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Tsai YC, Brown KA, Bernardi MT, Harting J, Clelland CD. Single-Molecule Sequencing of the C9orf72 Repeat Expansion in Patient iPSCs. Bio Protoc 2024; 14:e5060. [PMID: 39282230 PMCID: PMC11393041 DOI: 10.21769/bioprotoc.5060] [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: 05/14/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 09/18/2024] Open
Abstract
A hexanucleotide GGGGCC repeat expansion in the C9orf72 gene is the most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). C9orf72 repeat expansions are currently identified with long-range PCR or Southern blot for clinical and research purposes, but these methods lack accuracy and sensitivity. The GC-rich and repetitive content of the region cannot be amplified by PCR, which leads traditional sequencing approaches to fail. We turned instead to PacBio single-molecule sequencing to detect and size the C9orf72 repeat expansion without amplification. We isolated high molecular weight genomic DNA from patient-derived iPSCs of varying repeat lengths and then excised the region containing the C9orf72 repeat expansion from naked DNA with a CRISPR/Cas9 system. We added adapters to the cut ends, capturing the target region for sequencing on PacBio's Sequel, Sequel II, or Sequel IIe. This approach enriches the C9orf72 repeat region without amplification and allows the repeat expansion to be consistently and accurately sized, even for repeats in the thousands. Key features • This protocol is adapted from PacBio's previous "no-amp targeted sequencing utilizing the CRISPR-Cas9 system." • Optimized for sizing C9orf72 repeat expansions in patient-derived iPSCs and applicable to DNA from any cell type, blood, or tissue. • Requires high molecular weight naked DNA. • Compatible with Sequel I and II but not Revio.
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Affiliation(s)
| | - Katherine A Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Claire D Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
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2
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Chourpiliadis C, Seitz C, Lovik A, Joyce EE, Pan L, Hu Y, Kläppe U, Samuelsson K, Press R, Ingre C, Fang F. Lifestyle and medical conditions in relation to ALS risk and progression-an introduction to the Swedish ALSrisc Study. J Neurol 2024; 271:5447-5459. [PMID: 38878106 PMCID: PMC11319377 DOI: 10.1007/s00415-024-12496-w] [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: 02/15/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND This study was an introduction to the Swedish ALSrisc Study and explored the association of lifestyle and medical conditions, with risk and progression of amyotrophic lateral sclerosis (ALS). METHODS We included 265 newly diagnosed ALS patients during 2016-2022 in Stockholm and 207 ALS-free siblings and partners of the patients as controls. Information on body mass index (BMI), smoking, and history of head injuries, diabetes mellitus, hypercholesterolemia, and hypertension was obtained through the Euro-MOTOR questionnaire at recruitment. Patients were followed from diagnosis until death, invasive ventilation, or November 30, 2022. RESULTS Higher BMI at recruitment was associated with lower risk for ALS (OR 0.89, 95%CI 0.83-0.95), especially among those diagnosed after 65 years. One unit increase in the average BMI during the 3 decades before diagnosis was associated with a lower risk for ALS (OR 0.94, 95%CI 0.89-0.99). Diabetes was associated with lower risk of ALS (OR 0.38, 95%CI 0.16-0.90), while hypercholesterolemia was associated with higher risk of ALS (OR 2.10, 95%CI 1.13-3.90). Higher BMI at diagnosis was associated with lower risk of death (HR 0.91, 95%CI 0.84-0.98), while the highest level of smoking exposure (in pack-years) (HR 1.90, 95%CI 1.20-3.00), hypercholesterolemia (HR 1.84, 95%CI 1.06-3.19), and hypertension (HR 1.76, 95%CI 1.03-3.01) were associated with higher risk of death, following ALS diagnosis. CONCLUSIONS Higher BMI and diabetes were associated with lower risk of ALS. Higher BMI was associated with lower risk of death, whereas smoking (especially in high pack-years), hypercholesterolemia, and hypertension were associated with higher risk of death after ALS diagnosis.
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Affiliation(s)
| | - Christina Seitz
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anikó Lovik
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Institute of Psychology, Leiden University, Leiden, The Netherlands
| | - Emily E Joyce
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yihan Hu
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Kläppe
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Kristin Samuelsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Rayomand Press
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Ingre
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden.
| | - Fang Fang
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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Leighton DJ, Ansari M, Newton J, Cleary E, Stephenson L, Beswick E, Carod Artal J, Davenport R, Duncan C, Gorrie GH, Morrison I, Swingler R, Deary IJ, Porteous M, Chandran S, Pal S. Genotypes and phenotypes of motor neuron disease: an update of the genetic landscape in Scotland. J Neurol 2024; 271:5256-5266. [PMID: 38852112 PMCID: PMC11319561 DOI: 10.1007/s00415-024-12450-w] [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: 12/07/2023] [Revised: 05/09/2024] [Accepted: 05/16/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Using the Clinical Audit Research and Evaluation of Motor Neuron Disease (CARE-MND) database and the Scottish Regenerative Neurology Tissue Bank, we aimed to outline the genetic epidemiology and phenotypes of an incident cohort of people with MND (pwMND) to gain a realistic impression of the genetic landscape and genotype-phenotype associations. METHODS Phenotypic markers were identified from the CARE-MND platform. Sequence analysis of 48 genes was undertaken. Variants were classified using a structured evidence-based approach. Samples were also tested for C9orf72 hexanucleotide expansions using repeat-prime PCR methodology. RESULTS 339 pwMND donated a DNA sample: 44 (13.0%) fulfilled criteria for having a pathogenic variant/repeat expansion, 53.5% of those with a family history of MND and 9.3% of those without. The majority (30 (8.8%)) had a pathogenic C9orf72 repeat expansion, including two with intermediate expansions. Having a C9orf72 expansion was associated with a significantly lower Edinburgh Cognitive and Behavioural ALS Screen ALS-Specific score (p = 0.0005). The known pathogenic SOD1 variant p.(Ile114Thr), frequently observed in the Scottish population, was detected in 9 (2.7%) of total cases but in 17.9% of familial cases. Rare variants were detected in FUS and NEK1. One individual carried both a C9orf72 expansion and SOD1 variant. CONCLUSIONS Our results provide an accurate summary of MND demographics and genetic epidemiology. We recommend early genetic testing of people with cognitive impairment to ensure that C9orf72 carriers are given the best opportunity for informed treatment planning. Scotland is enriched for the SOD1 p.(Ile114Thr) variant and this has significant implications with regards to future genetically-targeted treatments.
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Affiliation(s)
- Danielle J Leighton
- School of Psychology & Neuroscience, University of Glasgow, Glasgow, UK.
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK.
- Anne Rowling Regenerative Neurology Clinic, Royal Infirmary, Edinburgh, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Institute of Neurological Sciences, Queen Elizabeth University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK.
| | - Morad Ansari
- South East Scotland Genetics Service, Western General Hospital, Edinburgh, UK
| | - Judith Newton
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, Royal Infirmary, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Elaine Cleary
- South East Scotland Genetics Service, Western General Hospital, Edinburgh, UK
| | - Laura Stephenson
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
| | - Emily Beswick
- Anne Rowling Regenerative Neurology Clinic, Royal Infirmary, Edinburgh, UK
| | | | - Richard Davenport
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, Royal Infirmary, Edinburgh, UK
| | - Callum Duncan
- Department of Neurology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - George H Gorrie
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
- Institute of Neurological Sciences, Queen Elizabeth University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK
| | - Ian Morrison
- Department of Neurology, NHS Tayside, Dundee, UK
| | - Robert Swingler
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts Group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Mary Porteous
- South East Scotland Genetics Service, Western General Hospital, Edinburgh, UK
| | - Siddharthan Chandran
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, Royal Infirmary, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | - Suvankar Pal
- The Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, Royal Infirmary, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
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4
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Ruiz de Sabando A, Ciosi M, Galbete A, Cumming SA, Monckton DG, Ramos-Arroyo MA. Somatic CAG repeat instability in intermediate alleles of the HTT gene and its potential association with a clinical phenotype. Eur J Hum Genet 2024; 32:770-778. [PMID: 38433266 PMCID: PMC11220145 DOI: 10.1038/s41431-024-01546-6] [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: 08/16/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 03/05/2024] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder caused by ≥36 CAGs in the HTT gene. Intermediate alleles (IAs) (27-35 CAGs) are not considered HD-causing, but their potential association with neurocognitive symptoms remains controversial. As HTT somatic CAG expansion influences HD onset, we hypothesised that IAs are somatically unstable, and that somatic CAG expansion may drive phenotypic presentation in some IA carriers. We quantified HTT somatic CAG expansions by MiSeq sequencing in the blood DNA of 164 HD subjects and 191 IA (symptomatic and control) carriers, and in the brain DNA of a symptomatic 33 CAG carrier. We also performed genotype-phenotype analysis. The phenotype of symptomatic IA carriers was characterised by motor (85%), cognitive (27%) and/or behavioural (29%) signs, with a late (58.7 ± 18.6 years), but not CAG-dependent, age at onset. IAs displayed somatic expansion that were CAG and age-dependent in blood DNA, with 0.4% and 0.01% of DNA molecules expanding by CAG and year, respectively. Somatic expansions of +1 and +2 CAGs were detected in the brain of the individual with 33 CAGs, with the highest expansion frequency in the putamen (10.3%) and the lowest in the cerebellum (4.8%). Somatic expansion in blood DNA was not different in symptomatic vs. control IA carriers. In conclusion, we show that HTT IAs are somatically unstable, but we found no association with HD-like phenotypes. It is plausible, however, that some IAs, close to the HD pathological threshold and with a predisposing genetic background, could manifest with neurocognitive symptoms.
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Affiliation(s)
- Ainara Ruiz de Sabando
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, 31008, Pamplona, Spain
- Department of Health Sciences, Universidad Pública de Navarra, IdiSNA, 31008, Pamplona, Spain
- Fundación Miguel Servet-Navarrabiomed, IdiSNA, 31008, Pamplona, Spain
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Arkaitz Galbete
- Department of Statistics, Informatics and Mathematics, Universidad Pública de Navarra, IdiSNA, 31006, Pamplona, Spain
| | - Sarah A Cumming
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Darren G Monckton
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Maria A Ramos-Arroyo
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, 31008, Pamplona, Spain.
- Fundación Miguel Servet-Navarrabiomed, IdiSNA, 31008, Pamplona, Spain.
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5
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Ruotolo G, D'Anzi A, Casamassa A, Mazzoni M, Ferrari D, Lombardi I, Carletti RM, D'Asdia C, Torrente I, Frezza K, Lattante S, Sabatelli M, Pennuto M, Vescovi AL, Rosati J. Generation of induced pluripotent stem cells (CSSi017-A)(12862) from an ALS patient carrying a repeat expansion in the C9orf72 gene. Stem Cell Res 2024; 77:103412. [PMID: 38613988 DOI: 10.1016/j.scr.2024.103412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 04/15/2024] Open
Abstract
Genetic expansions of the hexanucleotide repeats (GGGGCC) in the C9orf72 gene appear in approximately 40% of patients with familial ALS and 7% of patients with sporadic ALS in the European population, making this mutation one of the most prevalent genetic mutations in ALS. Here, we generated a human induced pluripotent stem cell (hiPSC) line from the dermal fibroblasts of a patient carrying a 56-repeat expansion in an ALS disease-causing allele of C9orf72. These iPSCs showed stable amplification in vitro with normal karyotype and high expression of pluripotent markers and differentiated spontaneously in vivo into three germ layers.
