2
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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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3
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Morello G, Gentile G, Spataro R, Spampinato AG, Guarnaccia M, Salomone S, La Bella V, Conforti FL, Cavallaro S. Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family. J Pers Med 2020; 10:jpm10040262. [PMID: 33276461 PMCID: PMC7712010 DOI: 10.3390/jpm10040262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Background: Repeat expansions in the spinocerebellar ataxia type 1 (SCA1) gene ATXN1 increases the risk for amyotrophic lateral sclerosis (ALS), supporting a relationship between these disorders. We recently reported the co-existence, in a large SCA1 family, of a clinically definite ALS individual bearing an intermediate ATXN1 expansion and SCA1 patients with a full expansion, some of which manifested signs of lower motor neuron involvement. Methods: In this study, we employed a systems biology approach that integrated multiple genomic analyses of the ALS patient and some SCA1 family members. Results: Our analysis identified common and distinctive candidate genes/variants and related biological processes that, in addition to or in combination with ATXN1, may contribute to motor neuron degeneration phenotype. Among these, we distinguished ALS-specific likely pathogenic variants in TAF15 and C9ORF72, two ALS-linked genes involved in the regulation of RNA metabolism, similarly to ATXN1, suggesting a selective role for this pathway in ALS pathogenesis. Conclusions: Overall, our work supports the utility to apply personal genomic information for characterizing complex disease phenotypes.
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Affiliation(s)
- Giovanna Morello
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (G.G.); (A.G.S.); (M.G.)
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, 95123 Catania, Italy;
| | - Giulia Gentile
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (G.G.); (A.G.S.); (M.G.)
| | - Rossella Spataro
- ALS Clinical Research Center and Neurochemistry Laboratory, BioNeC, University of Palermo, 90127 Palermo, Italy; (R.S.); (V.L.B.)
| | - Antonio Gianmaria Spampinato
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (G.G.); (A.G.S.); (M.G.)
- Department of Mathematics and Computer Science, University of Catania, 95123 Catania, Italy
| | - Maria Guarnaccia
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (G.G.); (A.G.S.); (M.G.)
| | - Salvatore Salomone
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, 95123 Catania, Italy;
| | - Vincenzo La Bella
- ALS Clinical Research Center and Neurochemistry Laboratory, BioNeC, University of Palermo, 90127 Palermo, Italy; (R.S.); (V.L.B.)
| | - Francesca Luisa Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, 87036 Rende, Italy
- Correspondence: (F.L.C.); (S.C.); Tel.: +39-0984-496204 (F.L.C.); +39-095-7338111 (S.C.); Fax: +39-0984-496203 (F.L.C.); +39-095-7338110 (S.C.)
| | - Sebastiano Cavallaro
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (G.G.); (A.G.S.); (M.G.)
- Correspondence: (F.L.C.); (S.C.); Tel.: +39-0984-496204 (F.L.C.); +39-095-7338111 (S.C.); Fax: +39-0984-496203 (F.L.C.); +39-095-7338110 (S.C.)
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4
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Tazelaar GHP, Boeynaems S, De Decker M, van Vugt JJFA, Kool L, Goedee HS, McLaughlin RL, Sproviero W, Iacoangeli A, Moisse M, Jacquemyn M, Daelemans D, Dekker AM, van der Spek RA, Westeneng HJ, Kenna KP, Assialioui A, Da Silva N, Povedano M, Pardina JSM, Hardiman O, Salachas F, Millecamps S, Vourc'h P, Corcia P, Couratier P, Morrison KE, Shaw PJ, Shaw CE, Pasterkamp RJ, Landers JE, Van Den Bosch L, Robberecht W, Al-Chalabi A, van den Berg LH, Van Damme P, Veldink JH, van Es MA. ATXN1 repeat expansions confer risk for amyotrophic lateral sclerosis and contribute to TDP-43 mislocalization. Brain Commun 2020; 2:fcaa064. [PMID: 32954321 PMCID: PMC7425293 DOI: 10.1093/braincomms/fcaa064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 02/01/2023] Open
Abstract
Increasingly, repeat expansions are being identified as part of the complex genetic architecture of amyotrophic lateral sclerosis. To date, several repeat expansions have been genetically associated with the disease: intronic repeat expansions in C9orf72, polyglutamine expansions in ATXN2 and polyalanine expansions in NIPA1. Together with previously published data, the identification of an amyotrophic lateral sclerosis patient with a family history of spinocerebellar ataxia type 1, caused by polyglutamine expansions in ATXN1, suggested a similar disease association for the repeat expansion in ATXN1. We, therefore, performed a large-scale international study in 11 700 individuals, in which we showed a significant association between intermediate ATXN1 repeat expansions and amyotrophic lateral sclerosis (P = 3.33 × 10-7). Subsequent functional experiments have shown that ATXN1 reduces the nucleocytoplasmic ratio of TDP-43 and enhances amyotrophic lateral sclerosis phenotypes in Drosophila, further emphasizing the role of polyglutamine repeat expansions in the pathophysiology of amyotrophic lateral sclerosis.
