43 and FUS. A transcriptome wide association study (TWAS) identified 6 loci associated with ALS, including in NUP50 encoding for the nucleopore basket protein NUP50. Independently, rare variants in NUP50 were associated with ALS risk (P = 3.71.10-03; odds ratio = 3.29; 95%CI, 1.37 to 7.87) in a cohort of 9,390 ALS/FTD patients and 4,594 controls. Cells from one patient carrying a NUP50 frameshift mutation displayed a decreased level of NUP50. Loss of NUP50 leads to death of cultured neurons, and motor defects in Drosophila and zebrafish. Thus, our study identifies alterations in splicing in neurons as critical in ALS and provides genetic evidence linking nuclear pore defects to ALS.
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Affiliation(s)
- Salim Megat
- Université de Strasbourg, Inserm, Mécanismes centraux et périphériques de la neurodégénérescence, UMR-S1118, Centre de Recherches en Biomédecine, Strasbourg, France.
| | - Natalia Mora
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Jason Sanogo
- Université de Strasbourg, Inserm, Mécanismes centraux et périphériques de la neurodégénérescence, UMR-S1118, Centre de Recherches en Biomédecine, Strasbourg, France
| | - Olga Roman
- Université de Strasbourg, Inserm, Mécanismes centraux et périphériques de la neurodégénérescence, UMR-S1118, Centre de Recherches en Biomédecine, Strasbourg, France
| | - Alberto Catanese
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Najwa Ouali Alami
- Clinical Neuroanatomy, Department of Neurology, Ulm University, Ulm, Germany
| | - Axel Freischmidt
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
- Department of Neurology, Ulm University, Ulm, Germany
| | - Xhuljana Mingaj
- Laboratory of Translational Research for Neurological Disorders, Imagine Institute, Université de Paris, INSERM UMR 1163, 75015, Paris, France
| | - Hortense De Calbiac
- Laboratory of Translational Research for Neurological Disorders, Imagine Institute, Université de Paris, INSERM UMR 1163, 75015, Paris, France
| | - François Muratet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Sylvie Dirrig-Grosch
- Université de Strasbourg, Inserm, Mécanismes centraux et périphériques de la neurodégénérescence, UMR-S1118, Centre de Recherches en Biomédecine, Strasbourg, France
| | - Stéphane Dieterle
- Université de Strasbourg, Inserm, Mécanismes centraux et périphériques de la neurodégénérescence, UMR-S1118, Centre de Recherches en Biomédecine, Strasbourg, France
| | - Nick Van Bakel
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Kathrin Müller
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | | | - Jochen Weishaupt
- Division for Neurodegenerative Diseases, Neurology Department, University Medicine Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Markus Weber
- Neuromuscular Disease Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Christoph Neuwirth
- Neuromuscular Disease Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Markus Margelisch
- Institute for Pathology, Kanstonsspital St. Gallen, St. Gallen, Switzerland
| | - Andreas Sommacal
- Institute for Pathology, Kanstonsspital St. Gallen, St. Gallen, Switzerland
| | - Kristel R Van Eijk
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Géraldine Lautrette
- Service de Neurologie, Centre de Référence SLA et autres maladies du neurone moteur, CHU Dupuytren 1, Limoges, France
| | - Philippe Couratier
- Service de Neurologie, Centre de Référence SLA et autres maladies du neurone moteur, CHU Dupuytren 1, Limoges, France
| | - Agnès Camuzat
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Isabelle Le Ber
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Maurizio Grassano
- ALS Center "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy
| | - Adriano Chio
- ALS Center "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy
| | - Tobias Boeckers
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Albert C Ludolph
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
- Department of Neurology, Ulm University, Ulm, Germany
| | - Francesco Roselli
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
- Department of Neurology, Ulm University, Ulm, Germany
| | | | - Stéphanie Millecamps
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Edor Kabashi
- Laboratory of Translational Research for Neurological Disorders, Imagine Institute, Université de Paris, INSERM UMR 1163, 75015, Paris, France
| | - Erik Storkebaum
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Chantal Sellier
- Université de Strasbourg, Inserm, Mécanismes centraux et périphériques de la neurodégénérescence, UMR-S1118, Centre de Recherches en Biomédecine, Strasbourg, France
| | - Luc Dupuis
- Université de Strasbourg, Inserm, Mécanismes centraux et périphériques de la neurodégénérescence, UMR-S1118, Centre de Recherches en Biomédecine, Strasbourg, France.
