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Gaur P, Bryois J, Calini D, Foo L, Hoozemans JJM, Malhotra D, Menon V. Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology. bioRxiv 2024:2024.04.23.590816. [PMID: 38712204 PMCID: PMC11071354 DOI: 10.1101/2024.04.23.590816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathological manifestations and is the leading cause of cognitive decline and dementia in elderly individuals. A major goal in AD research is to identify new therapeutic pathways by studying the molecular and cellular changes in the disease, either downstream or upstream of the pathological hallmarks. In this study, we present a comprehensive investigation of cellular heterogeneity from the temporal cortex region of 40 individuals, comprising healthy donors and individuals with differing tau and amyloid burden. Using single-nucleus transcriptome analysis of 430,271 nuclei from both gray and white matter of these individuals, we identified cell type-specific subclusters in both neuronal and glial cell types with varying degrees of association with AD pathology. In particular, these associations are present in layer specific glutamatergic (excitatory) neuronal types, along with GABAergic (inhibitory) neurons and glial subtypes. These associations were observed in early as well as late pathological progression. We extended this analysis by performing multiplexed in situ hybridization using the CARTANA platform, capturing 155 genes in 13 individuals with varying levels of tau pathology. By modeling the spatial distribution of these genes and their associations with the pathology, we not only replicated key findings from our snRNA data analysis, but also identified a set of cell type-specific genes that show selective enrichment or depletion near pathological inclusions. Together, our findings allow us to prioritize specific cell types and pathways for targeted interventions at various stages of pathological progression in AD.
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Affiliation(s)
- Pallavi Gaur
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Daniela Calini
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Lynette Foo
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Dheeraj Malhotra
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
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Rexach JE, Cheng Y, Chen L, Polioudakis D, Lin LC, Mitri V, Elkins A, Yin A, Calini D, Kawaguchi R, Ou J, Huang J, Williams C, Robinson J, Gaus SE, Spina S, Lee EB, Grinberg LT, Vinters H, Trojanowski JQ, Seeley WW, Malhotra D, Geschwind DH. Disease-specific selective vulnerability and neuroimmune pathways in dementia revealed by single cell genomics. bioRxiv 2023:2023.09.29.560245. [PMID: 37808727 PMCID: PMC10557766 DOI: 10.1101/2023.09.29.560245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The development of successful therapeutics for dementias requires an understanding of their shared and distinct molecular features in the human brain. We performed single-nuclear RNAseq and ATACseq in Alzheimer disease (AD), Frontotemporal degeneration (FTD), and Progressive Supranuclear Palsy (PSP), analyzing 40 participants, yielding over 1.4M cells from three brain regions ranging in vulnerability and pathological burden. We identify 35 shared disease-associated cell types and 14 that are disease-specific, replicating those previously identified in AD. Disease - specific cell states represent molecular features of disease-specific glial-immune mechanisms and neuronal vulnerability in each disorder, layer 4/5 intra-telencephalic neurons in AD, layer 2/3 intra-telencephalic neurons in FTD, and layer 5/6 near-projection neurons in PSP. We infer intrinsic disease-associated gene regulatory networks, which we empirically validate by chromatin footprinting. We find that causal genetic risk acts in specific neuronal and glial cells that differ across disorders, primarily non-neuronal cells in AD and specific neuronal subtypes in FTD and PSP. These data illustrate the heterogeneous spectrum of glial and neuronal composition and gene expression alterations in different dementias and identify new therapeutic targets by revealing shared and disease-specific cell states.
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Touil H, Roostaei T, Calini D, Diaconu C, Epstein S, Raposo C, Onomichi K, Thakur KT, Craveiro L, Callegari I, Bryois J, Riley CS, Menon V, Derfuss T, De Jager PL, Malhotra D. A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid. Cell Rep Methods 2023; 3:100533. [PMID: 37533636 PMCID: PMC10391561 DOI: 10.1016/j.crmeth.2023.100533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Single-cell transcriptomics allows characterization of cerebrospinal fluid (CSF) cells at an unprecedented level. Here, we report a robust cryopreservation protocol adapted for the characterization of fragile CSF cells by single-cell RNA sequencing (RNA-seq) in moderate- to large-scale studies. Fresh CSF was collected from twenty-one participants at two independent sites. Each CSF sample was split into two fractions: one was processed fresh, while the second was cryopreserved for months and profiled after thawing. B and T cell receptor sequencing was also performed. Our comparison of fresh and cryopreserved data from the same individuals demonstrates highly efficient recovery of all known CSF cell types. We find no significant difference in cell type proportions and cellular transcriptomes between fresh and cryopreserved cells. Results were comparable at both sites and with different single-cell sequencing chemistries. Cryopreservation did not affect recovery of T and B cell clonotype diversity. Our CSF cell cryopreservation protocol provides an important alternative to fresh processing of fragile CSF cells.
