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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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2
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Malloy C, Ahern M, Lin L, Hoffman DA. Neuronal Roles of the Multifunctional Protein Dipeptidyl Peptidase-like 6 (DPP6). Int J Mol Sci 2022; 23:ijms23169184. [PMID: 36012450 PMCID: PMC9409431 DOI: 10.3390/ijms23169184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
The concerted action of voltage-gated ion channels in the brain is fundamental in controlling neuronal physiology and circuit function. Ion channels often associate in multi-protein complexes together with auxiliary subunits, which can strongly influence channel expression and function and, therefore, neuronal computation. One such auxiliary subunit that displays prominent expression in multiple brain regions is the Dipeptidyl aminopeptidase-like protein 6 (DPP6). This protein associates with A-type K+ channels to control their cellular distribution and gating properties. Intriguingly, DPP6 has been found to be multifunctional with an additional, independent role in synapse formation and maintenance. Here, we feature the role of DPP6 in regulating neuronal function in the context of its modulation of A-type K+ channels as well as its independent involvement in synaptic development. The prevalence of DPP6 in these processes underscores its importance in brain function, and recent work has identified that its dysfunction is associated with host of neurological disorders. We provide a brief overview of these and discuss research directions currently underway to advance our understanding of the contribution of DPP6 to their etiology.
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3
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Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell 2022; 185:2035-2056.e33. [PMID: 35688132 DOI: 10.1016/j.cell.2022.05.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022]
Abstract
Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that αS directly modulates processing bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N terminus of αS, but not other synucleins, dictates mutually exclusive binding either to cellular membranes or to P-bodies in the cytosol. αS associates with multiple decapping proteins in close proximity on the Edc4 scaffold. As αS pathologically accumulates, aberrant interaction with Edc4 occurs at the expense of physiologic decapping-module interactions. mRNA decay kinetics within PD-relevant pathways are correspondingly disrupted in PD patient neurons and brain. Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, our data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
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Affiliation(s)
- Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sumaiya Nazeen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Xiou H Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zoe Sheinkopf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shubhangi Sathyakumar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Souvarish Sarkar
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xin Jiang
- Yumanity Therapeutics, Boston, MA 02135, USA
| | - Xianjun Dong
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Genomics and Bioinformatics Hub, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew T Keeney
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics and Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON M5T 3M7, Canada
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | | | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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4
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Gu B, Sun R, Fang X, Zhang J, Zhao Z, Huang D, Zhao Y, Zhao Y. Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats. Animals (Basel) 2022; 12:ani12050548. [PMID: 35268118 PMCID: PMC8908837 DOI: 10.3390/ani12050548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Body conformation traits are economically important in the goat meat industry. Good growth performance in goats, including an accelerated growth rate, can improve carcass weight and meat yield. The identification of genetic variants associated with these traits provides a basis for the genetic improvement of growth performance. In this study, we measured six body conformation traits, including body height, body length, cannon circumference, chest depth, chest width, and heart girth. By a genome-wide association study of a Chinese meat goat breed, 53 significant single nucleotide polymorphisms and 42 candidate genes associated with these traits were detected. These findings improve our understanding of the genetic basis of body conformation traits in goats. Abstract Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats.
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Affiliation(s)
- Bowen Gu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Ruifan Sun
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Xingqiang Fang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Deli Huang
- Tengda Animal Husbandry Co., Ltd., Chongqing 402360, China;
| | - Yuanping Zhao
- Dazu County Agriculture and Rural Committee, Chongqing 402360, China;
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
- Correspondence:
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Chen TH, Yang CC, Luo KH, Dai CY, Chuang YC, Chuang HY. The Mediation Effects of Aluminum in Plasma and Dipeptidyl Peptidase Like Protein 6 (DPP6) Polymorphism on Renal Function via Genome-Wide Typing Association. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10484. [PMID: 34639784 PMCID: PMC8507883 DOI: 10.3390/ijerph181910484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/03/2021] [Indexed: 11/30/2022]
Abstract
Aluminum (Al) toxicity is related to renal failure and the failure of other systems. Although there were some genome-wide association studies (GWAS) in Australia and England, there were no GWAS about Han Chinese to our knowledge. Thus, this research focused on using whole genomic genotypes from the Taiwan Biobank for exploring the association between Al concentrations in plasma and renal function. Participants, who underwent questionnaire interviews, biomarkers, and genotyping, were from the Taiwan Biobank database. Then, we measured their plasma Al concentrations with ICP-MS in the laboratory at Kaohsiung Medical University. We used this data to link genome-wide association (GWA) tests while looking for candidate genes and associated plasma Al concentration to renal function. Furthermore, we examined the path relationship between Single Nucleotide Polymorphisms (SNPs), Al concentrations, and estimated glomerular filtration rates (eGFR) through the mediation analysis with 3000 replication bootstraps. Following the principles of GWAS, we focused on three SNPs within the dipeptidyl peptidase-like protein 6 (DPP6) gene in chromosome 7, rs10224371, rs2316242, and rs10268004, respectively. The results of the mediation analysis showed that all of the selected SNPs have indirectly affected eGFR through a mediation of Al concentrations. Our analysis revealed the association between DPP6 SNPs, plasma Al concentrations, and eGFR. However, further longitudinal studies and research on mechanism are in need. Our analysis was still be the first study that explored the association between the DPP6, SNPs, and Al in plasma affecting eGFR.
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Affiliation(s)
- Ting-Hao Chen
- Department of Public Health and Environmental Medicine, Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-H.C.); (K.-H.L.)
| | - Chen-Cheng Yang
- Department of Occupational and Environmental Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; (C.-C.Y.); (C.-Y.D.)
| | - Kuei-Hau Luo
- Department of Public Health and Environmental Medicine, Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-H.C.); (K.-H.L.)
| | - Chia-Yen Dai
- Department of Occupational and Environmental Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; (C.-C.Y.); (C.-Y.D.)
| | - Yao-Chung Chuang
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan;
| | - Hung-Yi Chuang
- Department of Public Health and Environmental Medicine, Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-H.C.); (K.-H.L.)
- Department of Occupational and Environmental Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; (C.-C.Y.); (C.-Y.D.)
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Zhang J, Qiu W, Hu F, Zhang X, Deng Y, Nie H, Xu R. The rs2619566, rs10260404, and rs79609816 Polymorphisms Are Associated With Sporadic Amyotrophic Lateral Sclerosis in Individuals of Han Ancestry From Mainland China. Front Genet 2021; 12:679204. [PMID: 34421992 PMCID: PMC8378233 DOI: 10.3389/fgene.2021.679204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/25/2021] [Indexed: 11/21/2022] Open
Abstract
The pathogenesis of sporadic amyotrophic lateral sclerosis (sALS) remains unknown; however, recent research suggests that genetic factors may play an important role. This study aimed at investigating possible genetic risk factors for the pathogenesis of sALS. In our previous study, we conducted a genome-wide association study (GWAS) in 250 sALS patients and 250 control participants of Han ancestry from mainland China (HACM) and retrospectively analyzed the previously reported candidate loci related with sALS including our GWAS investigated results. In this study, twenty-seven candidate loci that were most likely associated with sALS were selected for further analysis in an independent case/control population of 239 sALS patients and 261 control subjects of HACM ethnicity using sequenom massARRAY methodology and DNA sequencing. We discovered that the polymorphism rs2619566 located within the contactin-4 (CNTN4) gene, rs10260404 in the dipeptidyl-peptidase 6 (DPP6) gene, and rs79609816 in the inositol polyphosphate-5-phosphatase B (INPP5B) gene were strongly associated with sALS in subjects of HACM ethnicity. Subjects harboring the minor C allele of rs2619566 and the minor T allele of rs79609816 exhibited an increased risk for sALS development, while carriers of the minor C allele of rs10260404 showed a decreased risk of sALS development compared to the subjects of other genotypes. The polymorphisms of rs2619566, rs10260404, and rs79609816 may change or affect the splicing, transcription, and translation of CNTN4, DPP6, and INPP5B genes and may play roles in the pathogenesis of sALS roles in the pathogenesis of sALS.
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Affiliation(s)
- Jie Zhang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Weiwen Qiu
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Fan Hu
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Xiong Zhang
- Department of Neurology, Maoming People's Hospital, Maoming, China
| | - Youqing Deng
- Department of Neurology, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongbing Nie
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Renshi Xu
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
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Rich KA, Roggenbuck J, Kolb SJ. Searching Far and Genome-Wide: The Relevance of Association Studies in Amyotrophic Lateral Sclerosis. Front Neurosci 2021; 14:603023. [PMID: 33584177 PMCID: PMC7873947 DOI: 10.3389/fnins.2020.603023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) and rare variant association studies (RVAS) are applied across many areas of complex disease to analyze variation in whole genomes of thousands of unrelated patients. These approaches are able to identify variants and/or biological pathways which are associated with disease status and, in contrast to traditional linkage studies or candidate gene approaches, do so without requiring multigenerational affected families, prior hypotheses, or known genes of interest. However, the novel associations identified by these methods typically have lower effect sizes than those found in classical family studies. In the motor neuron disease amyotrophic lateral sclerosis (ALS), GWAS, and RVAS have been used to identify multiple disease-associated genes but have not yet resulted in novel therapeutic interventions. There is significant urgency within the ALS community to identify additional genetic markers of disease to uncover novel biological mechanisms, stratify genetic subgroups of disease, and drive drug development. Given the widespread and increasing application of genetic association studies of complex disease, it is important to recognize the strengths and limitations of these approaches. Here, we review ALS gene discovery via GWAS and RVAS.
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Affiliation(s)
- Kelly A Rich
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Jennifer Roggenbuck
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Stephen J Kolb
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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8
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Mortezaei Z, Tavallaei M, Hosseini SM. Considering smoking status, coexpression network analysis of non-small cell lung cancer at different cancer stages, exhibits important genes and pathways. J Cell Biochem 2019; 120:19172-19185. [PMID: 31271232 DOI: 10.1002/jcb.29246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/23/2019] [Indexed: 02/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer among smokers, nonsmokers, women, and young individuals. Tobacco smoking and different stages of the NSCLC have important roles in cancer evolution and require different treatments. Existence of poorly effective therapeutic options for the NSCLC brings special attention to targeted therapies by considering genetic alterations. In this study, we used RNA-Seq data to compare expression levels of RefSeq genes and to find some genes with similar expression levels. We utilized the "Weighted Gene Co-expression Network Analysis" method for three different datasets to create coexpressed genetic modules having relations with the smoking status and different stages of the NSCLC. Our results indicate seven important genetic modules having important associations with the smoking status and cancer stages. Based on investigated genetic modules and their biological explanation, we then identified 13 newly candidate genes and 7 novel transcription factors in association with the NSCLC, the smoking status, and cancer stages. We then examined those results using other datasets and explained our results biologically to illustrate some important genes in relation with the smoking status and metastatic stage of the NSCLC that can bring some crucial information about cancer evolution. Our genetic findings also can be used as some therapeutic targets for different clinical conditions of the NSCLC.