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Udine E, Jain A, van Blitterswijk M. Advances in sequencing technologies for amyotrophic lateral sclerosis research. Mol Neurodegener 2023; 18:4. [PMID: 36635726 PMCID: PMC9838075 DOI: 10.1186/s13024-022-00593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is caused by upper and lower motor neuron loss and has a fairly rapid disease progression, leading to fatality in an average of 2-5 years after symptom onset. Numerous genes have been implicated in this disease; however, many cases remain unexplained. Several technologies are being used to identify regions of interest and investigate candidate genes. Initial approaches to detect ALS genes include, among others, linkage analysis, Sanger sequencing, and genome-wide association studies. More recently, next-generation sequencing methods, such as whole-exome and whole-genome sequencing, have been introduced. While those methods have been particularly useful in discovering new ALS-linked genes, methodological advances are becoming increasingly important, especially given the complex genetics of ALS. Novel sequencing technologies, like long-read sequencing, are beginning to be used to uncover the contribution of repeat expansions and other types of structural variation, which may help explain missing heritability in ALS. In this review, we discuss how popular and/or upcoming methods are being used to discover ALS genes, highlighting emerging long-read sequencing platforms and their role in aiding our understanding of this challenging disease.
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Affiliation(s)
- Evan Udine
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Angita Jain
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Center for Clinical and Translational Sciences, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL, 32224, USA.
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37
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Chen X, Zhou L, Cui C, Sun J. Evolving markers in amyotrophic lateral sclerosis. Adv Clin Chem 2023. [DOI: 10.1016/bs.acc.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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McCann EP, Grima N, Fifita JA, Chan Moi Fat S, Lehnert K, Henden L, Blair IP, Williams KL. Characterising the Genetic Landscape of Amyotrophic Lateral Sclerosis: A Catalogue and Assessment of Over 1,000 Published Genetic Variants. J Neuromuscul Dis 2023; 10:1127-1141. [PMID: 37638449 PMCID: PMC10657717 DOI: 10.3233/jnd-230148] [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] [Accepted: 08/07/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with genetic and phenotypic heterogeneity. Pathogenic genetic variants remain the only validated cause of disease, the majority of which were discovered in familial ALS patients. While causal gene variants are a lesser contributor to sporadic ALS, an increasing number of risk alleles (low penetrance genetic variants associated with a small increase in disease risk) and variants of uncertain significance have been reported. OBJECTIVE To examine the pathogenic potential of genetic variation in ALS, we sought to characterise variant- and gene-level attributes of previously reported ALS-implicated variants. METHODS A list of 1,087 genetic variants reported in ALS to March 2021 was compiled through comprehensive literature review. Individual variants were annotated using in silico tools and databases across variant features including pathogenicity scores, localisation to protein domains, evolutionary conservation, and minor allele frequencies. Gene level attributes of genic tolerance, gene expression in ALS-relevant tissues and gene ontology terms were assessed for 33 ALS genes. Statistical analysis was performed for each characteristic, and we compared the most penetrant variants found in familial cases with risk alleles exclusive to sporadic cases, to explore genetic variant features that associate with disease penetrance. RESULTS We provide spreadsheet (hg19 and GRCh38) and variant call format (GRCh38) resources for all 1,087 reported ALS-implicated variants, including detailed summaries for each attribute. We demonstrate that the characteristics of variants found exclusively in sporadic ALS cases are less severe than those observed in familial ALS. CONCLUSIONS We provide a comprehensive, literature-derived catalogue of genetic variation in ALS thus far and reveal crucial attributes that contribute to ALS pathogenicity. Our variant- and gene-level observations highlight the complexity of genetic variation in ALS, and we discuss important implications and considerations for novel variant interpretation.