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Affiliation(s)
- Hanane Touil
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tina Roostaei
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniela Calini
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Claudiu Diaconu
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samantha Epstein
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Catarina Raposo
- gRED OMNI-Biomarker Development, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, Basel, Switzerland
| | - Kaho Onomichi
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kiran T. Thakur
- Program in Neuroinfectious Diseases, Division of Critical Care and Hospitalist Neurology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Licinio Craveiro
- Product Development Medical Affairs (PDMA) Neuroscience, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Ilaria Callegari
- University Hospital Basel, Department of Neurology and Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Julien Bryois
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Claire S. Riley
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tobias Derfuss
- University Hospital Basel, Department of Neurology and Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dheeraj Malhotra
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA 02142, USA
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4
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Tiloca C, Goldwurm S, Calcagno N, Verde F, Peverelli S, Calini D, Zecchinelli AL, Sangalli D, Ratti A, Pezzoli G, Silani V, Ticozzi N. TARDBP mutations in a cohort of Italian patients with Parkinson’s disease and atypical parkinsonisms. Front Aging Neurosci 2022; 14:1020948. [PMID: 36247987 PMCID: PMC9557978 DOI: 10.3389/fnagi.2022.1020948] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAggregates of TAR DNA-binding protein of 43 kDa (TDP-43) represent the pathological hallmark of most amyotrophic lateral sclerosis (ALS) and of nearly 50% of frontotemporal dementia (FTD) cases but were also observed to occur as secondary neuropathology in the nervous tissue of patients with different neurodegenerative diseases, including Parkinson’s disease (PD) and atypical parkinsonism. Mutations of TARDBP gene, mainly in exon 6 hotspot, have been reported to be causative of some forms of ALS and FTD, with clinical signs of parkinsonism observed in few mutation carriers.MethodsDirect DNA sequencing of TARDBP exon 6 was performed in a large Italian cohort of 735 patients affected by PD (354 familial and 381 sporadic) and 142 affected by atypical parkinsonism, including 39 corticobasal syndrome (CBS) and 103 progressive sopranuclear palsy (PSP). Sequencing data from 1710 healthy, ethnically matched controls were already available.ResultsFour TARDBP missense variants (p.N267S, p. G294A, p.G295S, p.S393L) were identified in four patients with typical PD and in two individuals with atypical parkinsonism (1 CBS and 1 PSP). None of the detected mutations were found in healthy controls and only the variant p.N267S was previously described in association to idiopathic familial and sporadic PD and to CBS.ConclusionIn this study we provide further insight into the clinical phenotypic heterogeneity associated with TARDBP mutations, which expands beyond the classical ALS and FTD diseases to include also PD and atypical parkinsonism, although with a low mutational frequency, varying considerably in different Caucasian populations. In addition, our study extends the spectrum of TARDBP pathogenetic mutations found in familial and sporadic PD.
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Affiliation(s)
- Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Stefano Goldwurm
- Parkinson Institute of Milan, ASST Gaetano Pini/CTO, Milan, Italy
| | - Narghes Calcagno
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Neurology Residency Program, Università degli Studi di Milano, Milan, Italy
| | - Federico Verde
- 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
| | - Silvia Peverelli
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | | | - Davide Sangalli
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Neurology – Stroke Unit, A. Manzoni Hospital – ASST Lecco, Lecco, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Gianni Pezzoli
- Parkinson Institute of Milan, ASST Gaetano Pini/CTO, Milan, 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
| | - 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
- *Correspondence: Nicola Ticozzi,
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5
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Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby L, Calini D, Johnson MR, Corces MR, Montine TJ, Chen X, Chang HY, Malhotra D, Castelo-Branco G. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Neuron 2022; 110:1193-1210.e13. [PMID: 35093191 PMCID: PMC9810341 DOI: 10.1016/j.neuron.2021.12.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 01/05/2023]
Abstract
Multiple sclerosis (MS) is characterized by a targeted attack on oligodendroglia (OLG) and myelin by immune cells, which are thought to be the main drivers of MS susceptibility. We found that immune genes exhibit a primed chromatin state in single mouse and human OLG in a non-disease context, compatible with transitions to immune-competent states in MS. We identified BACH1 and STAT1 as transcription factors involved in immune gene regulation in oligodendrocyte precursor cells (OPCs). A subset of immune genes presents bivalency of H3K4me3/H3K27me3 in OPCs, with Polycomb inhibition leading to their increased activation upon interferon gamma (IFN-γ) treatment. Some MS susceptibility single-nucleotide polymorphisms (SNPs) overlap with these regulatory regions in mouse and human OLG. Treatment of mouse OPCs with IFN-γ leads to chromatin architecture remodeling at these loci and altered expression of interacting genes. Thus, the susceptibility for MS may involve OLG, which therefore constitutes novel targets for immunological-based therapies for MS.
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Affiliation(s)
- Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mukund Kabbe
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Cassandra A van Tuijn
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Abeer Heskol
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden; Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Chao Zheng
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's Associate Laboratory, PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Leslie Kirby
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Daniela Calini
- Roche Pharma Research and Early Development, 4070 Basel, Switzerland
| | - Michael R Johnson
- Faculty of Medicine, Department of Brain Sciences, Imperial College of London, SW7 2AZ London, UK
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Immunology, Genetics, and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5101, USA
| | - Dheeraj Malhotra
- Roche Pharma Research and Early Development, 4070 Basel, Switzerland
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, 171 77 Stockholm, Sweden.
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6
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Nolle A, van Dijken I, Waelti CM, Calini D, Bryois J, Lezan E, Golling S, Augustin A, Foo L, Hoozemans JJM. Enrichment of Glial Cells From Human Post-mortem Tissue for Transcriptome and Proteome Analysis Using Immunopanning. Front Cell Neurosci 2021; 15:772011. [PMID: 34966261 PMCID: PMC8711556 DOI: 10.3389/fncel.2021.772011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Glia cells have a crucial role in the central nervous system and are involved in the majority of neurological diseases. While glia isolation techniques are well established for rodent brain, only recent advances in isolating glial cells from human brain enabled analyses of human-specific glial-cell profiles. Immunopanning that is the prospective purification of cells using cell type-specific antibodies, has been successfully established for isolating glial cells from human fetal brain or from tissue obtained during brain surgeries. Here, we describe an immunopanning protocol to acutely isolate glial cells from post-mortem human brain tissue for e.g. transcriptome and proteome analyses. We enriched for microglia, oligodendrocytes and astrocytes from cortical gray matter tissue from three donors. For each enrichment, we assessed the presence of known glia-specific markers at the RNA and protein levels. In this study we show that immunopanning can be employed for acute isolation of glial cells from human post-mortem brain, which allows characterization of glial phenotypes depending on age, disease and brain regions.