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Affiliation(s)
- Zahra Mortezaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahmood Tavallaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sayed Mostafa Hosseini
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Pottier C, Ren Y, Perkerson RB, Baker M, Jenkins GD, van Blitterswijk M, DeJesus-Hernandez M, van Rooij JGJ, Murray ME, Christopher E, McDonnell SK, Fogarty Z, Batzler A, Tian S, Vicente CT, Matchett B, Karydas AM, Hsiung GYR, Seelaar H, Mol MO, Finger EC, Graff C, Öijerstedt L, Neumann M, Heutink P, Synofzik M, Wilke C, Prudlo J, Rizzu P, Simon-Sanchez J, Edbauer D, Roeber S, Diehl-Schmid J, Evers BM, King A, Mesulam MM, Weintraub S, Geula C, Bieniek KF, Petrucelli L, Ahern GL, Reiman EM, Woodruff BK, Caselli RJ, Huey ED, Farlow MR, Grafman J, Mead S, Grinberg LT, Spina S, Grossman M, Irwin DJ, Lee EB, Suh E, Snowden J, Mann D, Ertekin-Taner N, Uitti RJ, Wszolek ZK, Josephs KA, Parisi JE, Knopman DS, Petersen RC, Hodges JR, Piguet O, Geier EG, Yokoyama JS, Rissman RA, Rogaeva E, Keith J, Zinman L, Tartaglia MC, Cairns NJ, Cruchaga C, Ghetti B, Kofler J, Lopez OL, Beach TG, Arzberger T, Herms J, Honig LS, Vonsattel JP, Halliday GM, Kwok JB, White CL, Gearing M, Glass J, Rollinson S, Pickering-Brown S, Rohrer JD, Trojanowski JQ, Van Deerlin V, Bigio EH, Troakes C, Al-Sarraj S, Asmann Y, Miller BL, Graff-Radford NR, Boeve BF, Seeley WW, Mackenzie IRA, van Swieten JC, Dickson DW, Biernacka JM, Rademakers R. Genome-wide analyses as part of the international FTLD-TDP whole-genome sequencing consortium reveals novel disease risk factors and increases support for immune dysfunction in FTLD. Acta Neuropathol 2019; 137:879-899. [PMID: 30739198 PMCID: PMC6533145 DOI: 10.1007/s00401-019-01962-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/12/2022]
Abstract
Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) represents the most common pathological subtype of FTLD. We established the international FTLD-TDP whole-genome sequencing consortium to thoroughly characterize the known genetic causes of FTLD-TDP and identify novel genetic risk factors. Through the study of 1131 unrelated Caucasian patients, we estimated that C9orf72 repeat expansions and GRN loss-of-function mutations account for 25.5% and 13.9% of FTLD-TDP patients, respectively. Mutations in TBK1 (1.5%) and other known FTLD genes (1.4%) were rare, and the disease in 57.7% of FTLD-TDP patients was unexplained by the known FTLD genes. To unravel the contribution of common genetic factors to the FTLD-TDP etiology in these patients, we conducted a two-stage association study comprising the analysis of whole-genome sequencing data from 517 FTLD-TDP patients and 838 controls, followed by targeted genotyping of the most associated genomic loci in 119 additional FTLD-TDP patients and 1653 controls. We identified three genome-wide significant FTLD-TDP risk loci: one new locus at chromosome 7q36 within the DPP6 gene led by rs118113626 (p value = 4.82e - 08, OR = 2.12), and two known loci: UNC13A, led by rs1297319 (p value = 1.27e - 08, OR = 1.50) and HLA-DQA2 led by rs17219281 (p value = 3.22e - 08, OR = 1.98). While HLA represents a locus previously implicated in clinical FTLD and related neurodegenerative disorders, the association signal in our study is independent from previously reported associations. Through inspection of our whole-genome sequence data for genes with an excess of rare loss-of-function variants in FTLD-TDP patients (n ≥ 3) as compared to controls (n = 0), we further discovered a possible role for genes functioning within the TBK1-related immune pathway (e.g., DHX58, TRIM21, IRF7) in the genetic etiology of FTLD-TDP. Together, our study based on the largest cohort of unrelated FTLD-TDP patients assembled to date provides a comprehensive view of the genetic landscape of FTLD-TDP, nominates novel FTLD-TDP risk loci, and strongly implicates the immune pathway in FTLD-TDP pathogenesis.
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Affiliation(s)
- Cyril Pottier
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Yingxue Ren
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Ralph B Perkerson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Matt Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Gregory D Jenkins
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | | | - Jeroen G J van Rooij
- Department of Neurology, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Elizabeth Christopher
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | | | - Zachary Fogarty
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Anthony Batzler
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Cristina T Vicente
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Billie Matchett
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Anna M Karydas
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Ging-Yuek Robin Hsiung
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Harro Seelaar
- Department of Neurology, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Merel O Mol
- Department of Neurology, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Elizabeth C Finger
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 2E2, Canada
| | - Caroline Graff
- Division of Neurogeriatrics, Department NVS, Karolinska Institutet, Visionsgatan 4, J10:20, 171 64, Solna, Sweden
- Theme Aging, Unit for Hereditary Dementias, Karolinska University Hospital, Solna, Sweden
| | - Linn Öijerstedt
- Division of Neurogeriatrics, Department NVS, Karolinska Institutet, Visionsgatan 4, J10:20, 171 64, Solna, Sweden
- Theme Aging, Unit for Hereditary Dementias, Karolinska University Hospital, Solna, Sweden
| | - Manuela Neumann
- German Center for Neurodegenerative Diseases (DZNE), 18147, Rostock, Germany
- Department of Neuropathology, University of Tübingen, 72076, Tübingen, Germany
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), 18147, Rostock, Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076, Tübingen, Germany
| | - Matthis Synofzik
- German Center for Neurodegenerative Diseases (DZNE), 18147, Rostock, Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076, Tübingen, Germany
| | - Carlo Wilke
- German Center for Neurodegenerative Diseases (DZNE), 18147, Rostock, Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076, Tübingen, Germany
| | - Johannes Prudlo
- German Center for Neurodegenerative Diseases (DZNE), 18147, Rostock, Germany
- Department of Neurology, Rostock University Medical Center, 18147, Rostock, Germany
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), 18147, Rostock, Germany
| | - Javier Simon-Sanchez
- German Center for Neurodegenerative Diseases (DZNE), 18147, Rostock, Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076, Tübingen, Germany
| | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Str 17, 81377, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str 17, 81377, Munich, Germany
| | - Sigrun Roeber
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Straße 23, 81377, Munich, Germany
| | - Janine Diehl-Schmid
- Department of Psychiatry and Psychotherapy, Technische Universität München, Munich, Germany
| | - Bret M Evers
- Division of Neuropathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-9073, USA
| | - Andrew King
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
- Department of Clinical Neuropathology, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - M Marsel Mesulam
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Chicago, IL, 60611, USA
| | - Sandra Weintraub
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Chicago, IL, 60611, USA
- Department of Psychiatry and Behavioral Sciences and Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Chicago, IL, 60611, USA
| | - Kevin F Bieniek
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center San Antonio, San Antonio, TX, 78229, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Geoffrey L Ahern
- Department of Neurology, University of Arizona Health Sciences Center, 1501 North Campbell Avenue, Tucson, AZ, 85724-5023, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute, Phoenix, AZ, 85006, USA
| | - Bryan K Woodruff
- Department of Neurology, Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA
| | - Richard J Caselli
- Department of Neurology, Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA
| | - Edward D Huey
- Departments of Psychiatry and Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, 630 West 168th St P&S Box 16, New York, NY, 10032, USA
| | - Martin R Farlow
- Indiana University School of Medicine, 355 West 16th Street, GH 4700 Neurology, Indianapolis, IN, 46202, USA
| | - Jordan Grafman
- Department of Physical Medicine and Rehabilitation, Neurology, Cognitive Neurology and Alzheimer's Center, Department of Psychiatry, Feinberg School of Medicine, Northwestern University, 355 E Erie Street, Chicago, IL, 60611-5146, USA
| | - Simon Mead
- MRC Prion Unit at University College London, Institute of Prion Diseases, London, UK
| | - Lea T Grinberg
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Department of Pathology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Salvatore Spina
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Murray Grossman
- Penn Frontotemporal Degeneration Center, Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David J Irwin
- Penn Frontotemporal Degeneration Center, Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - EunRan Suh
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Julie Snowden
- Cerebral Function Unit, Greater Manchester Neurosciences Centre, Salford Royal Hospital, Salford, UK
| | - David Mann
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Salford Royal Hospital, Salford, UK
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Ryan J Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | | | - John R Hodges
- Central Clinical School and Brain and Mind Centre, The University of Sydney, Sydney, 2050, Australia
| | - Olivier Piguet
- School of Psychology and Brain and Mind Centre, The University of Sydney, Sydney, 2050, Australia
| | - Ethan G Geier
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Jennifer S Yokoyama
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Robert A Rissman
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, 92161, USA
| | - Ekaterina Rogaeva
- Krembil Discovery Tower, Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, 60 Leonard Av, 4th Floor - 4KD481, Toronto, ON, M5T 0S8, Canada
| | - Julia Keith
- Sunnybrook Health Sciences Centre, Toronto, ON, M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Lorne Zinman
- Sunnybrook Health Sciences Centre, Toronto, ON, M4N 3M5, Canada
| | - Maria Carmela Tartaglia
- Krembil Discovery Tower, Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, 60 Leonard Av, 4th Floor - 4KD481, Toronto, ON, M5T 0S8, Canada
- Krembil Neuroscience Center, Movement Disorder's Clinic, Toronto Western Hospital, 399 Bathurst Street, Toronto, ON, M5T 2S8, Canada
| | - Nigel J Cairns
- Department of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, Saint Louis, MO, 63108, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Knight Alzheimer Disease Research Center, Washington University School of Medicine, Saint Louis, MO, 63108, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 635 Barnhill Drive, MS A138, Indianapolis, IN, 46202, USA
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Oscar L Lopez