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Affiliation(s)
- Emily P. McCann
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Natalie Grima
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jennifer A. Fifita
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sandrine Chan Moi Fat
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Klaus Lehnert
- School of Biological Sciences, Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Lyndal Henden
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P. Blair
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L. Williams
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
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Liu H, Guan L, Deng M, Bolund L, Kristiansen K, Zhang J, Luo Y, Zhang Z. Integrative genetic and single cell RNA sequencing analysis provides new clues to the amyotrophic lateral sclerosis neurodegeneration. Front Neurosci 2023; 17:1116087. [PMID: 36875658 PMCID: PMC9983639 DOI: 10.3389/fnins.2023.1116087] [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: 12/05/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Introduction The gradual loss of motor neurons (MNs) in the brain and spinal cord is a hallmark of amyotrophic lateral sclerosis (ALS), but the mechanisms underlying neurodegeneration in ALS are still not fully understood. Methods Based on 75 ALS-pathogenicity/susceptibility genes and large-scale single-cell transcriptomes of human/mouse brain/spinal cord/muscle tissues, we performed an expression enrichment analysis to identify cells involved in ALS pathogenesis. Subsequently, we created a strictness measure to estimate the dosage requirement of ALS-related genes in linked cell types. Results Remarkably, expression enrichment analysis showed that α- and γ-MNs, respectively, are associated with ALS-susceptibility genes and ALS-pathogenicity genes, revealing differences in biological processes between sporadic and familial ALS. In MNs, ALS-susceptibility genes exhibited high strictness, as well as the ALS-pathogenicity genes with known loss of function mechanism, indicating the main characteristic of ALS-susceptibility genes is dosage-sensitive and the loss of function mechanism of these genes may involve in sporadic ALS. In contrast, ALS-pathogenicity genes with gain of function mechanism exhibited low strictness. The significant difference of strictness between loss of function genes and gain of function genes provided a priori understanding for the pathogenesis of novel genes without an animal model. Besides MNs, we observed no statistical evidence for an association between muscle cells and ALS-related genes. This result may provide insight into the etiology that ALS is not within the domain of neuromuscular diseases. Moreover, we showed several cell types linked to other neurological diseases [i.e., spinocerebellar ataxia (SA), hereditary motor neuropathies (HMN)] and neuromuscular diseases [i.e. hereditary spastic paraplegia (SPG), spinal muscular atrophy (SMA)], including an association between Purkinje cells in brain and SA, an association between α-MNs in spinal cord and SA, an association between smooth muscle cells and SA, an association between oligodendrocyte and HMN, a suggestive association between γ-MNs and HMN, a suggestive association between mature skeletal muscle and HMN, an association between oligodendrocyte in brain and SPG, and no statistical evidence for an association between cell type and SMA. Discussion These cellular similarities and differences deepened our understanding of the heterogeneous cellular basis of ALS, SA, HMN, SPG, and SMA.
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Affiliation(s)
- Hankui Liu
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China.,BGI-Shenzhen, Shenzhen, China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Min Deng
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China.,BGI-Shenzhen, Shenzhen, China
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Zhanchi Zhang
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Hebei Medical University, Shijiazhuang, China
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Al Khleifat A, Iacoangeli A, Jones AR, van Vugt JJFA, Moisse M, Shatunov A, Zwamborn RAJ, van der Spek RAA, Cooper-Knock J, Topp S, van Rheenen W, Kenna B, Van Eijk KR, Kenna K, Byrne R, López V, Opie-Martin S, Vural A, Campos Y, Weber M, Smith B, Fogh I, Silani V, Morrison KE, Dobson R, van Es MA, McLaughlin RL, Vourc’h P, Chio A, Corcia P, de Carvalho M, Gotkine M, Panades MP, Mora JS, Shaw PJ, Landers JE, Glass JD, Shaw CE, Basak N, Hardiman O, Robberecht W, Van Damme P, van den Berg LH, Veldink JH, Al-Chalabi A. Telomere length analysis in amyotrophic lateral sclerosis using large-scale whole genome sequence data. Front Cell Neurosci 2022; 16:1050596. [PMID: 36589292 PMCID: PMC9799999 DOI: 10.3389/fncel.2022.1050596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the loss of upper and lower motor neurons, leading to progressive weakness of voluntary muscles, with death following from neuromuscular respiratory failure, typically within 3 to 5 years. There is a strong genetic contribution to ALS risk. In 10% or more, a family history of ALS or frontotemporal dementia is obtained, and the Mendelian genes responsible for ALS in such families have now been identified in about 50% of cases. Only about 14% of apparently sporadic ALS is explained by known genetic variation, suggesting that other forms of genetic variation are important. Telomeres maintain DNA integrity during cellular replication, differ between sexes, and shorten naturally with age. Sex and age are risk factors for ALS and we therefore investigated telomere length in ALS. Methods Samples were from Project MinE, an international ALS whole genome sequencing consortium that includes phenotype data. For validation we used donated brain samples from motor cortex from people with ALS and controls. Ancestry and relatedness were evaluated by principal components analysis and relationship matrices of DNA microarray data. Whole genome sequence data were from Illumina HiSeq platforms and aligned using the Isaac pipeline. TelSeq was used to quantify telomere length using whole genome sequence data. We tested the association of telomere length with ALS and ALS survival using Cox regression. Results There were 6,580 whole genome sequences, reducing to 6,195 samples (4,315 from people with ALS and 1,880 controls) after quality control, and 159 brain samples (106 ALS, 53 controls). Accounting for age and sex, there was a 20% (95% CI 14%, 25%) increase of telomere length in people with ALS compared to controls (p = 1.1 × 10-12), validated in the brain samples (p = 0.03). Those with shorter telomeres had a 10% increase in median survival (p = 5.0×10-7). Although there was no difference in telomere length between sporadic ALS and familial ALS (p=0.64), telomere length in 334 people with ALS due to expanded C9orf72 repeats was shorter than in those without expanded C9orf72 repeats (p = 5.0×10-4). Discussion Although telomeres shorten with age, longer telomeres are a risk factor for ALS and worsen prognosis. Longer telomeres are associated with ALS.