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Affiliation(s)
- Anna Nolle
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Irene van Dijken
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Ciril M Waelti
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Daniela Calini
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Emmanuelle Lezan
- Pharmaceutical Sciences, Biomarkers, Bioinformatics and Omics and Pathology (MT, JL, AA), Roche Innovation Center Basel, Basel, Switzerland
| | - Sabrina Golling
- Pharmaceutical Sciences, Biomarkers, Bioinformatics and Omics and Pathology (MT, JL, AA), Roche Innovation Center Basel, Basel, Switzerland
| | - Angelique Augustin
- Pharmaceutical Sciences, Biomarkers, Bioinformatics and Omics and Pathology (MT, JL, AA), Roche Innovation Center Basel, Basel, Switzerland
| | - Lynette Foo
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
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Lütge A, Zyprych-Walczak J, Brykczynska Kunzmann U, Crowell HL, Calini D, Malhotra D, Soneson C, Robinson MD. CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data. Life Sci Alliance 2021; 4:e202001004. [PMID: 33758076 PMCID: PMC7994321 DOI: 10.26508/lsa.202001004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
A key challenge in single-cell RNA-sequencing (scRNA-seq) data analysis is batch effects that can obscure the biological signal of interest. Although there are various tools and methods to correct for batch effects, their performance can vary. Therefore, it is important to understand how batch effects manifest to adjust for them. Here, we systematically explore batch effects across various scRNA-seq datasets according to magnitude, cell type specificity, and complexity. We developed a cell-specific mixing score (cms) that quantifies mixing of cells from multiple batches. By considering distance distributions, the score is able to detect local batch bias as well as differentiate between unbalanced batches and systematic differences between cells of the same cell type. We compare metrics in scRNA-seq data using real and synthetic datasets and whereas these metrics target the same question and are used interchangeably, we find differences in scalability, sensitivity, and ability to handle differentially abundant cell types. We find that cell-specific metrics outperform cell type-specific and global metrics and recommend them for both method benchmarks and batch exploration.
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Affiliation(s)
- Almut Lütge
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Poznań, Poland
| | | | - Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Daniela Calini
- F. Hoffmann-LaRoche Ltd, Pharma Research and Early Development, Neuroscience, Ophthalmologyand Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Dheeraj Malhotra
- F. Hoffmann-LaRoche Ltd, Pharma Research and Early Development, Neuroscience, Ophthalmologyand Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Charlotte Soneson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
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8
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Crowell HL, Soneson C, Germain PL, Calini D, Collin L, Raposo C, Malhotra D, Robinson MD. muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nat Commun 2020; 11:6077. [PMID: 33257685 PMCID: PMC7705760 DOI: 10.1038/s41467-020-19894-4] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has become an empowering technology to profile the transcriptomes of individual cells on a large scale. Early analyses of differential expression have aimed at identifying differences between subpopulations to identify subpopulation markers. More generally, such methods compare expression levels across sets of cells, thus leading to cross-condition analyses. Given the emergence of replicated multi-condition scRNA-seq datasets, an area of increasing focus is making sample-level inferences, termed here as differential state analysis; however, it is not clear which statistical framework best handles this situation. Here, we surveyed methods to perform cross-condition differential state analyses, including cell-level mixed models and methods based on aggregated pseudobulk data. To evaluate method performance, we developed a flexible simulation that mimics multi-sample scRNA-seq data. We analyzed scRNA-seq data from mouse cortex cells to uncover subpopulation-specific responses to lipopolysaccharide treatment, and provide robust tools for multi-condition analysis within the muscat R package.
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Affiliation(s)
- Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Charlotte Soneson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
- Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Pierre-Luc Germain
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- D-HEST Institute for Neuroscience, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Daniela Calini
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Ludovic Collin
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Catarina Raposo
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Dheeraj Malhotra
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
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9
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Hamzeiy H, Savaş D, Tunca C, Şen NE, Gündoğdu Eken A, Şahbaz I, Calini D, Tiloca C, Ticozzi N, Ratti A, Silani V, Başak AN. Elevated Global DNA Methylation Is Not Exclusive to Amyotrophic Lateral Sclerosis and Is Also Observed in Spinocerebellar Ataxia Types 1 and 2. NEURODEGENER DIS 2018; 18:38-48. [PMID: 29428949 DOI: 10.1159/000486201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022] Open
Abstract
Adult-onset neurological disorders are caused and influenced by a multitude of different factors, including epigenetic modifications. Here, using an ELISA kit selected upon careful testing, we investigated global 5-methylcytosine (5-mC) levels in sporadic and familial amyotrophic lateral sclerosis (sALS and fALS), spinocerebellar ataxia types 1 and 2 (SCA1 and SCA2), Huntington's disease, Friedreich's ataxia, and myotonic dystrophy type 1. We report a significant elevation in global 5-mC levels of about 2-7% on average for sALS (p < 0.01 [F(1, 243) = 9.159, p = 0.0027]) and various forms of fALS along with SCA1 (p < 0.01 [F(1, 83) = 11.285], p = 0.0012) and SCA2 (p < 0.001 [F(1, 122) = 29.996, p = 0.0001]) when compared to age- and sex-matched healthy controls. C9orf72 expansion carrier ALS patients exhibit the highest global 5-mC levels along with C9orf72 promoter hypermethylation. We failed to measure global 5-hydroxymethylcytosine (5-hmC) levels in blood, probably due to the very low levels of 5-hmC and the limitations of the commercially available ELISA kits. Our results point towards a role for epigenetics modification in ALS, SCA1, and SCA2, and help conclude a dispute on the global 5-mC levels in sALS blood.
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Affiliation(s)
- Hamid Hamzeiy
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Doruk Savaş
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Ceren Tunca
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Nesli Ece Şen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Aslı Gündoğdu Eken
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Irmak Şahbaz
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, 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
| | - Antonia Ratti
- 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
| | - 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
| | - A Nazlı Başak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
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10
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van Doormaal PTC, Ticozzi N, Weishaupt JH, Kenna K, Diekstra FP, Verde F, Andersen PM, Dekker AM, Tiloca C, Marroquin N, Overste DJ, Pensato V, Nürnberg P, Pulit SL, Schellevis RD, Calini D, Altmüller J, Francioli LC, Muller B, Castellotti B, Motameny S, Ratti A, Wolf J, Gellera C, Ludolph AC, van den Berg LH, Kubisch C, Landers JE, Veldink JH, Silani V, Volk AE. The role of de novo mutations in the development of amyotrophic lateral sclerosis. Hum Mutat 2017; 38:1534-1541. [PMID: 28714244 DOI: 10.1002/humu.23295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/21/2017] [Accepted: 07/11/2017] [Indexed: 12/29/2022]
Abstract
The genetic basis combined with the sporadic occurrence of amyotrophic lateral sclerosis (ALS) suggests a role of de novo mutations in disease pathogenesis. Previous studies provided some evidence for this hypothesis; however, results were conflicting: no genes with recurrent occurring de novo mutations were identified and different pathways were postulated. In this study, we analyzed whole-exome data from 82 new patient-parents trios and combined it with the datasets of all previously published ALS trios (173 trios in total). The per patient de novo rate was not higher than expected based on the general population (P = 0.40). We showed that these mutations are not part of the previously postulated pathways, and gene-gene interaction analysis found no enrichment of interacting genes in this group (P = 0.57). Also, we were able to show that the de novo mutations in ALS patients are located in genes already prone for de novo mutations (P < 1 × 10-15 ). Although the individual effect of rare de novo mutations in specific genes could not be assessed, our results indicate that, in contrast to previous hypothesis, de novo mutations in general do not impose a major burden on ALS risk.