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Affiliation(s)
- G Ruotolo
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - A D'Anzi
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - A Casamassa
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - M Mazzoni
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - D Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - I Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - R M Carletti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - C D'Asdia
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - I Torrente
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - K Frezza
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - S Lattante
- Medical Genetics Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Section of Genomic Medicine, Department of Health Sciences and Public Health, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, Rome, Italy; Experimental Medicine Department, Università del Salento, Lecce, Italy
| | - M Sabatelli
- Neurology Unit, NeMO Clinical Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Section of Neurology, Department of Neurosciences, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, Rome, Italy
| | - M Pennuto
- Department of Biomedical Sciences, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - A L Vescovi
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - J Rosati
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
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6
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Sellier C, Corcia P, Vourc'h P, Dupuis L. C9ORF72 hexanucleotide repeat expansion: From ALS and FTD to a broader pathogenic role? Rev Neurol (Paris) 2024; 180:417-428. [PMID: 38609750 DOI: 10.1016/j.neurol.2024.03.008] [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: 03/20/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024]
Abstract
The major gene underlying monogenic forms of amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD) is C9ORF72. The causative mutation in C9ORF72 is an abnormal hexanucleotide (G4C2) repeat expansion (HRE) located in the first intron of the gene. The aim of this review is to propose a comprehensive update on recent developments on clinical, biological and therapeutics aspects related to C9ORF72 in order to highlight the current understanding of genotype-phenotype correlations, and also on biological machinery leading to neuronal death. We will particularly focus on the broad phenotypic presentation of C9ORF72-related diseases, that goes well beyond the classical phenotypes observed in ALS and FTD patients. Last, we will comment the possible therapeutical hopes for patients carrying a C9ORF72 HRE.
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Affiliation(s)
- C Sellier
- Centre de recherches en biomédecine de Strasbourg, UMR-S1329, Inserm, université de Strasbourg, Strasbourg, France
| | - P Corcia
- UMR 1253 iBrain, Inserm, université de Tours, Tours, France; Centre constitutif de coordination SLA, CHU de Bretonneau, 2, boulevard Tonnelle, 37044 Tours cedex 1, France
| | - P Vourc'h
- UMR 1253 iBrain, Inserm, université de Tours, Tours, France; Service de biochimie et biologie moléculaire, CHU de Tours, Tours, France
| | - L Dupuis
- Centre de recherches en biomédecine de Strasbourg, UMR-S1329, Inserm, université de Strasbourg, Strasbourg, France.
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7
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Novy C, Busk ØL, Tysnes OB, Landa SS, Aanjesen TN, Alstadhaug KB, Bjerknes TL, Bjørnå IK, Bråthen G, Dahl E, Demic N, Fahlström M, Flemmen HØ, Hallerstig E, HogenEsch I, Kampman MT, Kleveland G, Kvernmo HB, Ljøstad U, Maniaol A, Morsund AH, Nakken O, Olsen CG, Schlüter K, Utvik MS, Yaseen R, Holla ØL, Holmøy T, Høyer H. Repeat expansions in AR, ATXN1, ATXN2 and HTT in Norwegian patients diagnosed with amyotrophic lateral sclerosis. Brain Commun 2024; 6:fcae087. [PMID: 38585669 PMCID: PMC10998343 DOI: 10.1093/braincomms/fcae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/23/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Genetic repeat expansions cause neuronal degeneration in amyotrophic lateral sclerosis as well as other neurodegenerative disorders such as spinocerebellar ataxia, Huntington's disease and Kennedy's disease. Repeat expansions in the same gene can cause multiple clinical phenotypes. We aimed to characterize repeat expansions in a Norwegian amyotrophic lateral sclerosis cohort. Norwegian amyotrophic lateral sclerosis patients (n = 414) and neurologically healthy controls adjusted for age and gender (n = 713) were investigated for repeat expansions in AR, ATXN1, ATXN2 and HTT using short read exome sequencing and the ExpansionHunter software. Five amyotrophic lateral sclerosis patients (1.2%) and two controls (0.3%) carried ≥36 repeats in HTT (P = 0.032), and seven amyotrophic lateral sclerosis patients (1.7%) and three controls (0.4%) carried ≥29 repeats in ATXN2 (P = 0.038). One male diagnosed with amyotrophic lateral sclerosis carried a pathogenic repeat expansion in AR, and his diagnosis was revised to Kennedy's disease. In ATXN1, 50 amyotrophic lateral sclerosis patients (12.1%) and 96 controls (13.5%) carried ≥33 repeats (P = 0.753). None of the patients with repeat expansions in ATXN2 or HTT had signs of Huntington's disease or spinocerebellar ataxia type 2, based on a re-evaluation of medical records. The diagnosis of amyotrophic lateral sclerosis was confirmed in all patients, with the exception of one patient who had primary lateral sclerosis. Our findings indicate that repeat expansions in HTT and ATXN2 are associated with increased likelihood of developing amyotrophic lateral sclerosis. Further studies are required to investigate the potential relationship between HTT repeat expansions and amyotrophic lateral sclerosis.
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Affiliation(s)
- Camilla Novy
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Øyvind L Busk
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Ole-Bjørn Tysnes
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5009 Bergen, Norway
| | - Sigve S Landa
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Tori N Aanjesen
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | | | - Tale L Bjerknes
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5009 Bergen, Norway
- Institute of Clinical Medicine, University of Bergen, 5007 Bergen, Norway
| | - Ingrid K Bjørnå
- Department of Neurology, Vestre Viken Hospital Trust, 3004 Drammen, Norway
| | - Geir Bråthen
- Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Elin Dahl
- Department of Neurology, Telemark Hospital Trust, 3710 Skien, Norway
| | - Natasha Demic
- Department of Neurology, Vestfold Hospital Trust, 3103 Tønsberg, Norway
| | - Maria Fahlström
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Heidi Ø Flemmen
- Department of Neurology, Telemark Hospital Trust, 3710 Skien, Norway
| | - Erika Hallerstig
- Department of Neurology, Østfold Hospital Trust, 1714 Grålum, Norway
| | - Ineke HogenEsch
- Department of Neurology, Fonna Hospital Trust, 5528 Haugesund, Norway
| | - Margitta T Kampman
- Department of Neurology, University Hospital of North Norway, 9019 Tromsø, Norway
| | - Grethe Kleveland
- Department of Neurology, Innlandet Hospital Trust, 2609 Lillehammer, Norway
| | - Helene B Kvernmo
- Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Unn Ljøstad
- Institute of Clinical Medicine, University of Bergen, 5007 Bergen, Norway
- Department of Neurology, Sørlandet Hospital Trust, 4615 Kristiansand, Norway
| | - Angelina Maniaol
- Department of Neurology, Oslo University Hospital, 0450 Oslo, Norway
| | | | - Ola Nakken
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Cathrine G Olsen
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Katrin Schlüter
- Department of Neurology, Stavanger University Hospital, 4019 Stavanger, Norway
| | - May-Sissel Utvik
- Department of Neurology, Namsos Hospital Trust, 7803 Namsos, Norway
| | - Ryaz Yaseen
- Department of Neurology, Oslo University Hospital, 0450 Oslo, Norway
| | - Øystein L Holla
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Trygve Holmøy
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Helle Høyer
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
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8
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Chang YJ, Lin KT, Shih O, Yang CH, Chuang CY, Fang MH, Lai WB, Lee YC, Kuo HC, Hung SC, Yao CK, Jeng US, Chen YR. Sulfated disaccharide protects membrane and DNA damages from arginine-rich dipeptide repeats in ALS. SCIENCE ADVANCES 2024; 10:eadj0347. [PMID: 38394210 PMCID: PMC10889363 DOI: 10.1126/sciadv.adj0347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Hexanucleotide repeat expansion in C9ORF72 (C9) is the most prevalent mutation among amyotrophic lateral sclerosis (ALS) patients. The patients carry over ~30 to hundreds or thousands of repeats translated to dipeptide repeats (DPRs) where poly-glycine-arginine (GR) and poly-proline-arginine (PR) are most toxic. The structure-function relationship is still unknown. Here, we examined the minimal neurotoxic repeat number of poly-GR and found that extension of the repeat number led to a loose helical structure disrupting plasma and nuclear membrane. Poly-GR/PR bound to nucleotides and interfered with transcription. We screened and identified a sulfated disaccharide that bound to poly-GR/PR and rescued poly-GR/PR-induced toxicity in neuroblastoma and C9-ALS-iPSC-derived motor neurons. The compound rescued the shortened life span and defective locomotion in poly-GR/PR expressing Drosophila model and improved motor behavior in poly-GR-injected mouse model. Overall, our results reveal structural and toxicity mechanisms for poly-GR/PR and facilitate therapeutic development for C9-ALS.
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Affiliation(s)
- Yu-Jen Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
| | - Kai-Tai Lin
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
| | - Chi-Hua Yang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ming-Han Fang
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Wei-Bin Lai
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Neurology, National Yang Ming Chiao Tung University School of Medicine, Taipei, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | | | - Chi-Kuang Yao
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
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9
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Mohammadi S, Ghaderi S, Fatehi F. MRI biomarkers and neuropsychological assessments of hippocampal and parahippocampal regions affected by ALS: A systematic review. CNS Neurosci Ther 2024; 30:e14578. [PMID: 38334254 PMCID: PMC10853901 DOI: 10.1111/cns.14578] [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: 09/14/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Amyotrophic lateral sclerosis (ALS) is a progressive motor and extra-motor neurodegenerative disease. This systematic review aimed to examine MRI biomarkers and neuropsychological assessments of the hippocampal and parahippocampal regions in patients with ALS. METHODS A systematic review was conducted in the Scopus and PubMed databases for studies published between January 2000 and July 2023. The inclusion criteria were (1) MRI studies to assess hippocampal and parahippocampal regions in ALS patients, and (2) studies reporting neuropsychological data in patients with ALS. RESULTS A total of 46 studies were included. Structural MRI revealed hippocampal atrophy, especially in ALS-FTD, involving specific subregions (CA1, dentate gyrus). Disease progression and genetic factors impacted atrophy patterns. Diffusion tensor imaging (DTI) showed increased mean diffusivity (MD), axial diffusivity (AD), radial diffusivity (RD), and decreased fractional anisotropy (FA) in the hippocampal tracts and adjacent regions, indicating loss of neuronal and white matter integrity. Functional MRI (fMRI) revealed reduced functional connectivity (FC) between the hippocampus, parahippocampus, and other regions, suggesting disrupted networks. Perfusion MRI showed hypoperfusion in parahippocampal gyri. Magnetic resonance spectroscopy (MRS) found changes in the hippocampus, indicating neuronal loss. Neuropsychological tests showed associations between poorer memory and hippocampal atrophy or connectivity changes. CA1-2, dentate gyrus, and fimbria atrophy were correlated with worse memory. CONCLUSIONS The hippocampus and the connected regions are involved in ALS. Hippocampal atrophy disrupted connectivity and metabolite changes correlate with cognitive and functional decline. Specific subregions can be particularly affected. The hippocampus is a potential biomarker for disease monitoring and prognosis.