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Affiliation(s)
- Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Joke J. F. A. van Vugt
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, Leuven, Belgium
- VIB Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Aleksey Shatunov
- Institute of Medicine, North-Eastern Federal University, Yakutsk, Russia
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Ramona A. J. Zwamborn
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Rick A. A. van der Spek
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Brendan Kenna
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Kristel R. Van Eijk
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Kevin Kenna
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Ross Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Victoria López
- Computational Biology Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Atay Vural
- School of Medicine, Translational Medicine Research Center-NDAL, Koc University, Istanbul, Turkey
| | - Yolanda Campos
- Computational Biology Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Markus Weber
- School of Medicine, Translational Medicine Research Center-NDAL, Koc University, Istanbul, Turkey
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Bradley Smith
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Karen E. Morrison
- Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Richard Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
| | - Michael A. van Es
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Russell L. McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Adriano Chio
- Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Azienda Ospedaliera Citta della Salute e della Scienza, Turin, Italy
| | - Philippe Corcia
- Centre SLA, CHRU de Tours, Tours, France
- Federation des Centres SLA Tours and Limoges, LITORALS, Tours, France
| | - Mamede de Carvalho
- Physiology Institute, Faculty of Medicine, Instituto de Medicina Molecular, University of Lisbon, Lisbon, Portugal
| | - Marc Gotkine
- Department of Neurology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Jonathan D. Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, United States
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- King’s College Hospital, London, United Kingdom
| | - Nazli Basak
- School of Medicine, Translational Medicine Research Center-NDAL, Koc University, Istanbul, Turkey
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Leonard H. van den Berg
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Jan H. Veldink
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- King’s College Hospital, London, United Kingdom
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Savage AL, Iacoangeli A, Schumann GG, Rubio-Roldan A, Garcia-Perez JL, Al Khleifat A, Koks S, Bubb VJ, Al-Chalabi A, Quinn JP. Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis. Gene 2022; 843:146799. [PMID: 35963498 DOI: 10.1016/j.gene.2022.146799] [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: 03/24/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals' whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.
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Affiliation(s)
- Abigail L Savage
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Alejandro Rubio-Roldan
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain
| | - Jose L Garcia-Perez
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain; MRC-HGU Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, Western Australia 6009, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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Logroscino G, Urso D, Tortelli R. The challenge of amyotrophic lateral sclerosis descriptive epidemiology: to estimate low incidence rates across complex phenotypes in different geographic areas. Curr Opin Neurol 2022; 35:678-685. [PMID: 35946801 PMCID: PMC9593328 DOI: 10.1097/wco.0000000000001097] [Citation(s) in RCA: 1] [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] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW Amyotrophic lateral sclerosis (ALS) is a rare progressive neurodegenerative disease of motor neurons with a fatal outcome. The rareness of the disease and the rapidly fatal course are the main challenges for the ALS epidemiological research. The understanding of ALS has clearly advanced in the recent years both in the genetics and in the leading pathways of disease determinants. Epidemiological research has played a primary role in these discoveries. RECENT FINDINGS Epidemiological studies have shown a variation of incidence, mortality and prevalence of ALS between geographical areas and different populations, supporting the notion that genetic factors, linked to populations' ancestries, along with environmental and lifestyle factors, play a significant role in the occurrence of the disease. The burden of motor neuron diseases is increasing and currently more relevant in high-income countries but increasing at the highest rate in low and middle-income countries. The ALS phenotype is not restricted to motor functions. C9orf72 repeat expansion seems to present a recognizable phenotype characterized by earlier disease onset, the presence of cognitive and behavioural impairment. SUMMARY Population-based disease registries have played a major role in developing new knowledge on ALS, in characterizing genotype-phenotype correlations, in discovering new genetic modifiers and finally in planning research and health services, considering the high cost of motor neuron disease care. Epidemiological research based on multicentre international collaboration is essential to provide new data on ALS, especially in some regions of the world with poor data.