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Affiliation(s)
- Perry T C van Doormaal
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - 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
| | | | - Kevin Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Frank P Diekstra
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Federico Verde
- 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
| | - Peter M Andersen
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | - Annelot M Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | | | - Daniel J Overste
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Viviana Pensato
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Sara L Pulit
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Raymond D Schellevis
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Laurent C Francioli
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Barbara Castellotti
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Susanne Motameny
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Antonia Ratti
- 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
| | - Joachim Wolf
- Department of Neurology, Diakonissenkrankenhaus Mannheim, Mannheim, Germany
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | | | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christian Kubisch
- Institute of Human Genetics, Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - 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
| | - Alexander E Volk
- Institute of Human Genetics, Medical Centre Hamburg-Eppendorf, Hamburg, Germany
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11
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Kenna KP, van Doormaal PTC, Dekker AM, Ticozzi N, Kenna BJ, Diekstra FP, van Rheenen W, van Eijk KR, Jones AR, Keagle P, Shatunov A, Sproviero W, Smith BN, van Es MA, Topp SD, Kenna A, Miller JW, Fallini C, Tiloca C, McLaughlin RL, Vance C, Troakes C, Colombrita C, Mora G, Calvo A, Verde F, Al-Sarraj S, King A, Calini D, de Belleroche J, Baas F, van der Kooi AJ, de Visser M, Ten Asbroek ALMA, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Muñoz-Blanco JL, Strom TM, Meitinger T, Morrison KE, Lauria G, Williams KL, Leigh PN, Nicholson GA, Blair IP, Leblond CS, Dion PA, Rouleau GA, Pall H, Shaw PJ, Turner MR, Talbot K, Taroni F, Boylan KB, Van Blitterswijk M, Rademakers R, Esteban-Pérez J, García-Redondo A, Van Damme P, Robberecht W, Chio A, Gellera C, Drepper C, Sendtner M, Ratti A, Glass JD, Mora JS, Basak NA, Hardiman O, Ludolph AC, Andersen PM, Weishaupt JH, Brown RH, Al-Chalabi A, Silani V, Shaw CE, van den Berg LH, Veldink JH, Landers JE. NEK1 variants confer susceptibility to amyotrophic lateral sclerosis. Nat Genet 2016; 48:1037-42. [PMID: 27455347 PMCID: PMC5560030 DOI: 10.1038/ng.3626] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
To identify genetic factors contributing to amyotrophic lateral sclerosis (ALS), we conducted whole-exome analyses of 1,022 index familial ALS (FALS) cases and 7,315 controls. In a new screening strategy, we performed gene-burden analyses trained with established ALS genes and identified a significant association between loss-of-function (LOF) NEK1 variants and FALS risk. Independently, autozygosity mapping for an isolated community in the Netherlands identified a NEK1 p.Arg261His variant as a candidate risk factor. Replication analyses of sporadic ALS (SALS) cases and independent control cohorts confirmed significant disease association for both p.Arg261His (10,589 samples analyzed) and NEK1 LOF variants (3,362 samples analyzed). In total, we observed NEK1 risk variants in nearly 3% of ALS cases. NEK1 has been linked to several cellular functions, including cilia formation, DNA-damage response, microtubule stability, neuronal morphology and axonal polarity. Our results provide new and important insights into ALS etiopathogenesis and genetic etiology.
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Affiliation(s)
- Kevin P Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Perry T C van Doormaal
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Annelot M Dekker
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Nicola Ticozzi
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Brendan J Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Frank P Diekstra
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Wouter van Rheenen
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Pamela Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - William Sproviero
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Michael A van Es
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Simon D Topp
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Aoife Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jack W Miller
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Cinzia Tiloca
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Doctoral School in Molecular Medicine, Department of Sciences and Biomedical Technologies, Università degli Studi di Milano, Milan, Italy
| | - Russell L McLaughlin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Caroline Vance
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claire Troakes
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claudia Colombrita
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Gabriele Mora
- Salvatore Maugeri Foundation, IRCSS, Scientific Institute of Milano, Milan, Italy
| | - Andrea Calvo
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Federico Verde
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Safa Al-Sarraj
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Andrew King
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Daniela Calini
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | | | - Frank Baas
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Anneke J van der Kooi
- Department of Neurogenetics and Neurology, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Marianne de Visser
- Department of Neurogenetics and Neurology, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Anneloor L M A Ten Asbroek
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter C Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Seneshaw Asress
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - José Luis Muñoz-Blanco
- Unidad de ELA, Instituto de Investigación Hospital Gregorio Marañón de Madrid, Madrid, Spain
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | | | - Giuseppe Lauria
- 3rd Neurology Unit, Motor Neuron Diseases Center, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Kelly L Williams
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - P Nigel Leigh
- Trafford Centre for Medical Research, Brighton and Sussex Medical School, Falmer, UK
| | - Garth A Nicholson
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
- ANZAC Research Institute, Concord Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Ian P Blair
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Claire S Leblond
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Patrick A Dion
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Hardev Pall
- Institute of Clinical Studies, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Department of Neurology, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - Pamela J Shaw
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Kevin B Boylan
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Jesús Esteban-Pérez
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U-723, Madrid, Spain
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U-723, Madrid, Spain
| | - Phillip Van Damme
- Laboratory of Neurobiology, Department of Neurosciences, KU Leuven and Vesalius Research Centre, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals, Leuven, Belgium
| | - Wim Robberecht
- Laboratory of Neurobiology, Department of Neurosciences, KU Leuven and Vesalius Research Centre, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals, Leuven, Belgium
| | - Adriano Chio