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Affiliation(s)
- Sana Mohammadi
- Neuromuscular Research Center, Department of Neurology, Shariati HospitalTehran University of Medical SciencesTehranIran
- Department of Medical Sciences, School of MedicineIran University of Medical SciencesTehranIran
| | - Sadegh Ghaderi
- Neuromuscular Research Center, Department of Neurology, Shariati HospitalTehran University of Medical SciencesTehranIran
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
| | - Farzad Fatehi
- Neuromuscular Research Center, Department of Neurology, Shariati HospitalTehran University of Medical SciencesTehranIran
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10
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Giardina E, Mandich P, Ghidoni R, Ticozzi N, Rossi G, Fenoglio C, Tiziano FD, Esposito F, Capellari S, Nacmias B, Mineri R, Campopiano R, Di Pilla L, Sammarone F, Zampatti S, Peconi C, De Angelis F, Palmieri I, Galandra C, Nicodemo E, Origone P, Gotta F, Ponti C, Nicsanu R, Benussi L, Peverelli S, Ratti A, Ricci M, Di Fede G, Magri S, Serpente M, Lattante S, Domi T, Carrera P, Saltimbanco E, Bagnoli S, Ingannato A, Albanese A, Tagliavini F, Lodi R, Caltagirone C, Gambardella S, Valente EM, Silani V. Distribution of the C9orf72 hexanucleotide repeat expansion in healthy subjects: a multicenter study promoted by the Italian IRCCS network of neuroscience and neurorehabilitation. Front Neurol 2024; 15:1284459. [PMID: 38356886 PMCID: PMC10865370 DOI: 10.3389/fneur.2024.1284459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/05/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction High repeat expansion (HRE) alleles in C9orf72 have been linked to both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD); ranges for intermediate allelic expansions have not been defined yet, and clinical interpretation of molecular data lacks a defined genotype-phenotype association. In this study, we provide results from a large multicenter epidemiological study reporting the distribution of C9orf72 repeats in healthy elderly from the Italian population. Methods A total of 967 samples were collected from neurologically evaluated healthy individuals over 70 years of age in the 13 institutes participating in the RIN (IRCCS Network of Neuroscience and Neurorehabilitation) based in Italy. All samples were genotyped using the AmplideXPCR/CE C9orf72 Kit (Asuragen, Inc.), using standardized protocols that have been validated through blind proficiency testing. Results All samples carried hexanucleotide G4C2 expansion alleles in the normal range. All samples were characterized by alleles with less than 25 repeats. In particular, 93.7% of samples showed a number of repeats ≤10, 99.9% ≤20 repeats, and 100% ≤25 repeats. Conclusion This study describes the distribution of hexanucleotide G4C2 expansion alleles in an Italian healthy population, providing a definition of alleles associated with the neurological healthy phenotype. Moreover, this study provides an effective model of federation between institutes, highlighting the importance of sharing genomic data and standardizing analysis techniques, promoting translational research. Data derived from the study may improve genetic counseling and future studies on ALS/FTD.
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Affiliation(s)
- Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Paola Mandich
- IRCCS Ospedale Policlinico San Martino – UOC Genetica Medica, Genova, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Nicola Ticozzi
- 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
| | - Giacomina Rossi
- Unit of Neurology V – Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Fenoglio
- Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Francesco Danilo Tiziano
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
- Unit of Medical Genetics, Department of Laboratory Science and Infectious Diseases, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Federica Esposito
- Neurology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sabina Capellari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- DIBINEM Università di Bologna, Bologna, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Rossana Mineri
- Laboratory Medicine, Department of Cytogenetics and Molecular Genetics, IRCCS Humanitas Research Hospital, Milan, Italy
| | | | | | | | - Stefania Zampatti
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Cristina Peconi
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Flavio De Angelis
- Department of Mental, Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | | | | | | | - Paola Origone
- IRCCS Ospedale Policlinico San Martino – UOC Genetica Medica, Genova, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
| | - Fabio Gotta
- IRCCS Ospedale Policlinico San Martino – UOC Genetica Medica, Genova, Italy
| | - Clarissa Ponti
- IRCCS Ospedale Policlinico San Martino – UOC Genetica Medica, Genova, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
| | - Roland Nicsanu
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Silvia Peverelli
- 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 Molecular Medicine, Università degli Studi di Milano, Milan, Italy
| | - Martina Ricci
- Unit of Neurology V – Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giuseppe Di Fede
- Unit of Neurology V – Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Maria Serpente
- Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Serena Lattante
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Teuta Domi
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Carrera
- Laboratory of Clinical Molecular Biology, Unit of Genomics for Human Disease Diagnosis, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Saltimbanco
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Silvia Bagnoli
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Assunta Ingannato
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Alberto Albanese
- Department of Neurology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Raffaele Lodi
- Policlinico S. Orsola-Malpighi, Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Stefano Gambardella
- IRCCS Neuromed, Pozzilli, Italy
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Enza Maria Valente
- IRCCS Mondino Foundation, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - 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
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11
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Smeele PH, Cesare G, Vaccari T. ALS' Perfect Storm: C9orf72-Associated Toxic Dipeptide Repeats as Potential Multipotent Disruptors of Protein Homeostasis. Cells 2024; 13:178. [PMID: 38247869 PMCID: PMC10813877 DOI: 10.3390/cells13020178] [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: 12/13/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Protein homeostasis is essential for neuron longevity, requiring a balanced regulation between protein synthesis and degradation. The clearance of misfolded and aggregated proteins, mediated by autophagy and the ubiquitin-proteasome systems, maintains protein homeostasis in neurons, which are post-mitotic and thus cannot use cell division to diminish the burden of misfolded proteins. When protein clearance pathways are overwhelmed or otherwise disrupted, the accumulation of misfolded or aggregated proteins can lead to the activation of ER stress and the formation of stress granules, which predominantly attempt to restore the homeostasis by suppressing global protein translation. Alterations in these processes have been widely reported among studies investigating the toxic function of dipeptide repeats (DPRs) produced by G4C2 expansion in the C9orf72 gene of patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In this review, we outline the modalities of DPR-induced disruptions in protein homeostasis observed in a wide range of models of C9orf72-linked ALS/FTD. We also discuss the relative importance of each DPR for toxicity, possible synergies between DPRs, and discuss the possible functional relevance of DPR aggregation to disease pathogenesis. Finally, we highlight the interdependencies of the observed effects and reflect on the importance of feedback and feedforward mechanisms in their contribution to disease progression. A better understanding of DPR-associated disease pathogenesis discussed in this review might shed light on disease vulnerabilities that may be amenable with therapeutic interventions.
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Affiliation(s)
| | | | - Thomas Vaccari
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
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12
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Eck RJ, Stair JG, Kraemer BC, Liachko NF. Simple models to understand complex disease: 10 years of progress from Caenorhabditis elegans models of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Front Neurosci 2024; 17:1300705. [PMID: 38239833 PMCID: PMC10794587 DOI: 10.3389/fnins.2023.1300705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
The nematode Caenorhabditis elegans are a powerful model system to study human disease, with numerous experimental advantages including significant genetic and cellular homology to vertebrate animals, a short lifespan, and tractable behavioral, molecular biology and imaging assays. Beginning with the identification of SOD1 as a genetic cause of amyotrophic lateral sclerosis (ALS), C. elegans have contributed to a deeper understanding of the mechanistic underpinnings of this devastating neurodegenerative disease. More recently this work has expanded to encompass models of other types of ALS and the related disease frontotemporal lobar degeneration (FTLD-TDP), including those characterized by mutation or accumulation of the proteins TDP-43, C9orf72, FUS, HnRNPA2B1, ALS2, DCTN1, CHCHD10, ELP3, TUBA4A, CAV1, UBQLN2, ATXN3, TIA1, KIF5A, VAPB, GRN, and RAB38. In this review we summarize these models and the progress and insights from the last ten years of using C. elegans to study the neurodegenerative diseases ALS and FTLD-TDP.
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Affiliation(s)
- Randall J. Eck
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, United States
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jade G. Stair
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
| | - Brian C. Kraemer
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Nicole F. Liachko
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
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13
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Yuan Y, Bailey JM, Rivera-Lopez GM, Atchison WD. Preferential potentiation of AMPA-mediated currents in brainstem hypoglossal motoneurons by subchronic exposure of mice expressing the human superoxide dismutase 1 G93A gene mutation to neurotoxicant methylmercury in vivo. Neurotoxicology 2024; 100:72-84. [PMID: 38065418 PMCID: PMC10877233 DOI: 10.1016/j.neuro.2023.12.002] [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: 05/12/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
Abstract
The exact causes of Amyotrophic lateral sclerosis (ALS), a progressive and fatal neurological disorder due to loss of upper and/or lower motoneurons, remain elusive. Gene-environment interactions are believed to be an important factor in the development of ALS. We previously showed that in vivo exposure of mice overexpressing the human superoxide dismutase 1 (hSOD1) gene mutation (hSOD1G93A; G93A), a mouse model for ALS, to environmental neurotoxicant methylmercury (MeHg) accelerated the onset of ALS-like phenotype. Here we examined the time-course of effects of MeHg on AMPA receptor (AMPAR)-mediated currents in hypoglossal motoneurons in brainstem slices prepared from G93A, hSOD1wild-type (hWT) and non-carrier WT mice following in vivo exposure to MeHg. Mice were exposed daily to 3 ppm (approximately 0.7 mg/kg/day) MeHg via drinking water beginning at postnatal day 28 (P28) and continued until P47, 64 or 84, then acute brainstem slices were prepared, and spontaneous excitatory postsynaptic currents (sEPSCs) or AMPA-evoked currents were examined using whole cell patch-clamp recording technique. Brainstem slices of untreated littermates were prepared at the same time points to serve as control. MeHg exposure had no significant effect on either sEPSCs or AMPA-evoked currents in slices from hWT or WT mice during any of those exposure time periods under our experimental conditions. MeHg also did not cause any significant effect on sEPSCs or AMPA-currents in G93A hypoglossal motoneurons at P47 and P64. However, at P84, MeHg significantly increased amplitudes of both sEPSCs and AMPA-evoked currents in hypoglossal motineurons from G93A mice (p < 0.05), but not the sEPSC frequency, suggesting a postsynaptic action on AMPARs. MeHg exposure did not cause any significant effect on GABAergic spontaneous inhibitory postsynaptic currents (sIPSCs). Therefore, MeHg exposure in vivo caused differential effects on AMPARs in hypoglossal motoneurons from mice with different genetic backgrounds. MeHg appears to preferentially stimulate the AMPAR-mediated currents in G93A hypoglossal motoneurons in an exposure time-dependent manner, which may contribute to the AMPAR-mediated motoneuron excitotoxicity, thereby facilitating development of ALS-like phenotype.
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Affiliation(s)
- Yukun Yuan
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA.
| | - Jordan M Bailey
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA
| | - Gretchen M Rivera-Lopez
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA
| | - William D Atchison
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA
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14
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Panoyan MA, Wendt FR. The role of tandem repeat expansions in brain disorders. Emerg Top Life Sci 2023; 7:249-263. [PMID: 37401564 DOI: 10.1042/etls20230022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
The human genome contains numerous genetic polymorphisms contributing to different health and disease outcomes. Tandem repeat (TR) loci are highly polymorphic yet under-investigated in large genomic studies, which has prompted research efforts to identify novel variations and gain a deeper understanding of their role in human biology and disease outcomes. We summarize the current understanding of TRs and their implications for human health and disease, including an overview of the challenges encountered when conducting TR analyses and potential solutions to overcome these challenges. By shedding light on these issues, this article aims to contribute to a better understanding of the impact of TRs on the development of new disease treatments.