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Affiliation(s)
- Giancarlo Logroscino
- Center for Neurodegenerative Diseases and the Aging Brain, Department of Clinical Research in Neurology, University of Bari ’Aldo Moro’, “Pia Fondazione Cardinale G. Panico”, Tricase, Lecce
- Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari ’Aldo Moro’, Bari, Italy
| | - Daniele Urso
- Center for Neurodegenerative Diseases and the Aging Brain, Department of Clinical Research in Neurology, University of Bari ’Aldo Moro’, “Pia Fondazione Cardinale G. Panico”, Tricase, Lecce
- Department of Neurosciences, King's College London, Institute of Psychiatry, Psychology and Neuroscience, De Crespigny Park, London, UK
| | - Rosanna Tortelli
- Neuroscience and Rare Diseases Discovery and Translational Area, Roche Pharma Research and Early Development, F. Hoffmann-La Roche Ltd., Basel, Switzerland
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Abstract
PURPOSE OF REVIEW ALS genetics are highly dynamic and of great interest for the ALS research community. Each year, by using ever-growing datasets and cutting-edge methodology, an array of novel ALS-associated genes and downstream pathomechanisms are discovered. The increasing plenty and complexity of insights warrants regular summary by-reviews. RECENT FINDINGS Most recent disease gene discoveries constitute the candidate and risk genes SPTLC1 , KANK1 , CAV1 , HTT , and WDR7 , as well as seven novel risk loci. Cell type and functional enrichment analyses enlighten the genetic basis of selective motor neuron vulnerability in ALS demonstrating high expression of ALS-associated genes in cortical motor neurons and highlight the pathogenic significance of cell-autonomous processes. Major pathomechanistic insights have been gained regarding known ALS genes/proteins, specifically C9orf72 , TDP43, ANXA11 , and KIF5A . The first ASO-based gene-specific therapy trials in familial forms of ALS have yielded equivocal results stressing the re-evaluation of pathomechanisms linked to SOD1 and C9orf72 mutations. SUMMARY The genetic and molecular basis of ALS is increasingly examined on single-cell resolution. In the past 2 years, the understanding of the downstream mechanisms of several ALS genes and TDP-43 proteinopathy has been considerably extended. These insights will result in novel gene specific therapy approaches for sporadic ALS and genetic subtypes.
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Marshall JNG, Fröhlich A, Li L, Pfaff AL, Middlehurst B, Spargo TP, Iacoangeli A, Lang B, Al-Chalabi A, Koks S, Bubb VJ, Quinn JP. A polymorphic transcriptional regulatory domain in the amyotrophic lateral sclerosis risk gene CFAP410 correlates with differential isoform expression. Front Mol Neurosci 2022; 15:954928. [PMID: 36131690 PMCID: PMC9484465 DOI: 10.3389/fnmol.2022.954928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 11/15/2022] Open
Abstract
We describe the characterisation of a variable number tandem repeat (VNTR) domain within intron 1 of the amyotrophic lateral sclerosis (ALS) risk gene CFAP410 (Cilia and flagella associated protein 410) (previously known as C21orf2), providing insight into how this domain could support differential gene expression and thus be a modulator of ALS progression or risk. We demonstrated the VNTR was functional in a reporter gene assay in the HEK293 cell line, exhibiting both the properties of an activator domain and a transcriptional start site, and that the differential expression was directed by distinct repeat number in the VNTR. These properties embedded in the VNTR demonstrated the potential for this VNTR to modulate CFAP410 expression. We extrapolated these findings in silico by utilisation of tagging SNPs for the two most common VNTR alleles to establish a correlation with endogenous gene expression. Consistent with in vitro data, CFAP410 isoform expression was found to be variable in the brain. Furthermore, although the number of matched controls was low, there was evidence for one specific isoform being correlated with lower expression in those with ALS. To address if the genotype of the VNTR was associated with ALS risk, we characterised the variation of the CFAP410 VNTR in ALS cases and matched controls by PCR analysis of the VNTR length, defining eight alleles of the VNTR. No significant difference was observed between cases and controls, we noted, however, the cohort was unlikely to contain sufficient power to enable any firm conclusion to be drawn from this analysis. This data demonstrated that the VNTR domain has the potential to modulate CFAP410 expression as a regulatory element that could play a role in its tissue-specific and stimulus-inducible regulation that could impact the mechanism by which CFAP410 is involved in ALS.