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Carsten Drepper
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
- Department of Child and Adolescent Psychiatry, University Hospital of Würzburg, Würzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Antonia Ratti
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Jonathan D Glass
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Jesús S Mora
- ALS Unit/Neurology, Hospital San Rafael, Madrid, Spain
| | - Nazli A Basak
- NDAL, Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | | | - Peter M Andersen
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | | | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Vincenzo Silani
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Leonard H van den Berg
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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12
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Poletti B, Solca F, Carelli L, Madotto F, Lafronza A, Faini A, Monti A, Zago S, Calini D, Tiloca C, Doretti A, Verde F, Ratti A, Ticozzi N, Abrahams S, Silani V. The validation of the Italian Edinburgh Cognitive and Behavioural ALS Screen (ECAS). Amyotroph Lateral Scler Frontotemporal Degener 2016; 17:489-498. [PMID: 27219526 DOI: 10.1080/21678421.2016.1183679] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This study presents the Italian validation of the recently developed Edinburgh Cognitive and Behavioural ALS Screen (ECAS), a short screen for cognitive/behavioural alterations in patients with amyotrophic lateral sclerosis (ALS). We evaluated the psychometric properties of the ECAS Italian version in terms of reliability and convergent validity for both cognitive and behavioural features. Furthermore, we investigated the relationship with affective and clinical variables, in addition to ECAS usability and patients' insight into cognitive/behaviour changes. Finally, correlations between genetic and cognitive/behavioural data were analysed. We recruited 107 patients with ALS. Normative data were collected on 248 healthy subjects. Participants were administered the ECAS and two standard cognitive screening tools (FAB, MoCA), two psychological questionnaires (BDI, STAI/Y) and an ad hoc usability questionnaire. The FBI was also carried out with caregivers. Results showed that the ECAS Italian version discriminated well between patients and controls. The most prevalent deficit occurred in executive functions and fluency. Correlations were observed between the ECAS and standard cognitive screening tools and between the ECAS carer interview and the FBI, supporting its full convergent validity. In conclusion, the ECAS Italian version provides clinicians with a rapid, feasible and sensitive tool, useful to identify different profiles of cognitive-behavioural impairment in ALS.
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Affiliation(s)
- Barbara Poletti
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy
| | - Federica Solca
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy
| | - Laura Carelli
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy
| | - Fabiana Madotto
- b Research Centre on Public Health, Department of Medicine and Surgery , University of Milano-Bicocca , Milan , Italy
| | - Annalisa Lafronza
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy
| | - Andrea Faini
- c Department of Cardiovascular, Neural and Metabolic Sciences - IRCCS Istituto Auxologico Italiano , Milan , Italy
| | - Alessia Monti
- d Department of Neurorehabilitation Sciences , Casa Cura Policlinico , Milan , Italy
| | - Stefano Zago
- e Department of Neuroscience and Mental Health , Università degli Studi di Milano, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Daniela Calini
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy
| | - Cinzia Tiloca
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy
| | - Alberto Doretti
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy.,f Department of Pathophysiology and Transplantation , 'Dino Ferrari' Centre, Università degli Studi di Milano , Milan , Italy , and
| | - Federico Verde
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy.,f Department of Pathophysiology and Transplantation , 'Dino Ferrari' Centre, Università degli Studi di Milano , Milan , Italy , and
| | - Antonia Ratti
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy.,f Department of Pathophysiology and Transplantation , 'Dino Ferrari' Centre, Università degli Studi di Milano , Milan , Italy , and
| | - Nicola Ticozzi
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy.,f Department of Pathophysiology and Transplantation , 'Dino Ferrari' Centre, Università degli Studi di Milano , Milan , Italy , and
| | - Sharon Abrahams
- g Euan MacDonald Centre for Motor Neurone Disease Research, Anne Rowling Regenerate Neurology Clinic, Centre for Cognitive Ageing and Cognitive Epidemiology, Human Cognitive Neuroscience-PPLS, University of Edinburgh , Edinburgh , UK
| | - Vincenzo Silani
- a Department of Neurology and Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano , Milan , Italy.,f Department of Pathophysiology and Transplantation , 'Dino Ferrari' Centre, Università degli Studi di Milano , Milan , Italy , and
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13
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Pensato V, Tiloca C, Corrado L, Bertolin C, Sardone V, Del Bo R, Calini D, Mandrioli J, Lauria G, Mazzini L, Querin G, Ceroni M, Cantello R, Corti S, Castellotti B, Soldà G, Duga S, Comi GP, Cereda C, Sorarù G, D'Alfonso S, Taroni F, Shaw CE, Landers JE, Ticozzi N, Ratti A, Gellera C, Silani V. TUBA4A gene analysis in sporadic amyotrophic lateral sclerosis: identification of novel mutations. J Neurol 2015; 262:1376-8. [PMID: 25893256 DOI: 10.1007/s00415-015-7739-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Viviana Pensato
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Via Celoria 11, 20133, Milan, Italy
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14
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Smith BN, Ticozzi N, Fallini C, Gkazi AS, Topp S, Kenna KP, Scotter EL, Kost J, Keagle P, Miller JW, Calini D, Vance C, Danielson EW, Troakes C, Tiloca C, Al-Sarraj S, Lewis EA, King A, Colombrita C, Pensato V, Castellotti B, de Belleroche J, Baas F, ten Asbroek ALMA, Sapp PC, McKenna-Yasek D, McLaughlin RL, Polak M, Asress S, Esteban-Pérez J, Muñoz-Blanco JL, Simpson M, van Rheenen W, Diekstra FP, Lauria G, Duga S, Corti S, Cereda C, Corrado L, Sorarù G, Morrison KE, Williams KL, Nicholson GA, Blair IP, Dion PA, Leblond CS, Rouleau GA, Hardiman O, Veldink JH, van den Berg LH, Al-Chalabi A, Pall H, Shaw PJ, Turner MR, Talbot K, Taroni F, García-Redondo A, Wu Z, Glass JD, Gellera C, Ratti A, Brown RH, Silani V, Shaw CE, Landers JE. Exome-wide rare variant analysis identifies TUBA4A mutations associated with familial ALS. Neuron 2014; 84:324-31. [PMID: 25374358 DOI: 10.1016/j.neuron.2014.09.027] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2014] [Indexed: 12/11/2022]
Abstract
Exome sequencing is an effective strategy for identifying human disease genes. However, this methodology is difficult in late-onset diseases where limited availability of DNA from informative family members prohibits comprehensive segregation analysis. To overcome this limitation, we performed an exome-wide rare variant burden analysis of 363 index cases with familial ALS (FALS). The results revealed an excess of patient variants within TUBA4A, the gene encoding the Tubulin, Alpha 4A protein. Analysis of a further 272 FALS cases and 5,510 internal controls confirmed the overrepresentation as statistically significant and replicable. Functional analyses revealed that TUBA4A mutants destabilize the microtubule network, diminishing its repolymerization capability. These results further emphasize the role of cytoskeletal defects in ALS and demonstrate the power of gene-based rare variant analyses in situations where causal genes cannot be identified through traditional segregation analysis.