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Affiliation(s)
- Mary Anne Panoyan
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Frank R Wendt
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
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15
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Raguseo F, Wang Y, Li J, Petrić Howe M, Balendra R, Huyghebaert A, Vadukul DM, Tanase DA, Maher TE, Malouf L, Rubio-Sánchez R, Aprile FA, Elani Y, Patani R, Di Michele L, Di Antonio M. The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes. Nat Commun 2023; 14:8272. [PMID: 38092738 PMCID: PMC10719400 DOI: 10.1038/s41467-023-43872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases that exist on a clinico-pathogenetic spectrum, designated ALS/FTD. The most common genetic cause of ALS/FTD is expansion of the intronic hexanucleotide repeat (GGGGCC)n in C9orf72. Here, we investigate the formation of nucleic acid secondary structures in these expansion repeats, and their role in generating condensates characteristic of ALS/FTD. We observe significant aggregation of the hexanucleotide sequence (GGGGCC)n, which we associate to the formation of multimolecular G-quadruplexes (mG4s) by using a range of biophysical techniques. Exposing the condensates to G4-unfolding conditions leads to prompt disassembly, highlighting the key role of mG4-formation in the condensation process. We further validate the biological relevance of our findings by detecting an increased prevalence of G4-structures in C9orf72 mutant human motor neurons when compared to healthy motor neurons by staining with a G4-selective fluorescent probe, revealing signal in putative condensates. Our findings strongly suggest that RNA G-rich repetitive sequences can form protein-free condensates sustained by multimolecular G-quadruplexes, highlighting their potential relevance as therapeutic targets for C9orf72 mutation-related ALS/FTD.
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Affiliation(s)
- Federica Raguseo
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yiran Wang
- 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
| | - Jessica Li
- 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
| | - Marija Petrić Howe
- 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
| | - Rubika Balendra
- 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
| | - Anouk Huyghebaert
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Devkee M Vadukul
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Diana A Tanase
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Thomas E Maher
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Layla Malouf
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Roger Rubio-Sánchez
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Francesco A Aprile
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yuval Elani
- Imperial College London, Department of Chemical Engineering, South Kensington, London, SW7 2AZ, UK
| | - 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.
| | - Lorenzo Di Michele
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| | - Marco Di Antonio
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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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: 7] [Impact Index Per Article: 7.0] [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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König T, Leutmezer F, Berger T, Zimprich A, Schmied C, Stögmann E, Zrzavy T. No Association of Multiple Sclerosis with C9orf72 Hexanucleotide Repeat Size in an Austrian Cohort. Int J Mol Sci 2023; 24:11254. [PMID: 37511014 PMCID: PMC10378763 DOI: 10.3390/ijms241411254] [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: 06/09/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Multiple Sclerosis (MS) is a common immune-mediated disorder of the central nervous system that affects young adults and is characterized by demyelination and neurodegeneration. Recent studies have associated C9orf72 intermediate repeat expansions with MS. The objective of this study was to investigate whether C9orf72 repeat length is associated with MS or with a specific disease course in a monocentric Austrian MS cohort. Genotyping of 382 MS patients and 643 non-neurological controls for C9orf72 repeat expansions was performed. The study did not find a difference in the distribution of repeat numbers between controls and MS cases (median repeat units = 2; p = 0.39). Additionally, sub-analysis did not establish a link between intermediate repeats and MS (p = 0.23) and none of the patients with progressive disease course carried an intermediate allele (20-30 repeat units). Exploratory analysis for different cut-offs (of ≥7, ≥17, and ≥24) did not reveal any significant differences in allele frequencies between MS and controls. However, the study did identify a progressive MS patient with a pathogenic C9orf72 expansion and probable co-existing behavioral variant frontotemporal dementia (bvFTD) in a retrospective chart review. In conclusion, this study did not find evidence supporting an association between C9orf72 repeat length and MS or a specific disease course in the Austrian MS cohort. However, the identification of a progressive MS patient with a pathogenic C9orf72 expansion and probable co-existing with FTD highlights the complexity and challenges involved in recognizing distinct neurodegenerative diseases that may co-occur in MS patients.
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Affiliation(s)
- Theresa König
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, 1090 Vienna, Austria
| | - Fritz Leutmezer
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Berger
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, 1090 Vienna, Austria
| | - Alexander Zimprich
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, 1090 Vienna, Austria
| | - Christiane Schmied
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, 1090 Vienna, Austria
| | - Elisabeth Stögmann
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, 1090 Vienna, Austria
| | - Tobias Zrzavy
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, 1090 Vienna, Austria
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18
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Shi Y, Zhao Y, Lu L, Gao Q, Yu D, Sun M. CRISPR/Cas9: implication for modeling and therapy of amyotrophic lateral sclerosis. Front Neurosci 2023; 17:1223777. [PMID: 37483353 PMCID: PMC10359984 DOI: 10.3389/fnins.2023.1223777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a deadly neurological disease with a complicated and variable pathophysiology yet to be fully understood. There is currently no effective treatment available to either slow or terminate it. However, recent advances in ALS genomics have linked genes to phenotypes, encouraging the creation of novel therapeutic approaches and giving researchers more tools to create efficient animal models. Genetically engineered rodent models replicating ALS disease pathology have a high predictive value for translational research. This review addresses the history of the evolution of gene editing tools, the most recent ALS disease models, and the application of CRISPR/Cas9 against ALS disease.
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Affiliation(s)
- Yajun Shi
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yan Zhao
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Likui Lu
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qinqin Gao
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dongyi Yu
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Miao Sun
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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19
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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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20
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Proteomics Analysis of Lymphoblastoid Cell Lines from Patients with Amyotrophic Lateral Sclerosis. Molecules 2023; 28:molecules28052014. [PMID: 36903260 PMCID: PMC10004326 DOI: 10.3390/molecules28052014] [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: 11/28/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) consists of the progressive degeneration of motor neurons, caused by poorly understood mechanisms for which there is no cure. Some of the cellular perturbations associated with ALS can be detected in peripheral cells, including lymphocytes from blood. A related cell system that is very suitable for research consists of human lymphoblastoid cell lines (LCLs), which are immortalized lymphocytes. LCLs that can be easily expanded in culture and can be maintained for long periods as stable cultures. We investigated, on a small set of LCLs, if a proteomics analysis using liquid chromatography followed by tandem mass spectrometry reveals proteins that are differentially present in ALS versus healthy controls. We found that individual proteins, the cellular and molecular pathways in which these proteins participate, are detected as differentially present in the ALS samples. Some of these proteins and pathways are already known to be perturbed in ALS, while others are new and present interest for further investigations. These observations suggest that a more detailed proteomics analysis of LCLs, using a larger number of samples, represents a promising approach for investigating ALS mechanisms and to search for therapeutic agents. Proteomics data are available via ProteomeXchange with identifier PXD040240.
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21
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Bowles H, Kabiljo R, Al Khleifat A, Jones A, Quinn JP, Dobson RJB, Swanson CM, Al-Chalabi A, Iacoangeli A. An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data. FRONTIERS IN BIOINFORMATICS 2023; 2:1062328. [PMID: 36845320 PMCID: PMC9945273 DOI: 10.3389/fbinf.2022.1062328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/12/2022] [Indexed: 02/10/2023] Open
Abstract
There is a growing interest in the study of human endogenous retroviruses (HERVs) given the substantial body of evidence that implicates them in many human diseases. Although their genomic characterization presents numerous technical challenges, next-generation sequencing (NGS) has shown potential to detect HERV insertions and their polymorphisms in humans. Currently, a number of computational tools to detect them in short-read NGS data exist. In order to design optimal analysis pipelines, an independent evaluation of the available tools is required. We evaluated the performance of a set of such tools using a variety of experimental designs and datasets. These included 50 human short-read whole-genome sequencing samples, matching long and short-read sequencing data, and simulated short-read NGS data. Our results highlight a great performance variability of the tools across the datasets and suggest that different tools might be suitable for different study designs. However, specialized tools designed to detect exclusively human endogenous retroviruses consistently outperformed generalist tools that detect a wider range of transposable elements. We suggest that, if sufficient computing resources are available, using multiple HERV detection tools to obtain a consensus set of insertion loci may be ideal. Furthermore, given that the false positive discovery rate of the tools varied between 8% and 55% across tools and datasets, we recommend the wet lab validation of predicted insertions if DNA samples are available.
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Affiliation(s)
- Harry Bowles
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Renata Kabiljo
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ashley Jones
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre 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, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Neurology, King’s College Hospital, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
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22
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Wan M, He J, Huo J, Sun C, Fu Y, Fan D. Intermediate-Length GGC Repeat Expansion in NOTCH2NLC Was Identified in Chinese Patients with Amyotrophic Lateral Sclerosis. Brain Sci 2023; 13:brainsci13010085. [PMID: 36672065 PMCID: PMC9856391 DOI: 10.3390/brainsci13010085] [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: 11/15/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
GGC repeat expansions in the 5' untranslated region (5'UTR) of the Notch Homolog 2 N-terminal-like C gene (NOTCH2NLC) have been reported to be the genetic cause of neuronal intranuclear inclusion disease (NIID). However, whether they exist in other neurodegenerative disorders remains unclear. To determine whether there is a medium-length amplification of NOTCH2NLC in patients with amyotrophic lateral sclerosis (ALS), we screened 476 ALS patients and 210 healthy controls for the presence of a GGC repeat expansion in NOTCH2NLC by using repeat-primed polymerase chain reaction (RP-PCR) and fragment analysis. The repeat number in ALS patients was 16.11 ± 5.7 (range 7-46), whereas the repeat number in control subjects was 16.19 ± 3.79 (range 10-29). An intermediate-length GGC repeat expansion was observed in two ALS patients (numbers of repeats: 45, 46; normal repeat number ≤ 40) but not in the control group. The results suggested that the intermediate NOTCH2NLC GGC repeat expansion was associated with Chinese ALS patients, and further functional studies for intermediate-length variation are required to identify the mechanism.
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Affiliation(s)
- Mengxia Wan
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Beijing Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
| | - Ji He
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Beijing Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
| | - Junyan Huo
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Beijing Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
| | - Can Sun
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Beijing Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
| | - Yu Fu
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Beijing Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
- Correspondence: (Y.F.); (D.F.)
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Beijing Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission, Peking University, Beijing 100191, China
- Correspondence: (Y.F.); (D.F.)