- Department of Neurology, University of Arizona Health Sciences Center, 1501 North Campbell Avenue, Tucson, AZ, 85724-5023, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas Arzberger
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Str 17, 81377, Munich, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Straße 23, 81377, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University of Munich, Nussbaumstraße 7, 80336, Munich, Germany
| | - Jochen Herms
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Str 17, 81377, Munich, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Straße 23, 81377, Munich, Germany
| | - Lawrence S Honig
- Department of Neurology, Taub Institute, and GH Sergievsky Center, Columbia University Irving Medical Center, 630 West 168th St (P&S Unit 16), New York, NY, 10032, USA
| | - Jean Paul Vonsattel
- Department of Pathology and Taub Institute, Columbia University Irving Medical Center, 630 West 168th St, New York, NY, 10032, USA
| | - Glenda M Halliday
- Central Clinical School and Brain and Mind Centre, The University of Sydney, Sydney, 2050, Australia
- UNSW Medicine and NeuRA, Randwick, 2031, Australia
| | - John B Kwok
- Central Clinical School and Brain and Mind Centre, The University of Sydney, Sydney, 2050, Australia
- UNSW Medicine and NeuRA, Randwick, 2031, Australia
| | - Charles L White
- Division of Neuropathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-9073, USA
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine and Department of Neurology, Emory University, Atlanta, GA, 30322, USA
| | - Jonathan Glass
- Department of Pathology and Laboratory Medicine and Department of Neurology, Emory University, Atlanta, GA, 30322, USA
| | - Sara Rollinson
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Stuart Pickering-Brown
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jonathan D Rohrer
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vivianna Van Deerlin
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eileen H Bigio
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Chicago, IL, 60611, USA
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Safa Al-Sarraj
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
- Department of Clinical Neuropathology, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Yan Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Bruce L Miller
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | | | | | - William W Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Department of Pathology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Ian R A Mackenzie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - John C van Swieten
- Department of Neurology, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
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Pathophysiological consequences of isoform-specific IP 3 receptor mutations. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1707-1717. [PMID: 29906486 DOI: 10.1016/j.bbamcr.2018.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/06/2018] [Accepted: 06/11/2018] [Indexed: 12/11/2022]
Abstract
Ca2+ signaling governs a diverse range of cellular processes and, as such, is subject to tight regulation. A main component of the complex intracellular Ca2+-signaling network is the inositol 1,4,5-trisphosphate (IP3) receptor (IP3R), a tetrameric channel that mediates Ca2+ release from the endoplasmic reticulum (ER) in response to IP3. IP3R function is controlled by a myriad of factors, such as Ca2+, ATP, kinases and phosphatases and a plethora of accessory and regulatory proteins. Further complexity in IP3R-mediated Ca2+ signaling is the result of the existence of three main isoforms (IP3R1, IP3R2 and IP3R3) that display distinct functional characteristics and properties. Despite their abundant and overlapping expression profiles, IP3R1 is highly expressed in neurons, IP3R2 in cardiomyocytes and hepatocytes and IP3R3 in rapidly proliferating cells as e.g. epithelial cells. As a consequence, dysfunction and/or dysregulation of IP3R isoforms will have distinct pathophysiological outcomes, ranging from neurological disorders for IP3R1 to dysfunctional exocrine tissues and autoimmune diseases for IP3R2 and -3. Over the past years, several IP3R mutations have surfaced in the sequence analysis of patient-derived samples. Here, we aimed to provide an integrative overview of the clinically most relevant mutations for each IP3R isoform and the subsequent molecular mechanisms underlying the etiology of the disease.
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Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating, uniformly lethal degenerative disorder of motor neurons that overlaps clinically with frontotemporal dementia (FTD). Investigations of the 10% of ALS cases that are transmitted as dominant traits have revealed numerous gene mutations and variants that either cause these disorders or influence their clinical phenotype. The evolving understanding of the genetic architecture of ALS has illuminated broad themes in the molecular pathophysiology of both familial and sporadic ALS and FTD. These central themes encompass disturbances of protein homeostasis, alterations in the biology of RNA binding proteins, and defects in cytoskeletal dynamics, as well as numerous downstream pathophysiological events. Together, these findings from ALS genetics provide new insight into therapies that target genetically distinct subsets of ALS and FTD.
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Affiliation(s)
- Mehdi Ghasemi
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
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Klemann C, Visser J, Van Den Bosch L, Martens G, Poelmans G. Integrated molecular landscape of amyotrophic lateral sclerosis provides insights into disease etiology. Brain Pathol 2018; 28:203-211. [PMID: 28035716 PMCID: PMC8028446 DOI: 10.1111/bpa.12485] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe, progressive and ultimately fatal motor neuron disease caused by a combination of genetic and environmental factors, but its underlying mechanisms are largely unknown. To gain insight into the etiology of ALS, we here conducted genetic network and literature analyses of the top-ranked findings from six genome-wide association studies of sporadic ALS (involving 3589 cases and 8577 controls) as well as genes implicated in ALS etiology through other evidence, including familial ALS candidate gene association studies. We integrated these findings into a molecular landscape of ALS that allowed the identification of three main processes that interact with each other and are crucial to maintain axonal functionality, especially of the long axons of motor neurons, i.e. (1) Rho-GTPase signaling; (2) signaling involving the three regulatory molecules estradiol, folate, and methionine; and (3) ribonucleoprotein granule functioning and axonal transport. Interestingly, estradiol signaling is functionally involved in all three cascades and as such an important mediator of the molecular ALS landscape. Furthermore, epidemiological findings together with an analysis of possible gender effects in our own cohort of sporadic ALS patients indicated that estradiol may be a protective factor, especially for bulbar-onset ALS. Taken together, our molecular landscape of ALS suggests that abnormalities within three interconnected molecular processes involved in the functioning and maintenance of motor neuron axons are important in the etiology of ALS. Moreover, estradiol appears to be an important modulator of the ALS landscape, providing important clues for the development of novel disease-modifying treatments.
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Affiliation(s)
- C.J.H.M. Klemann
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
| | - J.E. Visser
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
- Department of NeurologyDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
- Department of NeurologyAmphia HospitalBredaThe Netherlands
| | - L. Van Den Bosch
- Department of NeurosciencesLaboratory of Neurobiology, Experimental Neurology, KU Leuven and VIB, Vesalius Research CenterLeuvenBelgium
| | - G.J.M. Martens
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
| | - G. Poelmans
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
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van Es MA, Hardiman O, Chio A, Al-Chalabi A, Pasterkamp RJ, Veldink JH, van den Berg LH. Amyotrophic lateral sclerosis. Lancet 2017; 390:2084-2098. [PMID: 28552366 DOI: 10.1016/s0140-6736(17)31287-4] [Citation(s) in RCA: 794] [Impact Index Per Article: 113.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 03/13/2017] [Accepted: 03/20/2017] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis is characterised by the progressive loss of motor neurons in the brain and spinal cord. This neurodegenerative syndrome shares pathobiological features with frontotemporal dementia and, indeed, many patients show features of both diseases. Many different genes and pathophysiological processes contribute to the disease, and it will be necessary to understand this heterogeneity to find effective treatments. In this Seminar, we discuss clinical and diagnostic approaches as well as scientific advances in the research fields of genetics, disease modelling, biomarkers, and therapeutic strategies.
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Affiliation(s)
- Michael A van Es
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Ireland; Department of Neurology, Beaumont Hospital, Beaumont, Ireland
| | - Adriano Chio
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy; Azienda Ospedaliero Universitaria Citta della Salute e della Scienza di Torino, Turin, Italy; Neuroscience Institute of Turin, Turin, Italy
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; NIHR Dementia Biomedical Research Unit, King's College London, London, UK
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands.
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14
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Calvo A, Moglia C, Canosa A, Cammarosano S, Ilardi A, Bertuzzo D, Traynor BJ, Brunetti M, Barberis M, Mora G, Casale F, Chiò A. Common polymorphisms of chemokine (C-X3-C motif) receptor 1 gene modify amyotrophic lateral sclerosis outcome: A population-based study. Muscle Nerve 2017; 57:212-216. [PMID: 28342179 DOI: 10.1002/mus.25653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 03/05/2017] [Accepted: 03/20/2017] [Indexed: 12/15/2022]
Abstract
INTRODUCTION In the brain, the chemokine (C-X3-C motif) receptor 1 (1CX3CR1) gene is expressed only by microglia, where it acts as a key mediator of the neuron-microglia interactions. We assessed whether the 2 common polymorphisms of the CX3CR1 gene (V249I and T280M) modify amyotrophic lateral sclerosis (ALS) phenotype. METHODS The study included 755 ALS patients diagnosed in Piemonte between 2007 and 2012 and 369 age-matched and sex-matched controls, all genotyped with the same chips. RESULTS Neither of the variants was associated with an increased risk of ALS. Patients with the V249I V/V genotype had a 6-month-shorter survival than those with I/I or V/I genotypes (dominant model, P = 0.018). The T280M genotype showed a significant difference among the 3 genotypes (additive model, P = 0.036). Cox multivariable analysis confirmed these findings. DISCUSSION We found that common variants of the CX3CR1 gene influence ALS survival. Our data provide further evidence for the role of neuroinflammation in ALS. Muscle Nerve 57: 212-216, 2018.