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Affiliation(s)
- Jack N. G. Marshall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Li Li
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Psychiatry, National Clinical Research Centre for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Abigail L. Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Thomas P. Spargo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, King's College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, King's College London, London, United Kingdom
| | - Bing Lang
- Department of Psychiatry, National Clinical Research Centre for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - 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, United Kingdom
- Department of Neurology, King's College Hospital, London, United Kingdom
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Synucleinopathy in Amyotrophic Lateral Sclerosis: A Potential Avenue for Antisense Therapeutics? Int J Mol Sci 2022; 23:ijms23169364. [PMID: 36012622 PMCID: PMC9409035 DOI: 10.3390/ijms23169364] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 01/02/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease classified as both a neurodegenerative and neuromuscular disorder. With a complex aetiology and no current cure for ALS, broadening the understanding of disease pathology and therapeutic avenues is required to progress with patient care. Alpha-synuclein (αSyn) is a hallmark for disease in neurodegenerative disorders, such as Parkinson's disease, Lewy body dementia, and multiple system atrophy. A growing body of evidence now suggests that αSyn may also play a pathological role in ALS, with αSyn-positive Lewy bodies co-aggregating alongside known ALS pathogenic proteins, such as SOD1 and TDP-43. This review endeavours to capture the scope of literature regarding the aetiology and development of ALS and its commonalities with "synucleinopathy disorders". We will discuss the involvement of αSyn in ALS and motor neuron disease pathology, and the current theories and strategies for therapeutics in ALS treatment, as well as those targeting αSyn for synucleinopathies, with a core focus on small molecule RNA technologies.
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Khani M, Nafissi S, Shamshiri H, Moazzeni H, Taheri H, Elahi E. Identification of RNF13 as cause of recessively inherited ALS in a multi-case pedigree. J Med Genet 2022; 60:jmedgenet-2022-108645. [PMID: 35879052 DOI: 10.1136/jmg-2022-108645] [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: 04/18/2022] [Accepted: 07/05/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is the most common motor neuron disease. The approximately 50 known ALS-associated genes do not fully explain its heritability, which suggests the existence of yet unidentified causative genes. We report results of studies aimed at identification of the genetic cause of ALS in a pedigree (three patients) without mutations in the common ALS-causative genes. METHODS Clinical investigations included thorough neurological and non-neurological examinations and testings. Genetic analysis was performed by exome sequencing. Functional studies included identification of altered splicing by PCR and sequencing, and mutated proteins by western blot analysis. Apoptosis in the presence and absence of tunicamycin was assessed in transfected HEK293T cells using an Annexin-PE-7AAD kit in conjunction with flow cytometry. RESULTS Clinical features are described in detail. Disease progression in the patients of the pedigree was relatively slow and survival was relatively long. An RNF13 mutation was identified as the cause of the recessively inherited ALS in the pedigree. The gene is highly conserved, and its encoded protein (RING finger protein 13) can potentially affect various neurodegenerative-relevant functions, including protein homeostasis. The RNF13 splice site mutation caused expression of two mis-spliced forms of RNF13 mRNA and an aberrant RNF13 protein, and affected apoptosis. CONCLUSION RNF13 was identified as a novel causative gene of recessively inherited ALS. The gene affects protein homeostasis, which is one of most important components of the pathology of neurodegeneration. The contribution of RNF13 to the aetiology of another neurodegenerative disease is discussed.