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23
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Meanti R, Bresciani E, Rizzi L, Coco S, Zambelli V, Dimitroulas A, Molteni L, Omeljaniuk RJ, Locatelli V, Torsello A. Potential Applications for Growth Hormone Secretagogues Treatment of Amyotrophic Lateral Sclerosis. Curr Neuropharmacol 2023; 21:2376-2394. [PMID: 36111771 PMCID: PMC10616926 DOI: 10.2174/1570159x20666220915103613] [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: 06/01/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) arises from neuronal death due to complex interactions of genetic, molecular, and environmental factors. Currently, only two drugs, riluzole and edaravone, have been approved to slow the progression of this disease. However, ghrelin and other ligands of the GHS-R1a receptor have demonstrated interesting neuroprotective activities that could be exploited in this pathology. Ghrelin, a 28-amino acid hormone, primarily synthesized and secreted by oxyntic cells in the stomach wall, binds to the pituitary GHS-R1a and stimulates GH secretion; in addition, ghrelin is endowed with multiple extra endocrine bioactivities. Native ghrelin requires esterification with octanoic acid for binding to the GHS-R1a receptor; however, this esterified form is very labile and represents less than 10% of circulating ghrelin. A large number of synthetic compounds, the growth hormone secretagogues (GHS) encompassing short peptides, peptoids, and non-peptidic moieties, are capable of mimicking several biological activities of ghrelin, including stimulation of GH release, appetite, and elevation of blood IGF-I levels. GHS have demonstrated neuroprotective and anticonvulsant effects in experimental models of pathologies both in vitro and in vivo. To illustrate, some GHS, currently under evaluation by regulatory agencies for the treatment of human cachexia, have a good safety profile and are safe for human use. Collectively, evidence suggests that ghrelin and cognate GHS may constitute potential therapies for ALS.
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Affiliation(s)
- Ramona Meanti
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | - Elena Bresciani
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | - Laura Rizzi
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | - Silvia Coco
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | - Vanessa Zambelli
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | - Anna Dimitroulas
- Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, GU2 7XH, United Kingdom
| | - Laura Molteni
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | - Robert J. Omeljaniuk
- Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, P7B 5E1, Canada
| | - Vittorio Locatelli
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | - Antonio Torsello
- School of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
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Mehta PR, Iacoangeli A, Opie-Martin S, van Vugt JJFA, Al Khleifat A, Bredin A, Ossher L, Andersen PM, Hardiman O, Mehta AR, Fratta P, Talbot K, Al-Chalabi A. The impact of age on genetic testing decisions in amyotrophic lateral sclerosis. Brain 2022; 145:4440-4447. [PMID: 36162820 PMCID: PMC9762932 DOI: 10.1093/brain/awac279] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/30/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a heterogeneous neurodegenerative syndrome. In up to 20% of cases, a family history is observed. Although Mendelian disease gene variants are found in apparently sporadic ALS, genetic testing is usually restricted to those with a family history or younger patients with sporadic disease. With the advent of therapies targeting genetic ALS, it is important that everyone treatable is identified. We therefore sought to determine the probability of a clinically actionable ALS genetic test result by age of onset, globally, but using the UK as an exemplar. Blood-derived DNA was sequenced for ALS genes, and the probability of a clinically actionable genetic test result estimated. For a UK subset, age- and sex-specific population incidence rates were used to determine the number of such results missed by restricting testing by age of onset according to UK's National Genomic Test Directory criteria. There were 6274 people with sporadic ALS, 1551 from the UK. The proportion with a clinically actionable genetic test result ranged between 0.21 [95% confidence interval (CI) 0.18-0.25] in the youngest age group to 0.15 (95% CI 0.13-0.17) in the oldest age group for a full gene panel. For the UK, the equivalent proportions were 0.23 (95% CI 0.13-0.33) in the youngest age group to 0.17 (95% CI 0.13-0.21) in the oldest age group. By limiting testing in those without a family history to people with onset below 40 years, 115 of 117 (98% of all, 95% CI 96%-101%) clinically actionable test results were missed. There is a significant probability of a clinically actionable genetic test result in people with apparently sporadic ALS at all ages. Although some countries limit testing by age, doing so results in a significant number of missed pathogenic test results. Age of onset and family history should not be a barrier to genetic testing in ALS.
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Affiliation(s)
- Puja R Mehta
- Correspondence may also be addressed to: Dr Puja R. Mehta UCL Queen Square Motor Neuron Disease Centre Department of Neuromuscular diseases UCL Queen Square Institute of Neurology London, WC1N 3BG, UK E-mail:
| | | | - Sarah Opie-Martin
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9RX, UK
| | - Joke J F A van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, 3584 CG, The Netherlands
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9RX, UK
| | - Andrea Bredin
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9RX, UK
| | - Lynn Ossher
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Peter M Andersen
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, SE-901 87, Sweden
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, D02 R590, Republic of Ireland
| | - Arpan R Mehta
- Department of Neurology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Ammar Al-Chalabi
- Correspondence to: Professor Ammar Al-Chalabi Department of Basic and Clinical Neuroscience Maurice Wohl Clinical Neuroscience Institute King’s College London London SE5 9RX, UK E-mail:
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25
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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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26
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Spargo TP, Opie-Martin S, Bowles H, Lewis CM, Iacoangeli A, Al-Chalabi A. Calculating variant penetrance from family history of disease and average family size in population-scale data. Genome Med 2022; 14:141. [PMID: 36522764 PMCID: PMC9753373 DOI: 10.1186/s13073-022-01142-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Genetic penetrance is the probability of a phenotype when harbouring a particular pathogenic variant. Accurate penetrance estimates are important across biomedical fields including genetic counselling, disease research, and gene therapy. However, existing approaches for penetrance estimation require, for instance, large family pedigrees or availability of large databases of people affected and not affected by a disease. METHODS We present a method for penetrance estimation in autosomal dominant phenotypes. It examines the distribution of a variant among people affected (cases) and unaffected (controls) by a phenotype within population-scale data and can be operated using cases only by considering family disease history. It is validated through simulation studies and candidate variant-disease case studies. RESULTS Our method yields penetrance estimates which align with those obtained via existing approaches in the Parkinson's disease LRRK2 gene and pulmonary arterial hypertension BMPR2 gene case studies. In the amyotrophic lateral sclerosis case studies, examining penetrance for variants in the SOD1 and C9orf72 genes, we make novel penetrance estimates which correspond closely to understanding of the disease. CONCLUSIONS The present approach broadens the spectrum of traits for which reliable penetrance estimates can be obtained. It has substantial utility for facilitating the characterisation of disease risks associated with rare variants with an autosomal dominant inheritance pattern. The yielded estimates avoid any kinship-specific effects and can circumvent ascertainment biases common when sampling rare variants among control populations.
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Affiliation(s)
- Thomas P Spargo
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RX, UK
| | - Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RX, UK
| | - Harry Bowles
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RX, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, de Crespigny Park, London, SE5 8AF, UK
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RX, UK.
- Department of Biostatistics and Health Informatics, King's College London, London, UK.
- NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust and King's College London, London, UK.
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RX, UK.
- King's College Hospital, Bessemer Road, London, SE5 9RS, UK.
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27
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Kabiljo R, Bowles H, Marriott H, Jones AR, Bouton CR, Dobson RJ, Quinn JP, Al Khleifat A, Swanson CM, Al-Chalabi A, Iacoangeli A. RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data. iScience 2022; 25:105289. [PMID: 36339261 PMCID: PMC9626663 DOI: 10.1016/j.isci.2022.105289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 12/02/2022] Open
Abstract
Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training. Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.
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Affiliation(s)
- Renata Kabiljo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Harry Bowles
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Heather Marriott
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Clement R. Bouton
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Richard J.B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust, London, UK
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
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28
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König T, Wurm R, Parvizi T, Silvaieh S, Hotzy C, Cetin H, Klotz S, Gelpi E, Bancher C, Benke T, Dal-Bianco P, Defrancesco M, Fischer P, Marksteiner J, Sutterlüty H, Ransmayr G, Schmidt R, Zimprich A, Stögmann E. C9orf72 repeat length might influence clinical sub-phenotypes in dementia patients. Neurobiol Dis 2022; 175:105927. [DOI: 10.1016/j.nbd.2022.105927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/27/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022] Open
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29
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Kaur K, Chen PC, Ko MW, Mei A, Chovatiya N, Huerta-Yepez S, Ni W, Mackay S, Zhou J, Maharaj D, Malarkannan S, Jewett A. The Potential Role of Cytotoxic Immune Effectors in Induction, Progression and Pathogenesis of Amyotrophic Lateral Sclerosis (ALS). Cells 2022; 11:3431. [PMID: 36359827 PMCID: PMC9656116 DOI: 10.3390/cells11213431] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an auto-immune neurodegenerative disorder affecting the motor-neuron system. The causes of ALS are heterogeneous, and are only partially understood. We studied different aspects of immune pathogenesis in ALS and found several basic mechanisms which are potentially involved in the disease. Our findings demonstrated that ALS patients' peripheral blood contains higher proportions of NK and B cells in comparison to healthy individuals. Significantly increased IFN-γ secretion by anti-CD3/28 mAbs-treated peripheral blood mononuclear cells (PBMCs) were observed in ALS patients, suggesting that hyper-responsiveness of T cell compartment could be a potential mechanism for ALS progression. In addition, elevated granzyme B and perforin secretion at a single cell level, and increased cytotoxicity and secretion of IFN-γ by patients' NK cells under specific treatment conditions were also observed. Increased IFN-γ secretion by ALS patients' CD8+ T cells in the absence of IFN-γ receptor expression, and increased CD8+ T cell effector/memory phenotype as well as increased granzyme B at the single cell level points to the CD8+ T cells as potential cells in targeting motor neurons. Along with the hyper-responsiveness of cytotoxic immune cells, significantly higher levels of inflammatory cytokines including IFN-γ was observed in peripheral blood-derived serum of ALS patients. Supernatants obtained from ALS patients' CD8+ T cells induced augmented cell death and differentiation of the epithelial cells. Weekly N-acetyl cysteine (NAC) infusion in patients decreased the levels of many inflammatory cytokines in peripheral blood of ALS patient except IFN-γ, TNF-α, IL-17a and GMCSF which remained elevated. Findings of this study indicated that CD8+ T cells and NK cells are likely culprits in targeting motor neurons and therefore, strategies should be designed to decrease their function, and eliminate the aggressive nature of these cells. Analysis of genetic mutations in ALS patient in comparison to identical twin revealed a number of differences and similarities which may be important in the pathogenesis of the disease.