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Affiliation(s)
- Bradley N Smith
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Athina Soragia Gkazi
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Simon Topp
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Kevin P Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Emma L Scotter
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Jason Kost
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Pamela Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jack W Miller
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Caroline Vance
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Eric W Danielson
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Claire Troakes
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy
| | - Safa Al-Sarraj
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Elizabeth A Lewis
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew King
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Claudia Colombrita
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Viviana Pensato
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Barbara Castellotti
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Jacqueline de Belleroche
- Neurogenetics Group, Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK
| | - Frank Baas
- Department of Genome analysis and Neurogenetics, Academic Medical Centre, Amsterdam, The Netherlands
| | | | - Peter C Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Russell L McLaughlin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Seneshaw Asress
- Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Jesús Esteban-Pérez
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), 28041 Madrid, Spain
| | - José Luis Muñoz-Blanco
- Unidad de ELA, Instituto de Investigación Hospital Gregorio Marañón de Madrid, SERMAS, 28007 Madrid, Spain
| | - Michael Simpson
- Department of Genetics and Molecular Medicine, King's College London, Tower Wing, Guy's Hospital, London, SE1 7EH, UK
| | | | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Frank P Diekstra
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Giuseppe Lauria
- 3rd Neurology Unit, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Stefano Duga
- Department of Medical Biotechnology and Translational Medicine - Università degli Studi di Milano, 20133 Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy; Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Cristina Cereda
- Experimental Neurobiology Laboratory, IRCCS 'C. Mondino' National Neurological Institute, 27100 Pavia, Italy
| | - Lucia Corrado
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), "A. Avogadro" University, 28100 Novara, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, 35122 Padova, Italy
| | - Karen E Morrison
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2WB, UK
| | - Kelly L Williams
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia; Northcott Neuroscience Laboratory, University of Sydney, ANZAC Research Institute, Sydney, NSW 2139, Australia
| | - Ian P Blair
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Patrick A Dion
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 Montreal, QC H3A 2B4, Canada
| | - Claire S Leblond
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 Montreal, QC H3A 2B4, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 Montreal, QC H3A 2B4, Canada
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Ammar Al-Chalabi
- Department of Clinical Neuroscience, Medical Research Council Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, WC2R 2LS, UK
| | - Hardev Pall
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), 28041 Madrid, Spain
| | - Zheyang Wu
- Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Christopher E Shaw
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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15
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Akimoto C, Volk AE, van Blitterswijk M, Van den Broeck M, Leblond CS, Lumbroso S, Camu W, Neitzel B, Onodera O, van Rheenen W, Pinto S, Weber M, Smith B, Proven M, Talbot K, Keagle P, Chesi A, Ratti A, van der Zee J, Alstermark H, Birve A, Calini D, Nordin A, Tradowsky DC, Just W, Daoud H, Angerbauer S, DeJesus-Hernandez M, Konno T, Lloyd-Jani A, de Carvalho M, Mouzat K, Landers JE, Veldink JH, Silani V, Gitler AD, Shaw CE, Rouleau GA, van den Berg LH, Van Broeckhoven C, Rademakers R, Andersen PM, Kubisch C. A blinded international study on the reliability of genetic testing for GGGGCC-repeat expansions in C9orf72 reveals marked differences in results among 14 laboratories. J Med Genet 2014; 51:419-24. [PMID: 24706941 PMCID: PMC4033024 DOI: 10.1136/jmedgenet-2014-102360] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background The GGGGCC-repeat expansion in C9orf72 is the most frequent mutation found in patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Most of the studies on C9orf72 have relied on repeat-primed PCR (RP-PCR) methods for detection of the expansions. To investigate the inherent limitations of this technique, we compared methods and results of 14 laboratories. Methods The 14 laboratories genotyped DNA from 78 individuals (diagnosed with ALS or FTD) in a blinded fashion. Eleven laboratories used a combination of amplicon-length analysis and RP-PCR, whereas three laboratories used RP-PCR alone; Southern blotting techniques were used as a reference. Results Using PCR-based techniques, 5 of the 14 laboratories got results in full accordance with the Southern blotting results. Only 50 of the 78 DNA samples got the same genotype result in all 14 laboratories. There was a high degree of false positive and false negative results, and at least one sample could not be genotyped at all in 9 of the 14 laboratories. The mean sensitivity of a combination of amplicon-length analysis and RP-PCR was 95.0% (73.9–100%), and the mean specificity was 98.0% (87.5–100%). Overall, a sensitivity and specificity of more than 95% was observed in only seven laboratories. Conclusions Because of the wide range seen in genotyping results, we recommend using a combination of amplicon-length analysis and RP-PCR as a minimum in a research setting. We propose that Southern blotting techniques should be the gold standard, and be made obligatory in a clinical diagnostic setting.