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Affiliation(s)
- Marzieh Khani
- School of Biology, College of Science, University of Tehran, Tehran, The Islamic Republic of Iran
| | - Shahriar Nafissi
- Department of Neurology, Tehran University of Medical Sciences, Tehran, The Islamic Republic of Iran
| | - Hosein Shamshiri
- Department of Neurology, Tehran University of Medical Sciences, Tehran, The Islamic Republic of Iran
| | - Hamidreza Moazzeni
- School of Biology, College of Science, University of Tehran, Tehran, The Islamic Republic of Iran
| | - Hanieh Taheri
- School of Biology, College of Science, University of Tehran, Tehran, The Islamic Republic of Iran
| | - Elahe Elahi
- School of Biology, College of Science, University of Tehran, Tehran, The Islamic Republic of Iran
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Tábuas-Pereira M, Santana I, Gibbons E, Paquette K, Almeida MR, Baldeiras I, Bras J, Guerreiro R. Exome Sequencing of a Portuguese Cohort of Frontotemporal Dementia Patients: Looking Into the ALS-FTD Continuum. Front Neurol 2022; 13:886379. [PMID: 35873773 PMCID: PMC9300853 DOI: 10.3389/fneur.2022.886379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction Frontotemporal dementia (FTD) is considered to be part of a continuum with amyotrophic lateral sclerosis (ALS). Many genes are associated with both ALS and FTD. Yet, many genes associated with ALS have not been shown to cause FTD. We aimed to study a Portuguese cohort of FTD patients, searching for variants in genes associated with both FTD and/or ALS. Methods We included 57 thoroughly characterized index FTD patients from our memory clinic, who were not carriers of pathogenic variants in GRN, MAPT or C9orf72. We performed exome sequencing and 1) prioritized potential FTD and ALS causing variants by using Exomiser to annotate and filter results; and 2) looked specifically at rare variability in genes associated with FTD (excluding GRN, MAPT and C9ORF72) and/or ALS. Results We identified 13 rare missense variants in 10 patients (three patients had two variants) in the following genes: FUS, OPTN, CCNF, DCTN1, TREM2, ERBB4, ANG, CHRNA4, CHRNB4 and SETX. We found an additional frameshift variant on GLT8D1 in one patient. One variant (ERBB4 p.Arg1112His) gathered enough evidence to be classified as likely pathogenic by the ACMG criteria. Discussion We report, for the first time, an expanded study of genes known to cause FTD-ALS, in the Portuguese population. Potentially pathogenic variants in ERBB4, FUS, SETX, ANG, CHRNA4 and CHRNB4 were identified in FTD patients. These findings provide additional evidence for the potential role of rare variability in ALS-associated genes in FTD, expanding the genetic spectrum between the two diseases.
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Affiliation(s)
- Miguel Tábuas-Pereira
- Neurology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Department of Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
- *Correspondence: Miguel Tábuas-Pereira
| | - Isabel Santana
- Neurology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Department of Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
- Department of Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
| | - Kimberly Paquette
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
| | - Maria Rosário Almeida
- Department of Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Inês Baldeiras
- Neurology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Department of Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
- Department of Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, United States
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, United States
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Coleman MP. Axon Biology in ALS: Mechanisms of Axon Degeneration and Prospects for Therapy. Neurotherapeutics 2022; 19:1133-1144. [PMID: 36207571 PMCID: PMC9587191 DOI: 10.1007/s13311-022-01297-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 10/10/2022] Open
Abstract
This review addresses the longstanding debate over whether amyotrophic lateral sclerosis (ALS) is a 'dying back' or 'dying forward' disorder in the light of new gene identifications and the increased understanding of mechanisms of action for previously identified ALS genes. While the topological pattern of pathology in animal models, and more anecdotally in patients is indeed 'dying back', this review discusses how this fits with the fact that many of the major initiating events are thought to occur within the soma. It also discusses how widely varying ALS risk factors, including some impacting axons directly, may combine to drive a common pathway involving TAR DNA binding protein 43 (TDP-43) and neuromuscular junction (NMJ) denervation. The emerging association between sterile alpha and TIR motif-containing 1 (SARM1), a protein so far mostly associated with axon degeneration, and sporadic ALS is another major theme. The strengths and limitations of the current evidence supporting an association are considered, along with ways in which SARM1 could become activated in ALS. The final section addresses SARM1-based therapies along with the prospects for targeting other axonal steps in ALS pathogenesis.
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Affiliation(s)
- Michael P Coleman
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Robinson Way, Cambridge, CB2 0PY, UK.