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Affiliation(s)
- Kawaljit Kaur
- Division of Oral Biology and Medicine, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, University of California School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Po-Chun Chen
- Division of Oral Biology and Medicine, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, University of California School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Meng-Wei Ko
- Division of Oral Biology and Medicine, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, University of California School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Ao Mei
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nishant Chovatiya
- Division of Oral Biology and Medicine, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, University of California School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Sara Huerta-Yepez
- Division of Oral Biology and Medicine, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, University of California School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Weiming Ni
- IsoPlexis, 35 North East Industrial Road, Branford, CT 06405, USA
| | - Sean Mackay
- IsoPlexis, 35 North East Industrial Road, Branford, CT 06405, USA
| | - Jing Zhou
- IsoPlexis, 35 North East Industrial Road, Branford, CT 06405, USA
| | - Dipanarine Maharaj
- South Florida Bone Marrow Stem Cell Transplant Institute, DBA Maharaj Institute of Immune Regenerative Medicine, 10301 Hagen Ranch Rd Ste. 600, Boynton Beach, FL 33437, USA
| | - Subramaniam Malarkannan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Versiti, Milwaukee, WI 53226, USA
| | - Anahid Jewett
- Division of Oral Biology and Medicine, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, University of California School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
- The Jonsson Comprehensive Cancer Center, UCLA School of Dentistry and Medicine, 10833 Le Conte Ave., Los Angeles, CA 90095, USA
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30
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Meijboom KE, Abdallah A, Fordham NP, Nagase H, Rodriguez T, Kraus C, Gendron TF, Krishnan G, Esanov R, Andrade NS, Rybin MJ, Ramic M, Stephens ZD, Edraki A, Blackwood MT, Kahriman A, Henninger N, Kocher JPA, Benatar M, Brodsky MH, Petrucelli L, Gao FB, Sontheimer EJ, Brown RH, Zeier Z, Mueller C. CRISPR/Cas9-mediated excision of ALS/FTD-causing hexanucleotide repeat expansion in C9ORF72 rescues major disease mechanisms in vivo and in vitro. Nat Commun 2022; 13:6286. [PMID: 36271076 PMCID: PMC9587249 DOI: 10.1038/s41467-022-33332-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/13/2022] [Indexed: 12/25/2022] Open
Abstract
A GGGGCC24+ hexanucleotide repeat expansion (HRE) in the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), fatal neurodegenerative diseases with no cure or approved treatments that substantially slow disease progression or extend survival. Mechanistic underpinnings of neuronal death include C9ORF72 haploinsufficiency, sequestration of RNA-binding proteins in the nucleus, and production of dipeptide repeat proteins. Here, we used an adeno-associated viral vector system to deliver CRISPR/Cas9 gene-editing machineries to effectuate the removal of the HRE from the C9ORF72 genomic locus. We demonstrate successful excision of the HRE in primary cortical neurons and brains of three mouse models containing the expansion (500-600 repeats) as well as in patient-derived iPSC motor neurons and brain organoids (450 repeats). This resulted in a reduction of RNA foci, poly-dipeptides and haploinsufficiency, major hallmarks of C9-ALS/FTD, making this a promising therapeutic approach to these diseases.
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Affiliation(s)
- Katharina E. Meijboom
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Abbas Abdallah
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Nicholas P. Fordham
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Hiroko Nagase
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Tomás Rodriguez
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Carolyn Kraus
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Tania F. Gendron
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Gopinath Krishnan
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Rustam Esanov
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Nadja S. Andrade
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Matthew J. Rybin
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Melina Ramic
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Zachary D. Stephens
- grid.66875.3a0000 0004 0459 167XDepartment of Quantitative Health Sciences. Mayo Clinic, Rochester, MN 55905 USA
| | - Alireza Edraki
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Meghan T. Blackwood
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Aydan Kahriman
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Nils Henninger
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Jean-Pierre A. Kocher
- grid.66875.3a0000 0004 0459 167XDepartment of Quantitative Health Sciences. Mayo Clinic, Rochester, MN 55905 USA
| | - Michael Benatar
- grid.26790.3a0000 0004 1936 8606Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael H. Brodsky
- grid.168645.80000 0001 0742 0364Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Leonard Petrucelli
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Fen-Biao Gao
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Erik J. Sontheimer
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Robert H. Brown
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Zane Zeier
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| | - Christian Mueller
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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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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Tang L, Chen L, Liu X, He J, Ma Y, Zhang N, Fan D. The repeat length of C9orf72 is associated with the survival of amyotrophic lateral sclerosis patients without C9orf72 pathological expansions. Front Neurol 2022; 13:939775. [PMID: 35989899 PMCID: PMC9381700 DOI: 10.3389/fneur.2022.939775] [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: 05/09/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveTo explore whether the repeat lengths of the chromosome 9 open reading frame 72 (C9orf72) gene and the ataxin-2 (ATXN2) gene in amyotrophic lateral sclerosis (ALS) patients without C9orf72 repeat expansions confer a risk of ALS or survival disadvantages in ALS.MethodsWe screened a hospital-based cohort of Chinese patients with sporadic ALS without C9orf72 repeat expansions and neurologically healthy controls for C9orf72 GGGGCC and AXTN2 CAG repeat length to compare the frequency of possible detrimental length alleles using several thresholds. Furthermore, the clinical features of ALS were compared between patients with ALS subgroups using different length thresholds of maximum C9orf72 and ATXN2 repeat alleles, such as sex, age of onset, diagnostic delay, and survival.ResultsOverall, 879 sporadic patients with ALS and 535 controls were included and the repeat lengths of the C9orf72 and ATXN2 were both detected. We found significant survival differences in patients using a series of C9orf72 repeat length thresholds from 2 to 5, among which the most significant difference was at the cutoff value of 2 (repeats 2 vs. >2: median survival 67 vs. 55 months, log-rank p = 0.032). Furthermore, Cox regression analysis revealed the role of age of onset [hazard ratio (HR) 1.04, 95% CI 1.03–1.05, p < 0.001], diagnostic delay (0.95, 0.94–0.96, p < 0.001), and carrying C9orf72 repeat length of 2 (0.72, 0.59–0.89, p = 0.002) in the survival of patients without C9orf72 repeat expansions. In addition, bulbar onset was associated with poorer survival when the patients carried the maximum C9orf72 repeat allele over 2 (1.81, 1.32–2.48, p < 0.001). However, no survival difference was found when applying a series of continuous cutoff values of ATXN2 or stratified by C9orf72 repeats of 2.ConclusionThe length of 2 in the maximum C9orf72 repeat allele was identified to be associated with favorable survival in ALS patients without C9orf72 repeat expansions. Our findings from the clinical setting implicated the possible cutoff definition of detrimental C9orf72 repeats, which should be helpful in the understanding of genetics in ALS and in clinical genetic counseling.
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Affiliation(s)
- Lu Tang
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | - Lu Chen
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | - Xiaolu Liu
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | - Ji He
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | - Yan Ma
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | - Nan Zhang
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- *Correspondence: Dongsheng Fan
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Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating motor neuron disease for which there is currently no robust therapy. Recent progress in understanding ALS disease mechanisms and genetics in combination with innovations in gene modulation strategies creates promising new options for the development of ALS therapies. In recent years, six gene modulation therapies have been tested in ALS patients. These target gain-of-function pathology of the most common ALS genes, SOD1, C9ORF72, FUS, and ATXN2, using adeno-associated virus (AAV)-mediated microRNAs and antisense oligonucleotides (ASOs). Here, we review the latest clinical and preclinical advances in gene modulation approaches for ALS, including gene silencing, gene correction, and gene augmentation. These techniques have the potential to positively impact the direction of future research trials and transform ALS treatments for this grave disease.
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Affiliation(s)
- Katharina E Meijboom
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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34
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Gene Therapy in Amyotrophic Lateral Sclerosis. Cells 2022; 11:cells11132066. [PMID: 35805149 PMCID: PMC9265980 DOI: 10.3390/cells11132066] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/30/2022] Open
Abstract
Since the discovery of Cu/Zn superoxide dismutase (SOD1) gene mutation, in 1993, as the first genetic abnormality in amyotrophic lateral sclerosis (ALS), over 50 genes have been identified as either cause or modifier in ALS and ALS/frontotemporal dementia (FTD) spectrum disease. Mutations in C9orf72, SOD1, TAR DNA binding protein 43 (TARDBP), and fused in sarcoma (FUS) genes are the four most common ones. During the last three decades, tremendous effort has been made worldwide to reveal biological pathways underlying the pathogenesis of these gene mutations in ALS/FTD. Accordingly, targeting etiologic genes (i.e., gene therapies) to suppress their toxic effects have been investigated widely. It includes four major strategies: (i) removal or inhibition of abnormal transcribed RNA using microRNA or antisense oligonucleotides (ASOs), (ii) degradation of abnormal mRNA using RNA interference (RNAi), (iii) decrease or inhibition of mutant proteins (e.g., using antibodies against misfolded proteins), and (iv) DNA genome editing with methods such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas). The promising results of these studies have led to the application of some of these strategies into ALS clinical trials, especially for C9orf72 and SOD1. In this paper, we will overview advances in gene therapy in ALS/FTD, focusing on C9orf72, SOD1, TARDBP, and FUS genes.
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35
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Breevoort S, Gibson S, Figueroa K, Bromberg M, Pulst S. Expanding Clinical Spectrum of C9ORF72-Related Disorders and Promising Therapeutic Strategies: A Review. Neurol Genet 2022; 8:e670. [PMID: 35620137 PMCID: PMC9128039 DOI: 10.1212/nxg.0000000000000670] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/18/2022] [Indexed: 11/15/2022]
Abstract
In 2011, a pathogenic hexanucleotide repeat expansion in the C9ORF72 gene was discovered to be the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Before this, the C9ORF72 gene and its protein were unknown. The repeat expansion was found to cause both haploinsufficiency and gain of toxicity through aggregating RNA products and dipeptide repeat proteins. A worldwide effort was then initiated to define C9ORF72 ALS/FTD and unravel the pathogenic mechanism for the development of therapeutic options. A decade later, C9ORF72 genetic testing is readily available. There is now an increasing appreciation that C9ORF72 not only is the leading genetic cause of ALS/FTD but may contribute to a spectrum of disorders. This article reviews what is currently known about the C9ORF72 expansion and how C9ORF72 expansion manifests in ALS, FTD, psychiatric disorders, and movement disorders. With therapeutic strategies fast approaching the clinic, earlier recognition of possible C9ORF72 expansion related disorders is even more paramount to improve patient care.
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Affiliation(s)
| | - Summer Gibson
- Department of Neurology, University of Utah, Salt Lake City
| | - Karla Figueroa
- Department of Neurology, University of Utah, Salt Lake City
| | - Mark Bromberg
- Department of Neurology, University of Utah, Salt Lake City
| | - Stefan Pulst
- Department of Neurology, University of Utah, Salt Lake City
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36
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How can we define the presymptomatic C9orf72 disease in 2022? An overview on the current definitions of preclinical and prodromal phases. Rev Neurol (Paris) 2022; 178:426-436. [PMID: 35525633 DOI: 10.1016/j.neurol.2022.03.007] [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: 01/20/2022] [Accepted: 03/08/2022] [Indexed: 11/24/2022]
Abstract
Repeat expansions in C9orf72 gene are the main genetic cause of frontotemporal dementia, amyotrophic lateral sclerosis and related phenotypes. With the advent of disease-modifying treatments, the presymptomatic disease phase is getting increasing interest as an ideal time window in which innovant therapeutic approaches could be administered. Recommendations issued from international study groups distinguish between a preclinical disease stage, during which lesions accumulate in absence of any symptoms or signs, and a prodromal stage, marked by the appearance the first subtle cognitive, behavioral, psychiatric and motor signs, before the full-blown disease. This paper summarizes the current definitions and criteria for these stages, in particular focusing on how fluid-based, neuroimaging and cognitive biomarkers can be useful to monitor disease trajectory across the presymptomatic phase, as well as to detect the earliest signs of clinical conversion. Continuous advances in the knowledge of C9orf72 pathophysiology, and the integration of biomarkers in the clinical evaluation of mutation carriers will allow a better diagnostic definition of C9orf72 disease spectrum from the earliest stages, with relevant impact on the possibility of disease prevention.