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Affiliation(s)
- Chizuru Akimoto
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | | | | | - Marleen Van den Broeck
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, University of Antwerp-CDE, Antwerp, Belgium Diagnostic Service Facility, Laboratory of neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Claire S Leblond
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Serge Lumbroso
- Department of Biochemistry, Nimes University Hospital, Nimes Cedex 9, France
| | - William Camu
- Center SLA, Montpellier University Hospital, Hôpital Gui-de-Chauliac, Montpellier Cedex 5, France
| | | | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susana Pinto
- Faculty of Medicine-University of Lisbon, Instituto de Medicina Molecular, Hospital de Santa Maria, University of Lisbon, Alameda Universidade, Lisbon, Portugal
| | - Markus Weber
- Department of neurology, Kantonsspital St. Gallen and University Hospital, St. Gallen, Switzerland
| | - Bradley Smith
- Institute of Psychiatry, King's College London and King's Health Partners, London, UK
| | - Melanie Proven
- Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford, England
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe hospital, Oxford, UK
| | - Pamela Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Alessandra Chesi
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Antonia Ratti
- Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Universtà degli Studi di Milano, Milan, Italy Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, , Milan, Italy
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, University of Antwerp-CDE, Antwerp, Belgium Diagnostic Service Facility, Laboratory of neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Helena Alstermark
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | - Anna Birve
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | - Daniela Calini
- Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Universtà degli Studi di Milano, Milan, Italy Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, , Milan, Italy
| | - Angelica Nordin
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | | | - Walter Just
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Hussein Daoud
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | | | | | - Takuya Konno
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Anjali Lloyd-Jani
- Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford, England
| | - Mamede de Carvalho
- Faculty of Medicine-University of Lisbon, Instituto de Medicina Molecular, Hospital de Santa Maria, University of Lisbon, Alameda Universidade, Lisbon, Portugal
| | - Kevin Mouzat
- Department of Biochemistry, Nimes University Hospital, Nimes Cedex 9, France
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vincenzo Silani
- Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Universtà degli Studi di Milano, Milan, Italy Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, , Milan, Italy
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Christopher E Shaw
- Institute of Psychiatry, King's College London and King's Health Partners, London, UK
| | - Guy A Rouleau
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, University of Antwerp-CDE, Antwerp, Belgium Diagnostic Service Facility, Laboratory of neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Rosa Rademakers
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden Institute of Human Genetics, Ulm University, Ulm, Germany Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, University of Antwerp-CDE, Antwerp, Belgium Diagnostic Service Facility, Laboratory of neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada Department of Biochemistry, Nimes University Hospital, Nimes Cedex 9, France Center SLA, Montpellier University Hospital, Hôpital Gui-de-Chauliac, Montpellier Cedex 5, France Medizinisch Genetisches Zentrum, München, Germany Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands Faculty of Medicine-University of Lisbon, Instituto de Medicina Molecular, Hospital de Santa Maria, University of Lisbon, Alameda Universidade, Lisbon, Portugal Department of neurology, Kantonsspital St. Gallen and University Hospital, St. Gallen, Switzerland Institute of Psychiatry, King's College London and King's Health Partners, London, UK Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford, England Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe hospital, Oxford, UK Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA Department of Genetics, Stanford University School of Medicine, Stanford, California, USA Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Universtà degli Studi di Milano, Milan, Italy Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, , Milan, Italy Department of Neurology, University of Ulm
| | - Peter M Andersen
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden Department of Neurology, University of Ulm, Ulm, Germany
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16
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Fogh I, Ratti A, Gellera C, Lin K, Tiloca C, Moskvina V, Corrado L, Sorarù G, Cereda C, Corti S, Gentilini D, Calini D, Castellotti B, Mazzini L, Querin G, Gagliardi S, Del Bo R, Conforti FL, Siciliano G, Inghilleri M, Saccà F, Bongioanni P, Penco S, Corbo M, Sorbi S, Filosto M, Ferlini A, Di Blasio AM, Signorini S, Shatunov A, Jones A, Shaw PJ, Morrison KE, Farmer AE, Van Damme P, Robberecht W, Chiò A, Traynor BJ, Sendtner M, Melki J, Meininger V, Hardiman O, Andersen PM, Leigh NP, Glass JD, Overste D, Diekstra FP, Veldink JH, van Es MA, Shaw CE, Weale ME, Lewis CM, Williams J, Brown RH, Landers JE, Ticozzi N, Ceroni M, Pegoraro E, Comi GP, D'Alfonso S, van den Berg LH, Taroni F, Al-Chalabi A, Powell J, Silani V. A genome-wide association meta-analysis identifies a novel locus at 17q11.2 associated with sporadic amyotrophic lateral sclerosis. Hum Mol Genet 2013; 23:2220-31. [PMID: 24256812 DOI: 10.1093/hmg/ddt587] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Identification of mutations at familial loci for amyotrophic lateral sclerosis (ALS) has provided novel insights into the aetiology of this rapidly progressing fatal neurodegenerative disease. However, genome-wide association studies (GWAS) of the more common (∼90%) sporadic form have been less successful with the exception of the replicated locus at 9p21.2. To identify new loci associated with disease susceptibility, we have established the largest association study in ALS to date and undertaken a GWAS meta-analytical study combining 3959 newly genotyped Italian individuals (1982 cases and 1977 controls) collected by SLAGEN (Italian Consortium for the Genetics of ALS) together with samples from Netherlands, USA, UK, Sweden, Belgium, France, Ireland and Italy collected by ALSGEN (the International Consortium on Amyotrophic Lateral Sclerosis Genetics). We analysed a total of 13 225 individuals, 6100 cases and 7125 controls for almost 7 million single-nucleotide polymorphisms (SNPs). We identified a novel locus with genome-wide significance at 17q11.2 (rs34517613 with P = 1.11 × 10(-8); OR 0.82) that was validated when combined with genotype data from a replication cohort (P = 8.62 × 10(-9); OR 0.833) of 4656 individuals. Furthermore, we confirmed the previously reported association at 9p21.2 (rs3849943 with P = 7.69 × 10(-9); OR 1.16). Finally, we estimated the contribution of common variation to heritability of sporadic ALS as ∼12% using a linear mixed model accounting for all SNPs. Our results provide an insight into the genetic structure of sporadic ALS, confirming that common variation contributes to risk and that sufficiently powered studies can identify novel susceptibility loci.