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Affiliation(s)
- Andrea Calvo
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, Torino, Italy
| | - Cristina Moglia
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, Torino, Italy
| | - Antonio Canosa
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy
| | - Stefania Cammarosano
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy
| | - Antonio Ilardi
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy
| | - Davide Bertuzzo
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Maura Brunetti
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy
| | - Marco Barberis
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy
| | - Gabriele Mora
- Salvatore Maugeri Foundation, IRCSS, Scientific Institute of Milano, Milano, Italy
| | - Federico Casale
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy
| | - Adriano Chiò
- "Rita Levi Montalcini" Department of Neuroscience, Neurology II, ALS Center, University of Torino, Via Cherasco 15, I-10126, Torino, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, Torino, Italy.,Institute of Cognitive Sciences and Technologies, National Council of Researches, Rome, Italy
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15
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Singh C, Glaab E, Linster CL. Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. J Biol Chem 2016; 292:1005-1028. [PMID: 27909055 DOI: 10.1074/jbc.m116.760744] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
Proteomes of even well characterized organisms still contain a high percentage of proteins with unknown or uncertain molecular and/or biological function. A significant fraction of those proteins is predicted to have catalytic properties. Here we aimed at identifying the function of the Saccharomyces cerevisiae Ydr109c protein and its human homolog FGGY, both of which belong to the broadly conserved FGGY family of carbohydrate kinases. Functionally identified members of this family phosphorylate 3- to 7-carbon sugars or sugar derivatives, but the endogenous substrate of S. cerevisiae Ydr109c and human FGGY has remained unknown. Untargeted metabolomics analysis of an S. cerevisiae deletion mutant of YDR109C revealed ribulose as one of the metabolites with the most significantly changed intracellular concentration as compared with a wild-type strain. In human HEK293 cells, ribulose could only be detected when ribitol was added to the cultivation medium, and under this condition, FGGY silencing led to ribulose accumulation. Biochemical characterization of the recombinant purified Ydr109c and FGGY proteins showed a clear substrate preference of both kinases for d-ribulose over a range of other sugars and sugar derivatives tested, including l-ribulose. Detailed sequence and structural analyses of Ydr109c and FGGY as well as homologs thereof furthermore allowed the definition of a 5-residue d-ribulokinase signature motif (TCSLV). The physiological role of the herein identified eukaryotic d-ribulokinase remains unclear, but we speculate that S. cerevisiae Ydr109c and human FGGY could act as metabolite repair enzymes, serving to re-phosphorylate free d-ribulose generated by promiscuous phosphatases from d-ribulose 5-phosphate. In human cells, FGGY can additionally participate in ribitol metabolism.
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Affiliation(s)
- Charandeep Singh
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
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16
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Sailer A, Scholz SW, Nalls MA, Schulte C, Federoff M, Price TR, Lees A, Ross OA, Dickson DW, Mok K, Mencacci NE, Schottlaender L, Chelban V, Ling H, O'Sullivan SS, Wood NW, Traynor BJ, Ferrucci L, Federoff HJ, Mhyre TR, Morris HR, Deuschl G, Quinn N, Widner H, Albanese A, Infante J, Bhatia KP, Poewe W, Oertel W, Höglinger GU, Wüllner U, Goldwurm S, Pellecchia MT, Ferreira J, Tolosa E, Bloem BR, Rascol O, Meissner WG, Hardy JA, Revesz T, Holton JL, Gasser T, Wenning GK, Singleton AB, Houlden H. A genome-wide association study in multiple system atrophy. Neurology 2016; 87:1591-1598. [PMID: 27629089 PMCID: PMC5067544 DOI: 10.1212/wnl.0000000000003221] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 06/15/2016] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To identify genetic variants that play a role in the pathogenesis of multiple system atrophy (MSA), we undertook a genome-wide association study (GWAS). METHODS We performed a GWAS with >5 million genotyped and imputed single nucleotide polymorphisms (SNPs) in 918 patients with MSA of European ancestry and 3,864 controls. MSA cases were collected from North American and European centers, one third of which were neuropathologically confirmed. RESULTS We found no significant loci after stringent multiple testing correction. A number of regions emerged as potentially interesting for follow-up at p < 1 × 10-6, including SNPs in the genes FBXO47, ELOVL7, EDN1, and MAPT. Contrary to previous reports, we found no association of the genes SNCA and COQ2 with MSA. CONCLUSIONS We present a GWAS in MSA. We have identified several potentially interesting gene loci, including the MAPT locus, whose significance will have to be evaluated in a larger sample set. Common genetic variation in SNCA and COQ2 does not seem to be associated with MSA. In the future, additional samples of well-characterized patients with MSA will need to be collected to perform a larger MSA GWAS, but this initial study forms the basis for these next steps.
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Affiliation(s)
- Anna Sailer
- Authors' affiliations are listed at the end of the article
| | - Sonja W Scholz
- Authors' affiliations are listed at the end of the article.
| | | | | | | | - T Ryan Price
- Authors' affiliations are listed at the end of the article
| | - Andrew Lees
- Authors' affiliations are listed at the end of the article
| | - Owen A Ross
- Authors' affiliations are listed at the end of the article
| | | | - Kin Mok
- Authors' affiliations are listed at the end of the article
| | | | | | | | - Helen Ling
- Authors' affiliations are listed at the end of the article
| | | | | | | | - Luigi Ferrucci
- Authors' affiliations are listed at the end of the article
| | | | | | - Huw R Morris
- Authors' affiliations are listed at the end of the article
| | | | - Niall Quinn
- Authors' affiliations are listed at the end of the article
| | - Hakan Widner
- Authors' affiliations are listed at the end of the article
| | | | - Jon Infante
- Authors' affiliations are listed at the end of the article
| | | | - Werner Poewe
- Authors' affiliations are listed at the end of the article
| | | | | | | | | | | | | | - Eduardo Tolosa
- Authors' affiliations are listed at the end of the article
| | | | - Olivier Rascol
- Authors' affiliations are listed at the end of the article
| | | | - John A Hardy
- Authors' affiliations are listed at the end of the article
| | - Tamas Revesz
- Authors' affiliations are listed at the end of the article
| | | | - Thomas Gasser
- Authors' affiliations are listed at the end of the article
| | | | | | - Henry Houlden
- Authors' affiliations are listed at the end of the article.
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17
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ALS and FTD: an epigenetic perspective. Acta Neuropathol 2016; 132:487-502. [PMID: 27282474 DOI: 10.1007/s00401-016-1587-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/17/2016] [Accepted: 06/02/2016] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two fatal neurodegenerative diseases seen in comorbidity in up to 50 % of cases. Despite tremendous efforts over the last two decades, no biomarkers or effective therapeutics have been identified to prevent, decelerate, or stop neuronal death in patients. While the identification of multiple mutations in more than two dozen genes elucidated the involvement of several mechanisms in the pathogenesis of both diseases, identifying the hexanucleotide repeat expansion in C9orf72, the most common genetic abnormality in ALS and FTD, opened the door to the discovery of several novel pathogenic biological routes, including chromatin remodeling and transcriptome alteration. Epigenetic processes regulate DNA replication and repair, RNA transcription, and chromatin conformation, which in turn further dictate transcriptional regulation and protein translation. Transcriptional and post-transcriptional epigenetic regulation is mediated by enzymes and chromatin-modifying complexes that control DNA methylation, histone modifications, and RNA editing. While the alteration of DNA methylation and histone modification has recently been reported in ALS and FTD, the assessment of epigenetic involvement in both diseases is still at an early stage, and the involvement of multiple epigenetic players still needs to be evaluated. As the epigenome serves as a way to alter genetic information not only during aging, but also following environmental signals, epigenetic mechanisms might play a central role in initiating ALS and FTD, especially for sporadic cases. Here, we provide a review of what is currently known about altered epigenetic processes in both ALS and FTD and discuss potential therapeutic strategies targeting epigenetic mechanisms. As approximately 85 % of ALS and FTD cases are still genetically unexplained, epigenetic therapeutics explored for other diseases might represent a profitable direction for the field.
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18
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Robertson DS, Prevost AT, Bowden J. Accounting for selection and correlation in the analysis of two-stage genome-wide association studies. Biostatistics 2016; 17:634-49. [PMID: 26993061 PMCID: PMC5031943 DOI: 10.1093/biostatistics/kxw012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/11/2015] [Accepted: 01/15/2016] [Indexed: 11/15/2022] Open
Abstract
The problem of selection bias has long been recognized in the analysis of two-stage trials, where promising candidates are selected in stage 1 for confirmatory analysis in stage 2. To efficiently correct for bias, uniformly minimum variance conditionally unbiased estimators (UMVCUEs) have been proposed for a wide variety of trial settings, but where the population parameter estimates are assumed to be independent. We relax this assumption and derive the UMVCUE in the multivariate normal setting with an arbitrary known covariance structure. One area of application is the estimation of odds ratios (ORs) when combining a genome-wide scan with a replication study. Our framework explicitly accounts for correlated single nucleotide polymorphisms, as might occur due to linkage disequilibrium. We illustrate our approach on the measurement of the association between 11 genetic variants and the risk of Crohn's disease, as reported in Parkes and others (2007. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat. Gen. 39: (7), 830-832.), and show that the estimated ORs can vary substantially if both selection and correlation are taken into account.
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Affiliation(s)
- David S Robertson
- MRC Biostatistics Unit, IPH Forvie Site, Robinson Way, Cambridge CB2 0SR, UK
| | - A Toby Prevost
- Imperial College London, 1st Floor, Stadium House, 68 Wood Lane, London W12 7RH, UK
| | - Jack Bowden
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol BS8 2BN, UK and MRC Biostatistics Unit, IPH Forvie Site, Robinson Way, Cambridge CB2 0SR, UK
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19
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Staats KA, Humblet-Baron S, Bento-Abreu A, Scheveneels W, Nikolaou A, Deckers K, Lemmens R, Goris A, Van Ginderachter JA, Van Damme P, Hisatsune C, Mikoshiba K, Liston A, Robberecht W, Van Den Bosch L. Genetic ablation of IP3 receptor 2 increases cytokines and decreases survival of SOD1G93A mice. Hum Mol Genet 2016; 25:3491-3499. [PMID: 27378687 PMCID: PMC5179944 DOI: 10.1093/hmg/ddw190] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating progressive neurodegenerative disease characterized by the selective death of motor neurons. Disease pathophysiology is complex and not yet fully understood. Higher gene expression of the inositol 1,4,5-trisphosphate receptor 2 gene (ITPR2), encoding the IP3 receptor 2 (IP3R2), was detected in sporadic ALS patients. Here, we demonstrate that IP3R2 gene expression was also increased in spinal cords of ALS mice. Moreover, an increase of IP3R2 expression was observed in other models of chronic and acute neurodegeneration. Upregulation of IP3R2 gene expression could be induced by lipopolysaccharide (LPS) in murine astrocytes, murine macrophages and human fibroblasts indicating that it may be a compensatory response to inflammation. Preventing this response by genetic deletion of ITPR2 from SOD1G93A mice had a dose-dependent effect on disease duration, resulting in a significantly shorter lifespan of these mice. In addition, the absence of IP3R2 led to increased innate immunity, which may contribute to the decreased survival of the SOD1G93A mice. Besides systemic inflammation, IP3R2 knockout mice also had increased IFNγ, IL-6 and IL1α expression. Altogether, our data indicate that IP3R2 protects against the negative effects of inflammation, suggesting that the increase in IP3R2 expression in ALS patients is a protective response.