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Pan S, Liu X, Liu T, Zhao Z, Dai Y, Wang YY, Jia P, Liu F. Causal Inference of Genetic Variants and Genes in Amyotrophic Lateral Sclerosis. Front Genet 2022; 13:917142. [PMID: 35812739 PMCID: PMC9257137 DOI: 10.3389/fgene.2022.917142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal progressive multisystem disorder with limited therapeutic options. Although genome-wide association studies (GWASs) have revealed multiple ALS susceptibility loci, the exact identities of causal variants, genes, cell types, tissues, and their functional roles in the development of ALS remain largely unknown. Here, we reported a comprehensive post-GWAS analysis of the recent large ALS GWAS (n = 80,610), including functional mapping and annotation (FUMA), transcriptome-wide association study (TWAS), colocalization (COLOC), and summary data-based Mendelian randomization analyses (SMR) in extensive multi-omics datasets. Gene property analysis highlighted inhibitory neuron 6, oligodendrocytes, and GABAergic neurons (Gad1/Gad2) as functional cell types of ALS and confirmed cerebellum and cerebellar hemisphere as functional tissues of ALS. Functional annotation detected the presence of multiple deleterious variants at three loci (9p21.2, 12q13.3, and 12q14.2) and highlighted a list of SNPs that are potentially functional. TWAS, COLOC, and SMR identified 43 genes at 24 loci, including 23 novel genes and 10 novel loci, showing significant evidence of causality. Integrating multiple lines of evidence, we further proposed that rs2453555 at 9p21.2 and rs229243 at 14q12 functionally contribute to the development of ALS by regulating the expression of C9orf72 in pituitary and SCFD1 in skeletal muscle, respectively. Together, these results advance our understanding of the biological etiology of ALS, feed into new therapies, and provide a guide for subsequent functional experiments.
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Affiliation(s)
- Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Tianzi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Yin-Ying Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- *Correspondence: Fan Liu, ; Peilin Jia,
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Fan Liu, ; Peilin Jia,
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Azari A, Goodarzi A, Jafarkhani B, Eghbali M, Karimi Z, Hosseini Balef SS, Irannejad H. Novel molecular targets and mechanisms for neuroprotective modulation in neurodegenerative disorders. Cent Nerv Syst Agents Med Chem 2022; 22:88-107. [PMID: 35713146 DOI: 10.2174/1871524922666220616092132] [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: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neuronal death underlies the symptoms of several human neurological disorders, including Alzheimer's, Parkinson's and Huntington's diseases, and amyotrophic lateral sclerosis that their precise pathophysiology have not yet been elucidated. According to various studies the prohibition is the best therapy with neuroprotective approaches which are advanced and safe methods. METHODS This review summarizes some of the already-known and newly emerged neuroprotective targets and strategies that their experimental effects have been reported. Accordingly, literature was studied from 2000 to 2021 and appropriate articles were searched in Google Scholar and Scopus with the keywords given in the Keywords section of the current review. RESULTS Lewy bodies are the histopathologic characteristics of neurodegenerative disorders and are protein-rich intracellular deposits in which Alpha-Synuclein is its major protein. Alpha-Synuclein's toxic potential provides a compelling rationale for therapeutic strategies aimed at decreasing its burden in neuronal cells through numerous pathways including ubiquitin-proteasome system and autophagy-lysosome Pathway, proteolytic breakdown via cathepsin D, kallikrein-6 (neurosin), calpain-1 or MMP9, heat shock proteins, and proteolysis targeting chimera which consists of a target protein ligand and an E3 ubiquitin ligase (E3) followed by target protein ubiquitination (PROTACs). Other targets that have been noticed recently are the mutant huntingtin, tau proteins and glycogen synthase kinase 3β that their accumulation proceeds extensive neuronal damage and up to the minute approach such as Proteolysis Targeting Chimera promotes its degradation in cells. As various studies demonstrated that Mendelian gene mutations can result into the neurodegenerative diseases, additional target that has gained much interest is epigenetics such as mutation, phosphodiesterase, RNA binding proteins and Nuclear respiratory factor 1. CONCLUSION The novel molecular targets and new strategies compiled and introduced here can be used by scientists to design and discover more efficient small molecule drugs against the neurodegenerative diseases. And also the genes in which their mutations can lead to the α-synuclein aggregation or accumulation are discussed and considered a valuable information of epigenetics in dementia.
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Affiliation(s)
- Aala Azari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amin Goodarzi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Behrouz Jafarkhani
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Eghbali
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zohreh Karimi
- Department of Obstetrics & Gynecology, Imam Khomeini hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Sajad Hosseini Balef
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hamid Irannejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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