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37
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Odeh HM, Fare CM, Shorter J. Nuclear-Import Receptors Counter Deleterious Phase Transitions in Neurodegenerative Disease. J Mol Biol 2022; 434:167220. [PMID: 34464655 PMCID: PMC8748273 DOI: 10.1016/j.jmb.2021.167220] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 01/17/2023]
Abstract
Nuclear-import receptors (NIRs) engage nuclear-localization signals (NLSs) of polypeptides in the cytoplasm and transport these cargo across the size-selective barrier of the nuclear-pore complex into the nucleoplasm. Beyond this canonical role in nuclear transport, NIRs operate in the cytoplasm to chaperone and disaggregate NLS-bearing clients. Indeed, NIRs can inhibit and reverse functional and deleterious phase transitions of their cargo, including several prominent neurodegenerative disease-linked RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as TDP-43, FUS, EWSR1, TAF15, hnRNPA1, and hnRNPA2. Importantly, elevated NIR expression can mitigate degenerative phenotypes connected to aberrant cytoplasmic aggregation of RBPs with PrLDs. Here, we review recent discoveries that NIRs can also antagonize aberrant interactions and toxicity of arginine-rich, dipeptide-repeat proteins that are associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) caused by G4C2 hexanucleotide repeat expansions in the first intron of C9ORF72. We also highlight recent findings that multiple NIR family members can prevent and reverse liquid-liquid phase separation of specific clients bearing RGG motifs in an NLS-independent manner. Finally, we discuss strategies to enhance NIR activity or expression, which could have therapeutic utility for several neurodegenerative disorders, including ALS, FTD, multisystem proteinopathy, limbic-predominant age-related TDP-43 encephalopathy, tauopathies, and related diseases.
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Affiliation(s)
- Hana M Odeh
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. https://twitter.com/CharlotteFare
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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38
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Liano D, Monti L, Chowdhury S, Raguseo F, Di Antonio M. Long-range DNA interactions: inter-molecular G-quadruplexes and their potential biological relevance. Chem Commun (Camb) 2022; 58:12753-12762. [PMID: 36281554 PMCID: PMC9671097 DOI: 10.1039/d2cc04872h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Guanine-rich DNA sequences are known to fold into secondary structures called G-quadruplexes (G4s), which can form from either individual DNA strands (intra-molecular) or multiple DNA strands (inter-molecular, iG4s). Intra-molecular G4s have been the object of extensive biological investigation due to their enrichment in gene-promoters and telomers. On the other hand, iG4s have never been considered in biological contexts, as the interaction between distal sequences of DNA to form an iG4 in cells was always deemed as highly unlikely. In this feature article, we challenge this dogma by presenting our recent discovery of the first human protein (CSB) displaying astonishing picomolar affinity and binding selectivity for iG4s. These findings suggest potential for iG4 structures to form in cells and highlight the need of further studies to unravel the fundamental biological roles of these inter-molecular DNA structures. Furthermore, we discuss how the potential for formation of iG4s in neuronal cells, triggered by repeat expansions in the C9orf72 gene, can lead to the formation of nucleic-acids based pathological aggregates in neurodegenerative diseases like ALS and FTD. Finally, based on our recent work on short LNA-modified probes, we provide a prespective on how the rational design of G4-selective chemical tools can be leveraged to further elucidate the biological relevance of iG4 structures in the context of ageing-related diseases. Intermolecular G-quadruplex structures can form within distal region of genomic DNA, contributing to chromatin looping. Herein, we discuss recent evidence supporting formation of iG4s in living cells and their potential biological function.![]()
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Affiliation(s)
- Denise Liano
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Ludovica Monti
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Souroprobho Chowdhury
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Federica Raguseo
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
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39
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Torres P, Cabral-Miranda F, Gonzalez-Teuber V, Hetz C. Proteostasis deregulation as a driver of C9ORF72 pathogenesis. J Neurochem 2021; 159:941-957. [PMID: 34679204 DOI: 10.1111/jnc.15529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two related neurodegenerative disorders that display overlapping features. The hexanucleotide repeat expansion GGGGCC (G4 C2 ) in C9ORF72 gene has been causally linked to both ALS and FTD emergence, thus opening a novel potential therapeutic target for disease intervention. The main driver of C9ORF72 pathology is the disruption of distinct cellular processes involved in the function of the proteostasis network. Here we discuss main findings relating to the induction of neurodegeneration by C9ORF72 mutation and proteostasis deregulation, highlighting the role of the endoplasmic reticulum stress, nuclear transport, and autophagy in the disease process. We further discuss possible points of intervention to target proteostasis mediators to treat C9ORF72-linked ALS/FTD.
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Affiliation(s)
- Paulina Torres
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile.,FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Science, University of Chile, Santiago, Chile
| | - Felipe Cabral-Miranda
- Instituto de Ciências Biomédicas, Universidade do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vicente Gonzalez-Teuber
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile.,FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Science, University of Chile, Santiago, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile.,FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Science, University of Chile, Santiago, Chile.,Buck Institute for Research on Aging, Novato, California, USA
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40
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Bartoletti-Stella A, Vacchiano V, De Pasqua S, Mengozzi G, De Biase D, Bartolomei I, Avoni P, Rizzo G, Parchi P, Donadio V, Chiò A, Pession A, Oppi F, Salvi F, Liguori R, Capellari S. Targeted sequencing panels in Italian ALS patients support different etiologies in the ALS/FTD continuum. J Neurol 2021; 268:3766-3776. [PMID: 33770234 PMCID: PMC8463338 DOI: 10.1007/s00415-021-10521-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/12/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND 5-10% of amyotrophic lateral sclerosis (ALS) patients presented a positive family history (fALS). More than 30 genes have been identified in association with ALS/frontotemporal dementia (FTD) spectrum, with four major genes accounting for 60-70% of fALS. In this paper, we aimed to assess the contribution to the pathogenesis of major and rare ALS/FTD genes in ALS patients. METHODS We analyzed ALS and ALS/FTD associated genes by direct sequencing or next-generation sequencing multigene panels in ALS patients. RESULTS Genetic abnormalities in ALS major genes included repeated expansions of hexanucleotide in C9orf72 gene (7.3%), mutations in SOD1 (4.9%), FUS (2.1%), and TARDBP (2.4%), whereas variants in rare ALS/FTD genes affected 15.5% of subjects overall, most frequently involving SQSTM1 (3.4%), and CHMP2B (1.9%). We found clustering of variants in ALS major genes in patients with a family history for "pure" ALS, while ALS/FTD related genes mainly occurred in patients with a family history for other neurodegenerative diseases (dementia and/or parkinsonism). CONCLUSIONS Our data support the presence of two different genetic components underlying ALS pathogenesis, related to the presence of a family history for ALS or other neurodegenerative diseases. Thus, family history may help in optimizing the genetic screening protocol to be applied.
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Affiliation(s)
- Anna Bartoletti-Stella
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
| | - Veria Vacchiano
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
| | - Silvia De Pasqua
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università Di Bologna, 40123, Bologna, Italy
| | - Giacomo Mengozzi
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
| | - Dario De Biase
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138, Bologna, Italy
| | - Ilaria Bartolomei
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
| | - Patrizia Avoni
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università Di Bologna, 40123, Bologna, Italy
| | - Giovanni Rizzo
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università Di Bologna, 40123, Bologna, Italy
| | - Piero Parchi
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138, Bologna, Italy
| | - Vincenzo Donadio
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Citta Della Salute E Della Scienza Di Torino, Turin, Italy
- Neuroscience Institute of Turin, Turin, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138, Bologna, Italy
| | - Federico Oppi
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
| | - Fabrizio Salvi
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
| | - Rocco Liguori
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università Di Bologna, 40123, Bologna, Italy
| | - Sabina Capellari
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bellaria Hospital, 40139, Bologna, Italy.
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università Di Bologna, 40123, Bologna, Italy.
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Arginine-rich dipeptide-repeat proteins as phase disruptors in C9-ALS/FTD. Emerg Top Life Sci 2021; 4:293-305. [PMID: 32639008 DOI: 10.1042/etls20190167] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022]
Abstract
A hexanucleotide repeat expansion GGGGCC (G4C2) within chromosome 9 open reading frame 72 (C9orf72) is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). This seminal realization has rapidly focused our attention to the non-canonical translation (RAN translation) of the repeat expansion, which yields dipeptide-repeat protein products (DPRs). The mechanisms by which DPRs might contribute to C9-ALS/FTD are widely studied. Arginine-rich DPRs (R-DPRs) are the most toxic of the five different DPRs produced in neurons, but how do R-DPRs promote C9-ALS/FTD pathogenesis? Proteomic analyses have uncovered potential pathways to explore. For example, the vast majority of the R-DPR interactome is comprised of disease-linked RNA-binding proteins (RBPs) with low-complexity domains (LCDs), strongly suggesting a link between R-DPRs and aberrations in liquid-liquid phase separation (LLPS). In this review, we showcase several potential mechanisms by which R-DPRs disrupt various phase-separated compartments to elicit deleterious neurodegeneration. We also discuss potential therapeutic strategies to counter R-DPR toxicity in C9-ALS/FTD.
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42
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Zaepfel BL, Rothstein JD. RNA Is a Double-Edged Sword in ALS Pathogenesis. Front Cell Neurosci 2021; 15:708181. [PMID: 34349625 PMCID: PMC8326408 DOI: 10.3389/fncel.2021.708181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease that affects upper and lower motor neurons. Familial ALS accounts for a small subset of cases (<10-15%) and is caused by dominant mutations in one of more than 10 known genes. Multiple genes have been causally or pathologically linked to both ALS and frontotemporal dementia (FTD). Many of these genes encode RNA-binding proteins, so the role of dysregulated RNA metabolism in neurodegeneration is being actively investigated. In addition to defects in RNA metabolism, recent studies provide emerging evidence into how RNA itself can contribute to the degeneration of both motor and cortical neurons. In this review, we discuss the roles of altered RNA metabolism and RNA-mediated toxicity in the context of TARDBP, FUS, and C9ORF72 mutations. Specifically, we focus on recent studies that describe toxic RNA as the potential initiator of disease, disease-associated defects in specific RNA metabolism pathways, as well as how RNA-based approaches can be used as potential therapies. Altogether, we highlight the importance of RNA-based investigations into the molecular progression of ALS, as well as the need for RNA-dependent structural studies of disease-linked RNA-binding proteins to identify clear therapeutic targets.
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Affiliation(s)
- Benjamin L Zaepfel
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Molecular Biology and Genetics Department, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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43
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Root J, Merino P, Nuckols A, Johnson M, Kukar T. Lysosome dysfunction as a cause of neurodegenerative diseases: Lessons from frontotemporal dementia and amyotrophic lateral sclerosis. Neurobiol Dis 2021; 154:105360. [PMID: 33812000 PMCID: PMC8113138 DOI: 10.1016/j.nbd.2021.105360] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are fatal neurodegenerative disorders that are thought to exist on a clinical and pathological spectrum. FTD and ALS are linked by shared genetic causes (e.g. C9orf72 hexanucleotide repeat expansions) and neuropathology, such as inclusions of ubiquitinated, misfolded proteins (e.g. TAR DNA-binding protein 43; TDP-43) in the CNS. Furthermore, some genes that cause FTD or ALS when mutated encode proteins that localize to the lysosome or modulate endosome-lysosome function, including lysosomal fusion, cargo trafficking, lysosomal acidification, autophagy, or TFEB activity. In this review, we summarize evidence that lysosomal dysfunction, caused by genetic mutations (e.g. C9orf72, GRN, MAPT, TMEM106B) or toxic-gain of function (e.g. aggregation of TDP-43 or tau), is an important pathogenic disease mechanism in FTD and ALS. Further studies into the normal function of many of these proteins are required and will help uncover the mechanisms that cause lysosomal dysfunction in FTD and ALS. Mutations or polymorphisms in genes that encode proteins important for endosome-lysosome function also occur in other age-dependent neurodegenerative diseases, including Alzheimer's (e.g. APOE, PSEN1, APP) and Parkinson's (e.g. GBA, LRRK2, ATP13A2) disease. A more complete understanding of the common and unique features of lysosome dysfunction across the spectrum of neurodegeneration will help guide the development of therapies for these devastating diseases.