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Affiliation(s)
- Gijs H P Tazelaar
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Steven Boeynaems
- Division of Experimental Neurology, Department of Neurosciences, KU
Leuven—University of Leuven, Leuven 3000, Belgium,Laboratory of Neurobiology, VIB, Center for Brain & Disease
Research, Leuven 3000, Belgium,Department of Genetics, Stanford University School of Medicine,
Stanford, CA 94305-5120, USA
| | - Mathias De Decker
- Division of Experimental Neurology, Department of Neurosciences, KU
Leuven—University of Leuven, Leuven 3000, Belgium,Laboratory of Neurobiology, VIB, Center for Brain & Disease
Research, Leuven 3000, Belgium
| | - Joke J F A van Vugt
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Lindy Kool
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - H Stephan Goedee
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Russell L McLaughlin
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College
Dublin, Dublin D02 PN40, Republic of Ireland
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical
Neuroscience Institute and United Kingdom Dementia Research Institute, King’s College
London, London SE5 9NU, UK
| | - Alfredo Iacoangeli
- Department of Biostatistics & Health Informatics, Institute of Psychiatry,
Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Matthieu Moisse
- Division of Experimental Neurology, Department of Neurosciences, KU
Leuven—University of Leuven, Leuven 3000, Belgium,Laboratory of Neurobiology, VIB, Center for Brain & Disease
Research, Leuven 3000, Belgium
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and
Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and
Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Annelot M Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Rick A van der Spek
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Kevin P Kenna
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Abdelilah Assialioui
- Servei de Neurologia, IDIBELL-Hospital de Bellvitge, Hospitalet de
Llobregat, Barcelona 08908, Spain
| | - Nica Da Silva
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical
Neuroscience Institute and United Kingdom Dementia Research Institute, King’s College
London, London SE5 9NU, UK
| | | | - Mónica Povedano
- Servei de Neurologia, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona 08908, Spain
| | | | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin D02 PN40, Republic of Ireland.,Department of Neurology, Beaumont Hospital, Dublin D02 PN40, Republic of Ireland
| | - François Salachas
- Centre de compétence SLA-Département de Neurologie, Hôpital Pitié-Salpêtrière, Paris 75651, France.,Institut du Cerveau et de la Moelle Epinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, Paris 75651, France
| | - Stéphanie Millecamps
- Institut du Cerveau et de la Moelle Epinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, Paris 75651, France
| | - Patrick Vourc'h
- INSERM U930, Université François Rabelais, Tours 92120, France
| | - Philippe Corcia
- Centre de compétence SLA-fédération Tours-Limoges, Tours 92120, France
| | - Philippe Couratier
- Centre de compétence SLA-fédération Tours-Limoges, Limoges 87100, France
| | - Karen E Morrison
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute, King's College London, London SE5 9NU, UK.,Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Utrecht University, 3508 GA, Utrecht, The Netherlands
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ludo Van Den Bosch
- Division of Experimental Neurology, Department of Neurosciences, KU Leuven-University of Leuven, Leuven 3000, Belgium.,Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Wim Robberecht
- Division of Experimental Neurology, Department of Neurosciences, KU Leuven-University of Leuven, Leuven 3000, Belgium.,Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium.,Department of Neurology, University Hospitals Leuven, Leuven 3000, Belgium
| | - 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 SE5 9NU, UK.,Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center, Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Philip Van Damme