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Affiliation(s)
- Kim A Staats
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND).,VIB, Vesalius Research Center, Laboratory of Neurobiology
| | | | - Andre Bento-Abreu
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND).,VIB, Vesalius Research Center, Laboratory of Neurobiology
| | - Wendy Scheveneels
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND).,VIB, Vesalius Research Center, Laboratory of Neurobiology
| | - Alexandros Nikolaou
- Molecular and Biochemical Pharmacology Laboratory, Vrije Universiteit Brussel.,Myeloid Cell Immunology Laboratory, VIB, Inflammation Research Center.,Cellular and Molecular Immunology Unit, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kato Deckers
- Center for Molecular and Vascular Biology, University of Leuven
| | - Robin Lemmens
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND).,VIB, Vesalius Research Center, Laboratory of Neurobiology.,University Hospitals Leuven, Department of Neurology
| | - An Goris
- KU Leuven - University of Leuven, Department of Neurosciences, Laboratory for Neuroimmunology, Leuven, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Laboratory, VIB, Inflammation Research Center.,Cellular and Molecular Immunology Unit, Vrije Universiteit Brussel, Brussels, Belgium
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND).,VIB, Vesalius Research Center, Laboratory of Neurobiology.,University Hospitals Leuven, Department of Neurology
| | - Chihiro Hisatsune
- Laboratory for Developmental Neurobiology, Brain Science Institute, RIKEN, Wako-shi, Saitama, Japan
| | - Katsuhiko Mikoshiba
- Laboratory for Developmental Neurobiology, Brain Science Institute, RIKEN, Wako-shi, Saitama, Japan
| | - Adrian Liston
- VIB and Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Wim Robberecht
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND).,VIB, Vesalius Research Center, Laboratory of Neurobiology.,University Hospitals Leuven, Department of Neurology
| | - Ludo Van Den Bosch
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND) .,VIB, Vesalius Research Center, Laboratory of Neurobiology
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20
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Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy. Proc Natl Acad Sci U S A 2016; 113:E3091-100. [PMID: 27185954 DOI: 10.1073/pnas.1600084113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Canine degenerative myelopathy (DM) is a naturally occurring neurodegenerative disease with similarities to some forms of amyotrophic lateral sclerosis (ALS). Most dogs that develop DM are homozygous for a common superoxide dismutase 1 gene (SOD1) mutation. However, not all dogs homozygous for this mutation develop disease. We performed a genome-wide association analysis in the Pembroke Welsh Corgi (PWC) breed comparing DM-affected and -unaffected dogs homozygous for the SOD1 mutation. The analysis revealed a modifier locus on canine chromosome 25. A haplotype within the SP110 nuclear body protein (SP110) was present in 40% of affected compared with 4% of unaffected dogs (P = 1.5 × 10(-5)), and was associated with increased probability of developing DM (P = 4.8 × 10(-6)) and earlier onset of disease (P = 1.7 × 10(-5)). SP110 is a nuclear body protein involved in the regulation of gene transcription. Our findings suggest that variations in SP110-mediated gene transcription may underlie, at least in part, the variability in risk for developing DM among PWCs that are homozygous for the disease-related SOD1 mutation. Further studies are warranted to clarify the effect of this modifier across dog breeds.
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21
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He F, Jones JM, Figueroa-Romero C, Zhang D, Feldman EL, Goutman SA, Meisler MH, Callaghan BC, Todd PK. Screening for novel hexanucleotide repeat expansions at ALS- and FTD-associated loci. NEUROLOGY-GENETICS 2016; 2:e71. [PMID: 27274540 PMCID: PMC4865132 DOI: 10.1212/nxg.0000000000000071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/01/2016] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To determine whether GGGGCC (G4C2) repeat expansions at loci other than C9orf72 serve as common causes of amyotrophic lateral sclerosis (ALS). METHODS We assessed G4C2 repeat number in 28 genes near known ALS and frontotemporal dementia (FTD) loci by repeat-primed PCR coupled with fluorescent fragment analysis in 199 patients with ALS (17 familial, 182 sporadic) and 136 healthy controls. We also obtained blood from patients with ALS4 for evaluation of repeats surrounding the SETX gene locus. C9orf72 expansions were evaluated in parallel. RESULTS Expansions of G4C2 repeats in C9orf72 explained 8.8% of sporadic and 47% of familial ALS cases analyzed. Repeat variance was observed at one other locus, RGS14, but no large expansions were observed, and repeat sizes were not different between cases and controls. No G4C2 repeat expansions were identified at other ALS or FTD risk loci or in ALS4 cases. CONCLUSIONS G4C2 expansions near known ALS and FTD loci other than C9orf72 are not a common cause of ALS.
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Affiliation(s)
- Fang He
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Julie M Jones
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Claudia Figueroa-Romero
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Dapeng Zhang
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Eva L Feldman
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Stephen A Goutman
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Miriam H Meisler
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Brian C Callaghan
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
| | - Peter K Todd
- Department of Neurology (F.H., C.F.-R., B.C.C., E.L.F., S.A.G., P.K.T.) and Department of Human Genetics (J.M.J., M.H.M.), University of Michigan, Ann Arbor; Veteran Association Health System (B.C.C., P.K.T.), Ann Arbor; and National Center for Biotechnology Information (D.Z.), National Institutes of Health, Bethesda, MD
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22
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Culminskaya I, Kulminski AM, Yashin AI. Coordinated Action of Biological Processes during Embryogenesis Can Cause Genome-Wide Linkage Disequilibrium in the Human Genome and Influence Age-Related Phenotypes. ANNALS OF GERONTOLOGY AND GERIATRIC RESEARCH 2016; 3:1035. [PMID: 28357417 PMCID: PMC5367637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A role of non-Mendelian inheritance in genetics of complex, age-related traits is becoming increasingly recognized. Recently, we reported on two inheritable clusters of SNPs in extensive genome-wide linkage disequilibrium (LD) in the Framingham Heart Study (FHS), which were associated with the phenotype of premature death. Here we address biologically-related properties of these two clusters. These clusters have been unlikely selected randomly because they are functionally and structurally different from matched sets of randomly selected SNPs. For example, SNPs in LD from each cluster are highly significantly enriched in genes (p=7.1×10-22 and p=5.8×10-18), in general, and in short genes (p=1.4×10-47 and p=4.6×10-7), in particular. Mapping of SNPs in LD to genes resulted in two, partly overlapping, networks of 1764 and 4806 genes. Both these networks were gene enriched in developmental processes and in biological processes tightly linked with development including biological adhesion, cellular component organization, locomotion, localization, signaling, (p<10-4, q<10-4 for each category). Thorough analysis suggests connections of these genetic networks with different stages of embryogenesis and highlights biological interlink of specific processes enriched for genes from these networks. The results suggest that coordinated action of biological processes during embryogenesis may generate genome-wide networks of genetic variants, which may influence complex age-related phenotypes characterizing health span and lifespan.
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Affiliation(s)
- Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, USA
| | - Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, USA
| | - Anatoli I. Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, USA
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23
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Deng L, Hou L, Zhang J, Tang X, Cheng Z, Li G, Fang X, Xu J, Zhang X, Xu R. Polymorphism of rs3737597 in DISC1 Gene on Chromosome 1q42.2 in sALS Patients: a Chinese Han Population Case-Control Study. Mol Neurobiol 2016; 54:3162-3179. [DOI: 10.1007/s12035-016-9869-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/17/2016] [Indexed: 01/10/2023]
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Browne EC, Abbott BM. Recent progress towards an effective treatment of amyotrophic lateral sclerosis using the SOD1 mouse model in a preclinical setting. Eur J Med Chem 2016; 121:918-925. [PMID: 27012524 DOI: 10.1016/j.ejmech.2016.02.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 02/18/2016] [Accepted: 02/18/2016] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, fatal and incurable neurodegenerative disorder. Motor neurone degeneration can be caused by genetic mutation but the exact etiology of the disease, particularly for sporadic illness, still remains unclear. Therapeutics which target known pathogenic mechanisms involved in ALS, such as protein aggregation, oxidative stress, apoptosis, inflammation, endoplasmic reticulum stress and mitochondria dysfunction, are currently being pursued in order to provide neuroprotection which may be able to slow down, or perhaps even halt, disease progression. This present review focuses on the compounds which have been recently evaluated using the SOD1 mouse model, the most widely used preclinical model for ALS research.
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Affiliation(s)
- Elisse C Browne
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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25
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Zou ZY, Liu CY, Che CH, Huang HP. Toward precision medicine in amyotrophic lateral sclerosis. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:27. [PMID: 26889480 PMCID: PMC4731596 DOI: 10.3978/j.issn.2305-5839.2016.01.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022]
Abstract
Precision medicine is an innovative approach that uses emerging biomedical technologies to deliver optimally targeted and timed interventions, customized to the molecular drivers of an individual's disease. This approach is only just beginning to be considered for treating amyotrophic lateral sclerosis (ALS). The clinical and biological complexities of ALS have hindered development of effective therapeutic strategies. In this review we consider applying the key elements of precision medicine to ALS: phenotypic classification, comprehensive risk assessment, presymptomatic period detection, potential molecular pathways, disease model development, biomarker discovery and molecularly tailored interventions. Together, these would embody a precision medicine approach, which may provide strategies for optimal targeting and timing of efforts to prevent, stop or slow progression of ALS.