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Affiliation(s)
- Jessica Root
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Paola Merino
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Austin Nuckols
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Michelle Johnson
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia; Department of Neurology, Emory University, School of Medicine, Atlanta 30322, Georgia.
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44
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C9orf72 Intermediate Repeats Confer Genetic Risk for Severe COVID-19 Pneumonia Independently of Age. Int J Mol Sci 2021; 22:ijms22136991. [PMID: 34209673 PMCID: PMC8268051 DOI: 10.3390/ijms22136991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
A cytokine storm, autoimmune features and dysfunctions of myeloid cells significantly contribute to severe coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Genetic background of the host seems to be partly responsible for severe phenotype and genes related to innate immune response seem critical host determinants. The C9orf72 gene has a role in vesicular trafficking, autophagy regulation and lysosome functions, is highly expressed in myeloid cells and is involved in immune functions, regulating the lysosomal degradation of mediators of innate immunity. A large non-coding hexanucleotide repeat expansion (HRE) in this gene is the main genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), both characterized by neuroinflammation and high systemic levels of proinflammatory cytokines, while HREs of intermediate length, although rare, are more frequent in autoimmune disorders. C9orf72 full mutation results in haploinsufficiency and intermediate HREs seem to modulate gene expression as well and impair autophagy. Herein, we sought to explore whether intermediate HREs in C9orf72 may be a risk factor for severe COVID-19. Although we found intermediate HREs in only a small portion of 240 patients with severe COVID-19 pneumonia, the magnitude of risk for requiring non-invasive or mechanical ventilation conferred by harboring intermediate repeats >10 units in at least one C9orf72 allele was more than twice respect to having shorter expansions, when adjusted for age (odds ratio (OR) 2.36; 95% confidence interval (CI) 1.04-5.37, p = 0.040). The association between intermediate repeats >10 units and more severe clinical outcome (p = 0.025) was also validated in an independent cohort of 201 SARS-CoV-2 infected patients. These data suggest that C9orf72 HREs >10 units may influence the pathogenic process driving more severe COVID-19 phenotypes.
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45
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Chintalaphani SR, Pineda SS, Deveson IW, Kumar KR. An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics. Acta Neuropathol Commun 2021; 9:98. [PMID: 34034831 PMCID: PMC8145836 DOI: 10.1186/s40478-021-01201-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR) expansion disorders are an important cause of human neurological disease. They have an established role in more than 40 different phenotypes including the myotonic dystrophies, Fragile X syndrome, Huntington's disease, the hereditary cerebellar ataxias, amyotrophic lateral sclerosis and frontotemporal dementia. MAIN BODY STR expansions are difficult to detect and may explain unsolved diseases, as highlighted by recent findings including: the discovery of a biallelic intronic 'AAGGG' repeat in RFC1 as the cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS); and the finding of 'CGG' repeat expansions in NOTCH2NLC as the cause of neuronal intranuclear inclusion disease and a range of clinical phenotypes. However, established laboratory techniques for diagnosis of repeat expansions (repeat-primed PCR and Southern blot) are cumbersome, low-throughput and poorly suited to parallel analysis of multiple gene regions. While next generation sequencing (NGS) has been increasingly used, established short-read NGS platforms (e.g., Illumina) are unable to genotype large and/or complex repeat expansions. Long-read sequencing platforms recently developed by Oxford Nanopore Technology and Pacific Biosciences promise to overcome these limitations to deliver enhanced diagnosis of repeat expansion disorders in a rapid and cost-effective fashion. CONCLUSION We anticipate that long-read sequencing will rapidly transform the detection of short tandem repeat expansion disorders for both clinical diagnosis and gene discovery.
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Affiliation(s)
- Sanjog R. Chintalaphani
- School of Medicine, University of New South Wales, Sydney, 2052 Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Brain and Mind Centre, University of Sydney, Camperdown, NSW 2050 Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Faculty of Medicine, St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010 Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Molecular Medicine Laboratory and Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW 2137 Australia
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46
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Disease Mechanisms and Therapeutic Approaches in C9orf72 ALS-FTD. Biomedicines 2021; 9:biomedicines9060601. [PMID: 34070550 PMCID: PMC8229688 DOI: 10.3390/biomedicines9060601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/15/2023] Open
Abstract
A hexanucleotide repeat expansion mutation in the first intron of C9orf72 is the most common known genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Since the discovery in 2011, numerous pathogenic mechanisms, including both loss and gain of function, have been proposed. The body of work overall suggests that toxic gain of function arising from bidirectionally transcribed repeat RNA is likely to be the primary driver of disease. In this review, we outline the key pathogenic mechanisms that have been proposed to date and discuss some of the novel therapeutic approaches currently in development.
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47
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Cicardi ME, Marrone L, Azzouz M, Trotti D. Proteostatic imbalance and protein spreading in amyotrophic lateral sclerosis. EMBO J 2021; 40:e106389. [PMID: 33792056 PMCID: PMC8126909 DOI: 10.15252/embj.2020106389] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/18/2020] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder whose exact causative mechanisms are still under intense investigation. Several lines of evidence suggest that the anatomical and temporal propagation of pathological protein species along the neural axis could be among the main driving mechanisms for the fast and irreversible progression of ALS pathology. Many ALS-associated proteins form intracellular aggregates as a result of their intrinsic prion-like properties and/or following impairment of the protein quality control systems. During the disease course, these mutated proteins and aberrant peptides are released in the extracellular milieu as soluble or aggregated forms through a variety of mechanisms. Internalization by recipient cells may seed further aggregation and amplify existing proteostatic imbalances, thus triggering a vicious cycle that propagates pathology in vulnerable cells, such as motor neurons and other susceptible neuronal subtypes. Here, we provide an in-depth review of ALS pathology with a particular focus on the disease mechanisms of seeding and transmission of the most common ALS-associated proteins, including SOD1, FUS, TDP-43, and C9orf72-linked dipeptide repeats. For each of these proteins, we report historical, biochemical, and pathological evidence of their behaviors in ALS. We further discuss the possibility to harness pathological proteins as biomarkers and reflect on the implications of these findings for future research.
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Affiliation(s)
- Maria Elena Cicardi
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Lara Marrone
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Mimoun Azzouz
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Davide Trotti
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
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48
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Serpente M, Fenoglio C, Arighi A, Fumagalli GG, Arcaro M, Sorrentino F, Visconte C, Scarpini E, Galimberti D. Analysis of C9orf72 Intermediate Alleles in a Retrospective Cohort of Neurological Patients: Risk Factors for Alzheimer's Disease? J Alzheimers Dis 2021; 81:1445-1451. [PMID: 33935096 DOI: 10.3233/jad-210249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND C9orf72 hexanucleotide GGGGCC (G4C2) large repeat expansions within the first intron of the gene are a major cause of familial frontotemporal dementia, but also of apparently sporadic cases. Alleles with > 30 repeats are often considered pathogenic, but the repeat length threshold is still undefined. It is also unclear if C9orf72 intermediate alleles (9-30 repeats) have clinically significant effects. OBJECTIVES We correlated the presence of C9orf72 intermediate alleles with clinical diagnoses in a perspective cohort referred to a secondary memory clinic. METHODS All samples were genotyped with AmplideXPCR/CE C9ORF72 Kit (Asuragen, Inc), an optimized C9orf72 PCR amplification reagent. RESULTS We showed that in patients with Alzheimer's disease (AD) the frequency of the intermediate repeat alleles was significantly increased versus controls (34/54, 63%AD versus 16/39, 41%CTRLs, *p = 0.01, OR 2.91 CI 95%1.230-6.077), whereas no significant differences (p > 0.05) were observed when comparing all other dementias with non-demented individuals. CONCLUSION Our findings suggest that C9orf72 intermediate repeat units may represent a genetic risk factor, contributing to the occurrence of AD. Nevertheless, further longitudinal studies, including larger cohort of subjects with intermediate alleles with long-term follow-up, would be needed to confirm these results.
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Affiliation(s)
- Maria Serpente
- Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Milan, Italy.,Dino Ferrari Center, University of Milan, Milan, Italy
| | | | - Andrea Arighi
- Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Milan, Italy
| | | | - Marina Arcaro
- Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Milan, Italy
| | | | | | - Elio Scarpini
- Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Milan, Italy.,Dino Ferrari Center, University of Milan, Milan, Italy
| | - Daniela Galimberti
- Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Milan, Italy.,Dino Ferrari Center, University of Milan, Milan, Italy
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49
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Role of SNAREs in Neurodegenerative Diseases. Cells 2021; 10:cells10050991. [PMID: 33922505 PMCID: PMC8146804 DOI: 10.3390/cells10050991] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases are pathologies of the central and peripheral nervous systems characterized by loss of brain functions and problems in movement which occur due to the slow and progressive degeneration of cellular elements. Several neurodegenerative diseases are known such as Alzheimer’s disease, Parkinson’s disease and amyotrophic lateral sclerosis and many studies on the molecular mechanisms underlying these pathologies have been conducted. Altered functions of some key proteins and the presence of intraneuronal aggregates have been identified as responsible for the development of the diseases. Interestingly, the formation of the SNARE complex has been discovered to be fundamental for vesicle fusion, vesicle recycling and neurotransmitter release. Indeed, inhibition of the formation of the SNARE complex, defects in the SNARE-dependent exocytosis and altered regulation of SNARE-mediated vesicle fusion have been associated with neurodegeneration. In this review, the biological aspects of neurodegenerative diseases and the role of SNARE proteins in relation to the onset of these pathologies are described.
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50
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Marshall JN, Lopez AI, Pfaff AL, Koks S, Quinn JP, Bubb VJ. Variable number tandem repeats - Their emerging role in sickness and health. Exp Biol Med (Maywood) 2021; 246:1368-1376. [PMID: 33794697 PMCID: PMC8239992 DOI: 10.1177/15353702211003511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Understanding the mechanisms regulating tissue specific and stimulus inducible
regulation is at the heart of understanding human biology and how this
translates to wellbeing, the ageing process, and disease progression.
Polymorphic DNA variation is superimposed as an extra layer of complexity in
such processes which underpin our individuality and are the focus of
personalized medicine. This review focuses on the role and action of repetitive
DNA, specifically variable number tandem repeats and
SINE-VNTR-Alu domains, highlighting their role in
modification of gene structure and gene expression in addition to their
polymorphic nature being a genetic modifier of disease risk and progression.
Although the literature focuses on their role in disease, it illustrates their
potential to be major contributors to normal physiological function. To date,
these elements have been under-reported in genomic analysis due to the
difficulties in their characterization with short read DNA sequencing methods.
However, recent advances in long read sequencing methods should resolve these
problems allowing for a greater understanding of their contribution to a host of
genomic and functional mechanisms underlying physiology and disease.
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Affiliation(s)
- Jack Ng Marshall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ana Illera Lopez
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
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