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17
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Ticozzi N, Tiloca C, Calini D, Gagliardi S, Altieri A, Colombrita C, Cereda C, Ratti A, Pezzoli G, Borroni B, Goldwurm S, Padovani A, Silani V. C9orf72 repeat expansions are restricted to the ALS-FTD spectrum. Neurobiol Aging 2013; 35:936.e13-7. [PMID: 24169076 DOI: 10.1016/j.neurobiolaging.2013.09.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 12/12/2022]
Abstract
Expansion of a GGGGCC repeat (RE) in the C9orf72 gene has been recently reported as the main genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Given the growing evidence of genetic and clinicopathologic overlap among ALS, FTD, and other neurodegenerative diseases, we investigated the occurrence of RE in a subset of 9 patients with ALS-plus syndromes, including Parkinson's disease (PD), progressive supranuclear palsy (PSP), corticobasal syndrome (CBS), and multiple system atrophy. We identified RE in 2 ALS-plus individuals (22.2%) displaying PSP and CBS features. On the basis of this finding, we extended our analysis to a cohort composed of 190 PD, 103 CBS, 107 PSP, and 177 Alzheimer's disease cases. We did not identify any RE in these patients, indicating that C9orf72 is in all probability not involved in the pathogenesis of these disorders. However, the high frequency of C9orf72 RE in patients with ALS-plus syndromes suggests that, similar to ALS-FTD patients, individuals with combined motor neuron and extrapyramidal features should be screened for RE, independent of their family history.
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Affiliation(s)
- Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Auxologico Italiano, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Auxologico Italiano, Milan, Italy; Doctoral School in Molecular Medicine, Department of Sciences and Biomedical Technologies, University of Milan, Milan, Italy
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Auxologico Italiano, Milan, Italy
| | - Stella Gagliardi
- Laboratory of Experimental Neurology, Istituto di Ricovero e Cura a Carattere Scientifico C. Mondino National Neurological Institute, Pavia, Italy
| | - Alessandra Altieri
- Department of Neurology and Laboratory of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Auxologico Italiano, Milan, Italy
| | - Claudia Colombrita
- Department of Neurology and Laboratory of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Auxologico Italiano, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Cristina Cereda
- Laboratory of Experimental Neurology, Istituto di Ricovero e Cura a Carattere Scientifico C. Mondino National Neurological Institute, Pavia, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Auxologico Italiano, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianni Pezzoli
- Parkinson Institute, Istituti Clinici di Perfezionamento, Milan, Italy
| | - Barbara Borroni
- Centre for Neurodegenerative Disorders, University of Brescia, Brescia, Italy
| | - Stefano Goldwurm
- Parkinson Institute, Istituti Clinici di Perfezionamento, Milan, Italy
| | - Alessandro Padovani
- Centre for Neurodegenerative Disorders, University of Brescia, Brescia, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Auxologico Italiano, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
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Calini D, Corrado L, Del Bo R, Gagliardi S, Pensato V, Verde F, Corti S, Mazzini L, Milani P, Castellotti B, Bertolin C, Sorarù G, Cereda C, Comi GP, D'Alfonso S, Gellera C, Ticozzi N, Landers JE, Ratti A, Silani V. Analysis of hnRNPA1, A2/B1, and A3 genes in patients with amyotrophic lateral sclerosis. Neurobiol Aging 2013; 34:2695.e11-2. [PMID: 23827524 DOI: 10.1016/j.neurobiolaging.2013.05.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 05/27/2013] [Indexed: 11/18/2022]
Abstract
Mutations in the prion-like domain (PrLD) of hnRNPA1 and A2/B1 genes were recently identified in 2 families with inclusion body myopathy associated with Paget disease of bone, frontotemporal dementia (FTD), and amyotrophic lateral sclerosis, and in ALS patients. These mutations were shown to increase the propensity of hnRNPA1 and A2/B1 proteins, which are TDP-43-binding partners, to self-aggregate. hnRNPA3 protein contains a similar PrLD and was recently described in the p62-positive/TDP-43-negative inclusions in affected tissues of C9orf72-mutated ALS/FTD patients. We screened hnRNPA1, A2/B1, and A3 genes in a cohort of 113 familial ALS (FALS) individuals without mutations in other known ALS-causative genes. We extended our analysis to 108 FALS with mutations in other ALS-associated genes and to 622 sporadic cases by screening specifically the PrLDs of hnRNPA1, A2/B1, and A3. We failed to find variants in each cohort. Our results suggest that mutations in hnRNPA1, A2/B1, and A3 genes are a rare finding in ALS.
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Affiliation(s)
- Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, 20095 Cusano Milanino, Milan, Italy
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Ratti A, Corrado L, Castellotti B, Del Bo R, Fogh I, Cereda C, Tiloca C, D'Ascenzo C, Bagarotti A, Pensato V, Ranieri M, Gagliardi S, Calini D, Mazzini L, Taroni F, Corti S, Ceroni M, Oggioni GD, Lin K, Powell JF, Sorarù G, Ticozzi N, Comi GP, D'Alfonso S, Gellera C, Silani V. C9ORF72 repeat expansion in a large Italian ALS cohort: evidence of a founder effect. Neurobiol Aging 2012; 33:2528.e7-14. [PMID: 22766072 DOI: 10.1016/j.neurobiolaging.2012.06.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/28/2012] [Accepted: 06/07/2012] [Indexed: 12/12/2022]
Abstract
A hexanucleotide repeat expansion (RE) in C9ORF72 gene was recently reported as the main cause of amyotrophic lateral sclerosis (ALS) and cases with frontotemporal dementia. We screened C9ORF72 in a large cohort of 259 familial ALS, 1275 sporadic ALS, and 862 control individuals of Italian descent. We found RE in 23.9% familial ALS, 5.1% sporadic ALS, and 0.2% controls. Two cases carried the RE together with mutations in other ALS-associated genes. The phenotype of RE carriers was characterized by bulbar-onset, shorter survival, and association with cognitive and behavioral impairment. Extrapyramidal and cerebellar signs were also observed in few patients. Genotype data revealed that 95% of RE carriers shared a restricted 10-single nucleotide polymorphism haplotype within the previously reported 20-single nucleotide polymorphism risk haplotype, detectable in only 27% of nonexpanded ALS cases and in 28% of controls, suggesting a common founder with cohorts of North European ancestry. Although C9ORF72 RE segregates with disease, the identification of RE both in controls and in patients carrying additional pathogenic mutations suggests that penetrance and phenotypic expression of C9ORF72 RE may depend on additional genetic risk factors.
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Affiliation(s)
- Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.
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