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Affiliation(s)
- Zhang-Yu Zou
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 350001, China
| | - Chang-Yun Liu
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 350001, China
| | - Chun-Hui Che
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 350001, China
| | - Hua-Pin Huang
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 350001, China
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26
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Ju XD, Liu T, Chen J, Li XG, Liu XX, Liu WC, Wang K, Deng M. Single-nucleotide Polymorphism rs2275294 in ZNF512B is not Associated with Susceptibility to Amyotrophic Lateral Sclerosis in a Large Chinese Cohort. Chin Med J (Engl) 2015; 128:3305-9. [PMID: 26668144 PMCID: PMC4797505 DOI: 10.4103/0366-6999.171421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that primarily affects motor neurons and has no effective treatment. Recently, Iida et al. identified a single-nucleotide polymorphism (SNP) rs2275294 in the ZNF512B gene that is significantly associated with susceptibility to ALS in the Japanese population. Here, we performed a case–control study examining the possible association of rs2275294 with risk of sporadic ALS (SALS) in a large Chinese cohort. Methods: To assess this association, we performed a replication study in 953 SALS patients and 1039 age- and gender-matched healthy control subjects, who were recruited from Peking University Third Hospital and the First Affiliated Hospital of Anhui Medical University from January 2004 to December 2013 throughout China. We genotyped the rs2275294 SNP using polymerase chain reaction and direct sequencing. Results: The allele frequency of rs2275294 in ZNF512B was different between Japanese and Chinese. The association in Chinese between ALS patients and controls did not reach statistical significance (P = 0.54; odds ratio = 0.94; 95% confidence interval = 0.76–1.15). Conclusions: The SNP rs2275294 in ZNF512B is not considered to be associated with ALS susceptibility in the Chinese population. Our study highlights genetic heterogeneity in ALS susceptibility in different population. Given our negative results, further replication study involving larger and more homogeneous samples in different ethnicities should be performed in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Min Deng
- Medical Research Center, Peking University Third Hospital, Beijing 100191, China
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27
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Chen CJ, Chen CM, Pai TW, Chang HT, Hwang CS. A genome-wide association study on amyotrophic lateral sclerosis in the Taiwanese Han population. Biomark Med 2015; 10:597-611. [PMID: 26580837 DOI: 10.2217/bmm.15.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Identification of mutations in patients with amyotrophic lateral sclerosis (ALS) in a genome-wide association study can reveal possible biomarkers of such a rapidly progressive and fatal neurodegenerative disease. It was observed that significant single nucleotide polymorphisms vary when the tested population changes from one ethnic group to another. To identify new loci associated with ALS susceptibility in the Taiwanese Han population, we performed a genome-wide association study on 94 patients with sporadic ALS and 376 matched controls. We uncovered two new susceptibility loci at 13q14.3 (rs2785946) and 11q25 (rs11224052). In addition, we analyzed the functions of all the associated genes among 54 significant single nucleotide polymorphisms using Gene Ontology annotations, and the results showed several statistically significant neural- and muscle-related Gene Ontology terms and the associated diseases.
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Affiliation(s)
- Chi-Jim Chen
- Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Chien-Ming Chen
- Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Tun-Wen Pai
- Department of Computer Science & Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Hao-Teng Chang
- Graduate Institute of Basic Medical Sciences, China Medical University, Taichung, Taiwan.,Department of Computer Science & Information Engineering, Asia University, Taichung, Taiwan
| | - Chi-Shin Hwang
- Department of Neurology, Taipei City Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
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28
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Chen X, Chen Y, Guo X, Cao B, Wei Q, Ou R, Zhao B, Song W, Wu Y, Shang HF. Replication analysis of genetic variants on 17q11.2 and 9p21.2 with sporadic amyotrophic lateral sclerosis and Parkinson's disease in a Chinese population. Neurobiol Aging 2015; 36:3116.e1-3116.e3. [PMID: 26304631 DOI: 10.1016/j.neurobiolaging.2015.07.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 02/05/2023]
Abstract
We performed a replication study of the 2 genetic variants, rs34517613 on 17q11.2 and rs3849942 on 9p21.2 in patients with sporadic amyotrophic lateral sclerosis (ALS) and Parkinson's disease in a Chinese population. These 2 variants are identified to be associated with increased risk of ALS in European-descended populations by genome-wide association studies. Both rs34517613 and rs3849942 showed no evidence of association in Chinese. These loci are not risk factors for sporadic ALS and Parkinson's disease in the western Han Chinese population.
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Affiliation(s)
- Xueping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoyan Guo
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ruwei Ou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bi Zhao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei Song
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ying Wu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hui-Fang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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29
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Amy M, Staehlin O, René F, Blasco H, Marouillat S, Daoud H, Vourc'h P, Gordon PH, Camu W, Corcia P, Loeffler JP, Palkovits M, Sommer WH, Andres CR. A common functional allele of the Nogo receptor gene, reticulon 4 receptor (RTN4R), is associated with sporadic amyotrophic lateral sclerosis in a French population. Amyotroph Lateral Scler Frontotemporal Degener 2015; 16:490-6. [PMID: 26083872 DOI: 10.3109/21678421.2015.1051988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis is sporadic (SALS) in 90% of cases and has complex environmental and genetic influences. Nogo protein inhibits neurite outgrowth and is overexpressed in muscle in ALS. Our aims were to study the reticulon 4 receptor gene RTN4R which encodes Nogo 1 receptor (NgR1) in SALS, to test if the variants were associated with variable expression of the gene and whether NgR1 protein expression was modified in a transgenic mouse model of ALS. We genotyped three single nucleotide polymorphisms (SNPs; rs701421, rs701427, and rs1567871) of the RTN4R gene in 364 SALS French patients and 430 controls. We examined expression of RTN4R mRNA by quantitative PCR in control post mortem human brain tissue. We determined the expression of NgR1 protein in spinal motor neurons from a SOD1 G86R ALS mouse model. We observed significant associations between SALS and RTN4R alleles. Messenger RNA expression from RTN4R in human cortical brain tissue correlated significantly with the genotypes of rs701427. NgR1 protein expression was reduced in Nogo A positive motor neurons from diseased transgenic animals. In conclusion, these observations suggest that a functional RTN4R gene variant is associated with SALS. This variant may act in concert with other genetic variants or environmental influences.
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Affiliation(s)
- Maïté Amy
- a INSERM U930 , Tours , France.,b Université François Rabelais , Tours , France
| | - Oliver Staehlin
- c Institute of Psychopharmacology at Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg , Mannheim , Germany
| | - Frédérique René
- d INSERM U1118, Mécanismes Centraux et Périphériques de la Neurodégénérescence , Strasbourg , France.,e Université de Strasbourg, UMRS 1118 , Strasbourg , France
| | - Hélène Blasco
- a INSERM U930 , Tours , France.,b Université François Rabelais , Tours , France.,f Service de Biochimie et Biologie Moléculaire, Hôpital Bretonneau , CHRU de Tours, Tours , France
| | | | | | - Patrick Vourc'h
- a INSERM U930 , Tours , France.,b Université François Rabelais , Tours , France.,f Service de Biochimie et Biologie Moléculaire, Hôpital Bretonneau , CHRU de Tours, Tours , France
| | - Paul H Gordon
- g Northern Navajo Medical Center , Shiprock NM , USA
| | - William Camu
- h ALS Centre, Hôpital Gui de Chauliac, CHU de Montpellier , Montpellier , France
| | - Philippe Corcia
- a INSERM U930 , Tours , France.,b Université François Rabelais , Tours , France.,i ALS Centre, Department of Neurology , CHRU de Tours, France
| | - Jean-Philippe Loeffler
- d INSERM U1118, Mécanismes Centraux et Périphériques de la Neurodégénérescence , Strasbourg , France.,e Université de Strasbourg, UMRS 1118 , Strasbourg , France
| | - Miklós Palkovits
- j Laboratory of Neuromorphology, Semmelweis University and the Hungarian Academy of Sciences , Budapest , Hungary
| | - Wolfgang H Sommer
- c Institute of Psychopharmacology at Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg , Mannheim , Germany
| | - Christian R Andres
- a INSERM U930 , Tours , France.,b Université François Rabelais , Tours , France.,f Service de Biochimie et Biologie Moléculaire, Hôpital Bretonneau , CHRU de Tours, Tours , France
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30
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Marangi G, Traynor BJ. Genetic causes of amyotrophic lateral sclerosis: new genetic analysis methodologies entailing new opportunities and challenges. Brain Res 2015; 1607:75-93. [PMID: 25316630 PMCID: PMC5916786 DOI: 10.1016/j.brainres.2014.10.009] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 10/03/2014] [Accepted: 10/05/2014] [Indexed: 12/11/2022]
Abstract
The genetic architecture of amyotrophic lateral sclerosis (ALS) is being increasingly understood. In this far-reaching review, we examine what is currently known about ALS genetics and how these genes were initially identified. We also discuss the various types of mutations that might underlie this fatal neurodegenerative condition and outline some of the strategies that might be useful in untangling them. These include expansions of short repeat sequences, common and low-frequency genetic variations, de novo mutations, epigenetic changes, somatic mutations, epistasis, oligogenic and polygenic hypotheses. This article is part of a Special Issue entitled ALS complex pathogenesis.
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Affiliation(s)
- Giuseppe Marangi
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA; Institute of Medical Genetics, Catholic University, Roma, Italy.
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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31
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Corcia P, Vourc’h P, Couratier P. Que peut-on attendre des nouvelles technologies dans le domaine de la génétique de la SLA ? Rev Neurol (Paris) 2015; 171:401-3. [DOI: 10.1016/j.neurol.2015.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 11/25/2022]
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32
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Nalls MA, Escott-Price V, Williams N, Lubbe S, Keller MF, Morris HR, Singleton AB. Genetic risk and age in Parkinson's disease: Continuum not stratum. Mov Disord 2015; 30:850-4. [PMID: 25778492 PMCID: PMC5217457 DOI: 10.1002/mds.26192] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/26/2014] [Accepted: 01/29/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent genomewide association study meta-analyses have identified 28 loci associated with risk of Parkinson's disease (PD). We sought to investigate whether these genetic risk factors are associated with PD age at onset. METHODS Genetic risk scores from these loci were calculated for 6,249 cases. Linear regression tested associations between cumulative genetic risk and PD age at onset. RESULTS Increasing genetic risk scores were associated with earlier age at onset (beta = -0.10, P = 2.92 × 10(-8) , adjusted r(2) = 0.27). Single standard deviation increase in genetic risk score is associated with 37.44 d earlier age at onset. Highest genetic risk was found at 31 to 60 y, onset slightly below average age at onset (AAO). CONCLUSIONS Common genetic risk factors have a small but consistent association with AAO in PD.