- Division of Experimental Neurology, Department of Neurosciences, KU Leuven-University of Leuven, Leuven 3000, Belgium.,Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium.,Department of Neurology, University Hospitals Leuven, Leuven 3000, Belgium
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center, Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Michael A van Es
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center, Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
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5
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Sánchez I, Balagué E, Matilla-Dueñas A. Ataxin-1 regulates the cerebellar bioenergetics proteome through the GSK3β-mTOR pathway which is altered in Spinocerebellar ataxia type 1 (SCA1). Hum Mol Genet 2016; 25:4021-4040. [PMID: 27466200 DOI: 10.1093/hmg/ddw242] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/21/2016] [Accepted: 07/11/2016] [Indexed: 12/17/2022] Open
Abstract
A polyglutamine expansion within the ataxin-1 protein (ATXN1) underlies spinocerebellar ataxia type-1 (SCA1), a neurological disorder mainly characterized by ataxia and cerebellar deficits. In SCA1, both loss and gain of ATXN1 biological functions contribute to cerebellar pathogenesis. However, the critical ATXN1 functions and pathways involved remain unclear. To further investigate the early signalling pathways regulated by ATXN1, we performed an unbiased proteomic study of the Atxn1-KO 5-week-old mice cerebellum. Here, we show that lack of ATXN1 expression induces early alterations in proteins involved in glycolysis [pyruvate kinase, muscle, isoform 1 protein (PKM-i1), citrate synthase (CS), glycerol-3-phosphate dehydrogenase 2 (GPD2), glucose-6-phosphate isomerase (GPI), alpha -: enolase (ENO1)], ATP synthesis [CS, Succinate dehydrogenase complex,subunit A (SDHA), ATP synthase subunit d, mitochondrial (ATP5H)] and oxidative stress [peroxiredoxin-6 (PRDX6), aldehyde dehydrogenase family 1, subfamily A1, 10-formyltetrahydrofolate dehydrogenase]. In the SCA1 mice, several of these proteins (PKM-i1, ATP5H, PRDX6, proteome subunit A6) were down-regulated and ATP levels decreased. The underlying mechanism does not involve modulation of mitochondrial biogenesis, but dysregulation of the activity of the metabolic regulators glycogen synthase kinase 3B (GSK3β), decreased in Atxn1-KO and increased in SCA1 mice, and mechanistic target of rapamycin (serine/threonine kinase) (mTOR), unchanged in the Atxn1-KO and decreased in SCA1 mice cerebellum before the onset of ataxic symptoms. Pharmacological inhibition of GSK3β and activation of mTOR in a SCA1 cell model ameliorated identified ATXN1-regulated metabolic proteome and ATP alterations. Taken together, these results point to an early role of ATXN1 in the regulation of bioenergetics homeostasis in the mouse cerebellum. Moreover, data suggest GSK3β and mTOR pathways modulate this ATXN1 function in SCA1 pathogenesis that could be targeted therapeutically prior to the onset of disease symptoms in SCA1 and other pathologies involving dysregulation of ATXN1 functions.
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Affiliation(s)
- Ivelisse Sánchez
- Functional and Translational Neurogenetics Unit, Department of Neurosciences, Health Sciences Research Institute Germans Trias i Pujol (IGTP)-Universitat Autonoma de Barcelona, Crta. de Can Ruti, camí de les escoles s/n, 08916 Badalona, Barcelona, Spain
| | - Eudald Balagué
- Functional and Translational Neurogenetics Unit, Department of Neurosciences, Health Sciences Research Institute Germans Trias i Pujol (IGTP)-Universitat Autonoma de Barcelona, Crta. de Can Ruti, camí de les escoles s/n, 08916 Badalona, Barcelona, Spain
| | - Antoni Matilla-Dueñas
- Functional and Translational Neurogenetics Unit, Department of Neurosciences, Health Sciences Research Institute Germans Trias i Pujol (IGTP)-Universitat Autonoma de Barcelona, Crta. de Can Ruti, camí de les escoles s/n, 08916 Badalona, Barcelona, Spain
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