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Affiliation(s)
- Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Nigel Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff, Wales, UK
| | - Steven Lubbe
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, England, UK
| | - Margaux F. Keller
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Huw R. Morris
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, England, UK
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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33
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Steinberg KM, Yu B, Koboldt DC, Mardis ER, Pamphlett R. Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS. Sci Rep 2015; 5:9124. [PMID: 25773295 PMCID: PMC4360641 DOI: 10.1038/srep09124] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/20/2015] [Indexed: 12/13/2022] Open
Abstract
The contribution of genetic variants to sporadic amyotrophic lateral sclerosis (ALS) remains largely unknown. Either recessive or de novo variants could result in an apparently sporadic occurrence of ALS. In an attempt to find such variants we sequenced the exomes of 44 ALS-unaffected-parents trios. Rare and potentially damaging compound heterozygous variants were found in 27% of ALS patients, homozygous recessive variants in 14% and coding de novo variants in 27%. In 20% of patients more than one of the above variants was present. Genes with recessive variants were enriched in nucleotide binding capacity, ATPase activity, and the dynein heavy chain. Genes with de novo variants were enriched in transcription regulation and cell cycle processes. This trio study indicates that rare private recessive variants could be a mechanism underlying some case of sporadic ALS, and that de novo mutations are also likely to play a part in the disease.
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Affiliation(s)
| | - Bing Yu
- Department of Medical Genomics, Royal Prince Alfred Hospital and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Roger Pamphlett
- The Stacey MND Laboratory, Department of Pathology, The University of Sydney, Sydney, New South Wales, Australia
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34
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Nalls MA, Bras J, Hernandez DG, Keller MF, Majounie E, Renton AE, Saad M, Jansen I, Guerreiro R, Lubbe S, Plagnol V, Gibbs JR, Schulte C, Pankratz N, Sutherland M, Bertram L, Lill CM, DeStefano AL, Faroud T, Eriksson N, Tung JY, Edsall C, Nichols N, Brooks J, Arepalli S, Pliner H, Letson C, Heutink P, Martinez M, Gasser T, Traynor BJ, Wood N, Hardy J, Singleton AB. NeuroX, a fast and efficient genotyping platform for investigation of neurodegenerative diseases. Neurobiol Aging 2015; 36:1605.e7-12. [PMID: 25444595 PMCID: PMC4317375 DOI: 10.1016/j.neurobiolaging.2014.07.028] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 12/11/2022]
Abstract
Our objective was to design a genotyping platform that would allow rapid genetic characterization of samples in the context of genetic mutations and risk factors associated with common neurodegenerative diseases. The platform needed to be relatively affordable, rapid to deploy, and use a common and accessible technology. Central to this project, we wanted to make the content of the platform open to any investigator without restriction. In designing this array we prioritized a number of types of genetic variability for inclusion, such as known risk alleles, disease-causing mutations, putative risk alleles, and other functionally important variants. The array was primarily designed to allow rapid screening of samples for disease-causing mutations and large population studies of risk factors. Notably, an explicit aim was to make this array widely available to facilitate data sharing across and within diseases. The resulting array, NeuroX, is a remarkably cost and time effective solution for high-quality genotyping. NeuroX comprises a backbone of standard Illumina exome content of approximately 240,000 variants, and over 24,000 custom content variants focusing on neurologic diseases. Data are generated at approximately $50-$60 per sample using a 12-sample format chip and regular Infinium infrastructure; thus, genotyping is rapid and accessible to many investigators. Here, we describe the design of NeuroX, discuss the utility of NeuroX in the analyses of rare and common risk variants, and present quality control metrics and a brief primer for the analysis of NeuroX derived data.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew B. Singleton
- Corresponding author at: Laboratory of Neurogenetics, National Institute on Aging, 35 Lincoln Drive, Bethesda, MD, USA. Tel.: +301 451 6079; fax: +301 451 5466. (A.B. Singleton)
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35
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Jones AR, Troakes C, King A, Sahni V, De Jong S, Bossers K, Papouli E, Mirza M, Al-Sarraj S, Shaw CE, Shaw PJ, Kirby J, Veldink JH, Macklis JD, Powell JF, Al-Chalabi A. Stratified gene expression analysis identifies major amyotrophic lateral sclerosis genes. Neurobiol Aging 2015; 36:2006.e1-9. [PMID: 25801576 DOI: 10.1016/j.neurobiolaging.2015.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/15/2015] [Indexed: 01/10/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons resulting in progressive paralysis. Gene expression studies of ALS only rarely identify the same gene pathways as gene association studies. We hypothesized that analyzing tissues by matching on degree of disease severity would identify different patterns of gene expression from a traditional case-control comparison. We analyzed gene expression changes in 4 postmortem central nervous system regions, stratified by severity of motor neuron loss. An overall comparison of cases (n = 6) and controls (n = 3) identified known ALS gene, SOX5, as showing differential expression (log2 fold change = 0.09, p = 5.5 × 10(-5)). Analyses stratified by disease severity identified expression changes in C9orf72 (p = 2.77 × 10(-3)), MATR3 (p = 3.46 × 10(-3)), and VEGFA (p = 8.21 × 10(-4)), all implicated in ALS through genetic studies, and changes in other genes in pathways involving RNA processing and immune response. These findings suggest that analysis of gene expression stratified by disease severity can identify major ALS genes and may be more efficient than traditional case-control comparison.
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Affiliation(s)
- Ashley R Jones
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Claire Troakes
- MRC London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | - Andrew King
- MRC London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | - Vibhu Sahni
- Department of Stem Cell and Regenerative Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Simone De Jong
- MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Koen Bossers
- Synaptic Plasticity and Behavior Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Efterpi Papouli
- Biomedical Research Centre, King's College London, Guy's Hospital, London, UK; Cambridge Epigenetix Ltd, Babraham, UK
| | - Muddassar Mirza
- Biomedical Research Centre, King's College London, Guy's Hospital, London, UK
| | - Safa Al-Sarraj
- MRC London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - John F Powell
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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36
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Yang X, Xi J, An R, Yu L, Lin Z, Zhou H, Xu Y. Lack of evidence for an association between the V393A variant of COQ2 and amyotrophic lateral sclerosis in a Han Chinese population. Neurol Sci 2015; 36:1211-5. [PMID: 25613861 DOI: 10.1007/s10072-015-2083-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/15/2015] [Indexed: 02/05/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive disorder involving the degeneration of motor neurons. ALS shares pathogenic characteristics and genetic risk factors with multiple system atrophy (MSA). Here we examine whether a variant of the COQ2 gene associated with MSA in Japanese is also associated with ALS in Han Chinese. The ligase detection reaction was used to measure the frequency of the V393A variant of COQ2 in 282 patients with ALS and 491 healthy controls. The ALS and control groups showed no significant differences in genotype frequencies (OR 1.298, 95 %CI 0.396-4.253, p = 0.666) or allele frequencies (OR 1.314, 95 %CI 0.403-4.286, p = 0.650) at the V393A locus of COQ2. We also conducted a meta-analysis and combined our data with the previous Japanese research, but still failed to detect an association between V393A and ALS. In conclusion, This case-control study shows no evidence for an association between ALS and the V393A variant of COQ2 in Han Chinese and together with the Japanese research suggests that this polymorphism may not be linked to the risk of ALS in East Asians in general.
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Affiliation(s)
- Xinglong Yang
- Department of Neurology, West China Hospital, Sichuan University, 37 Guo Xue Xiang, Chengdu, Sichuan Province, 610041, People's Republic of China,
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Tan MS, Jiang T, Tan L, Yu JT. Genome-wide association studies in neurology. ANNALS OF TRANSLATIONAL MEDICINE 2015; 2:124. [PMID: 25568877 DOI: 10.3978/j.issn.2305-5839.2014.11.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 03/04/2013] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWAS) are a powerful tool for understanding the genetic underpinnings of human disease. In this article, we briefly review the role and findings of GWAS in common neurological diseases, including Stroke, Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, migraine, amyotrophic lateral sclerosis, frontotemporal lobar degeneration, restless legs syndrome, intracranial aneurysm, human prion diseases and moyamoya disease. We then discuss the present and future implications of these findings with regards to disease prediction, uncovering basic biology, and the development of potential therapeutic agents.
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Affiliation(s)
- Meng-Shan Tan
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Teng Jiang
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Lan Tan
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Jin-Tai Yu
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
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Kariuki SN, Ghodke-Puranik Y, Dorschner JM, Chrabot BS, Kelly JA, Tsao BP, Kimberly RP, Alarcón-Riquelme ME, Jacob CO, Criswell LA, Sivils KL, Langefeld CD, Harley JB, Skol AD, Niewold TB. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. Genes Immun 2015; 16:15-23. [PMID: 25338677 PMCID: PMC4305028 DOI: 10.1038/gene.2014.57] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon-alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. About 40-50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs low IFN-α in over 1550 SLE cases, including genome-wide association study and replication cohorts. In meta-analysis, the top associations in European ancestry were protein kinase, cyclic GMP-dependent, type I (PRKG1) rs7897633 (P(Meta) = 2.75 × 10(-8)) and purine nucleoside phosphorylase (PNP) rs1049564 (P(Meta) = 1.24 × 10(-7)). We also found evidence for cross-ancestral background associations with the ankyrin repeat domain 44 (ANKRD44) and pleckstrin homology domain containing, family F member 2 gene (PLEKHF2) loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic sub-phenotypes becomes an attractive strategy for genetic discovery in complex disease.
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Affiliation(s)
| | | | - Jessica M. Dorschner
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN
| | - Beverly S. Chrabot
- Gwen Knapp Center for Lupus Research, University of Chicago, Chicago, IL
| | - Jennifer A. Kelly
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Betty P. Tsao
- Department of Medicine, University of California, Los Angeles, CA
| | | | - Marta E. Alarcón-Riquelme
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government
| | - Chaim O. Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA
| | - Lindsey A. Criswell
- Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA
| | - Kathy L. Sivils
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Carl D. Langefeld
- Department of Biostatistical Sciences, Wake Forest University, Winston-Salem, NC
| | - John B. Harley
- Cincinnati Children’s Hospital Medical Center and Cincinnati VA Medical Center, Cincinnati, OH
| | - Andrew D. Skol
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - Timothy B. Niewold
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN
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39
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Dissection of genetic factors associated with amyotrophic lateral sclerosis. Exp Neurol 2014; 262 Pt B:91-101. [DOI: 10.1016/j.expneurol.2014.04.013] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 03/31/2014] [Accepted: 04/14/2014] [Indexed: 12/11/2022]
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Keller MF, Ferrucci L, Singleton AB, Tienari PJ, Laaksovirta H, Restagno G, Chiò A, Traynor BJ, Nalls MA. Genome-wide analysis of the heritability of amyotrophic lateral sclerosis. JAMA Neurol 2014; 71:1123-34. [PMID: 25023141 DOI: 10.1001/jamaneurol.2014.1184] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IMPORTANCE Considerable advances have been made in our understanding of the genetics underlying amyotrophic lateral sclerosis (ALS). Nevertheless, for the majority of patients who receive a diagnosis of ALS, the role played by genetics is unclear. Further elucidation of the genetic architecture of this disease will help clarify the role of genetic variation in ALS populations. OBJECTIVE To estimate the relative importance of genetic factors in a complex disease such as ALS by accurately quantifying heritability using genome-wide data derived from genome-wide association studies. DESIGN, SETTING, AND PARTICIPANTS We applied the genome-wide complex trait analysis algorithm to 3 genome-wide association study data sets that were generated from ALS case-control cohorts of European ancestry to estimate the heritability of ALS. Cumulatively, these data sets contained genotype data from 1223 cases and 1591 controls that had been previously generated and are publically available on the National Center for Biotechnology Information database of genotypes and phenotypes website (http://www.ncbi.nlm.nih.gov/gap). The cohorts genotyped as part of these genome-wide association study efforts include the InCHIANTI (aging in the Chianti area) Study, the Piemonte and Valle d'Aosta Register for Amyotrophic Lateral Sclerosis, the National Institute of Neurological Disorders and Stroke Repository, and an ALS specialty clinic in Helsinki, Finland. MAIN OUTCOMES AND MEASURES A linear mixed model was used to account for all known single-nucleotide polymorphisms simultaneously and to quantify the phenotypic variance present in ostensibly outbred individuals. Variance measures were used to estimate heritability. RESULTS With our meta-analysis, which is based on genome-wide genotyping data, we estimated the overall heritability of ALS to be approximately 21.0% (95% CI, 17.1-24.9) (SE = 2.0%), indicating that additional genetic variation influencing risk of ALS loci remains to be identified. Furthermore, we identified 17 regions of the genome that display significantly high heritability estimates. Eleven of these regions represent novel candidate regions for ALS risk. CONCLUSIONS AND RELEVANCE We found the heritability of ALS to be significantly higher than previously reported. We also identified multiple, novel genomic regions that we hypothesize may contain causative risk variants that influence susceptibility to ALS.
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Affiliation(s)
- Margaux F Keller
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland2Department of Biological Anthropology, Temple University, Philadelphia, Pennsylvania
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Pentti J Tienari
- Department of Neurology, Helsinki University Central Hospital and Molecular Neurology, Research Programs Unit, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Hannu Laaksovirta
- Department of Neurology, Helsinki University Central Hospital and Molecular Neurology, Research Programs Unit, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Gabriella Restagno
- Molecular Genetics Unit, Department of Clinical Pathology, ASO OIRM-St Anna, Turin, Italy
| | - Adriano Chiò
- Rita Levi-Montalcini Department of Neuroscience, University of Turin, Turin, Italy
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Michael A Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
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41
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He J, Mangelsdorf M, Fan D, Bartlett P, Brown MA. Amyotrophic Lateral Sclerosis Genetic Studies: From Genome-wide Association Mapping to Genome Sequencing. Neuroscientist 2014; 21:599-615. [PMID: 25378359 DOI: 10.1177/1073858414555404] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of obscure etiology. Multiple genetic studies have been conducted to advance our understanding of the disease, employing a variety of techniques such as linkage mapping in families, to genome-wide association studies and sequencing based approaches such as whole exome sequencing and whole genome sequencing and a few epigenetic analyses. While major progress has been made, the majority of the genetic variation involved in ALS is yet to be undefined. The optimal study designs to investigate ALS depend on the genetic model for the disease, and it is likely that different approaches will be required to map genes involved in familial and sporadic disease. The potential approaches and their strengths and weaknesses are discussed.
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Affiliation(s)
- Ji He
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia Department of Neurology, Peking University Third Hospital, Beijing, China University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Brisbane, Australia
| | - Marie Mangelsdorf
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
| | - Perry Bartlett
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Matthew A Brown
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Brisbane, Australia
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Abstract
Our understanding of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease, is expanding rapidly as its genetic causes are uncovered. The pace of new gene discovery over the last 5 years has accelerated, providing new insights into the pathogenesis of disease and highlighting biological pathways as targets for therapeutic development. This article reviews our current understanding of the heritability of ALS and provides an overview of each of the major ALS genes, highlighting their phenotypic characteristics and frequencies as a guide for clinicians evaluating patients with ALS.
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Affiliation(s)
- Matthew B Harms
- Neuromuscular Division, Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA.
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43
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Deng H, Gao K, Jankovic J. The role of FUS gene variants in neurodegenerative diseases. Nat Rev Neurol 2014; 10:337-48. [DOI: 10.1038/nrneurol.2014.78] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Jerng HH, Pfaffinger PJ. Modulatory mechanisms and multiple functions of somatodendritic A-type K (+) channel auxiliary subunits. Front Cell Neurosci 2014; 8:82. [PMID: 24723849 PMCID: PMC3973911 DOI: 10.3389/fncel.2014.00082] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/03/2014] [Indexed: 12/13/2022] Open
Abstract
Auxiliary subunits are non-conducting, modulatory components of the multi-protein ion channel complexes that underlie normal neuronal signaling. They interact with the pore-forming α-subunits to modulate surface distribution, ion conductance, and channel gating properties. For the somatodendritic subthreshold A-type potassium (ISA) channel based on Kv4 α-subunits, two types of auxiliary subunits have been extensively studied: Kv channel-interacting proteins (KChIPs) and dipeptidyl peptidase-like proteins (DPLPs). KChIPs are cytoplasmic calcium-binding proteins that interact with intracellular portions of the Kv4 subunits, whereas DPLPs are type II transmembrane proteins that associate with the Kv4 channel core. Both KChIPs and DPLPs genes contain multiple start sites that are used by various neuronal populations to drive the differential expression of functionally distinct N-terminal variants. In turn, these N-terminal variants generate tremendous functional diversity across the nervous system. Here, we focus our review on (1) the molecular mechanism underlying the unique properties of different N-terminal variants, (2) the shaping of native ISA properties by the concerted actions of KChIPs and DPLP variants, and (3) the surprising ways that KChIPs and DPLPs coordinate the activity of multiple channels to fine-tune neuronal excitability. Unlocking the unique contributions of different auxiliary subunit N-terminal variants may provide an important opportunity to develop novel targeted therapeutics to treat numerous neurological disorders.
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Affiliation(s)
- Henry H. Jerng
- Department of Neuroscience, Baylor College of MedicineHouston, TX, USA
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45
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Renton AE, Chiò A, Traynor BJ. State of play in amyotrophic lateral sclerosis genetics. Nat Neurosci 2014; 17:17-23. [PMID: 24369373 PMCID: PMC4544832 DOI: 10.1038/nn.3584] [Citation(s) in RCA: 1115] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 10/22/2013] [Indexed: 12/11/2022]
Abstract
Considerable progress has been made in unraveling the genetic etiology of amyotrophic lateral sclerosis (ALS), the most common form of adult-onset motor neuron disease and the third most common neurodegenerative disease overall. Here we review genes implicated in the pathogenesis of motor neuron degeneration and how this new information is changing the way we think about this fatal disorder. Specifically, we summarize current literature of the major genes underlying ALS, SOD1, TARDBP, FUS, OPTN, VCP, UBQLN2, C9ORF72 and PFN1, and evaluate the information being gleaned from genome-wide association studies. We also outline emerging themes in ALS research, such as next-generation sequencing approaches to identify de novo mutations, the genetic convergence of familial and sporadic ALS, the proposed oligogenic basis for the disease, and how each new genetic discovery is broadening the phenotype associated with the clinical entity we know as ALS.
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Affiliation(s)
- Alan E Renton
- Neuromuscular Diseases Research Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
| | - Bryan J Traynor
- 1] Neuromuscular Diseases Research Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA. [2] Department of Neurology, Brain Sciences Institute, Johns Hopkins University, Baltimore, Maryland, USA
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46
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Mok K, Laaksovirta H, Tienari PJ, Peuralinna T, Myllykangas L, Chiò A, Traynor BJ, Nalls MA, Gurunlian N, Shatunov A, Restagno G, Mora G, Nigel Leigh P, Shaw CE, Morrison KE, Shaw PJ, Al-Chalabi A, Hardy J, Orrell RW. Homozygosity analysis in amyotrophic lateral sclerosis. Eur J Hum Genet 2013; 21:1429-35. [PMID: 23612577 PMCID: PMC3829775 DOI: 10.1038/ejhg.2013.59] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 02/21/2013] [Accepted: 02/28/2013] [Indexed: 01/20/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) may appear to be familial or sporadic, with recognised dominant and recessive inheritance in a proportion of cases. Sporadic ALS may be caused by rare homozygous recessive mutations. We studied patients and controls from the UK and a multinational pooled analysis of GWAS data on homozygosity in ALS to determine any potential recessive variant leading to the disease. Six-hundred and twenty ALS and 5169 controls were studied in the UK cohort. A total of 7646 homozygosity segments with length >2 Mb were identified, and 3568 rare segments remained after filtering 'common' segments. The mean total of the autosomal genome with homozygosity segments was longer in ALS than in controls (unfiltered segments, P=0.05). Two-thousand and seventeen ALS and 6918 controls were studied in the pooled analysis. There were more regions of homozygosity segments per case (P=1 × 10(-5)), a greater proportion of cases harboured homozygosity (P=2 × 10(-5)), a longer average length of segment (P=1 × 10(-5)), a longer total genome coverage (P=1 × 10(-5)), and a higher rate of these segments overlapped with RefSeq gene regions (P=1 × 10(-5)), in ALS patients than controls. Positive associations were found in three regions. The most significant was in the chromosome 21 SOD1 region, and also chromosome 1 2.9-4.8 Mb, and chromosome 5 in the 65 Mb region. There are more than twenty potential genes in these regions. These findings point to further possible rare recessive genetic causes of ALS, which are not identified as common variants in GWAS.
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Affiliation(s)
- Kin Mok
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Hannu Laaksovirta
- Helsinki University Central Hospital, Department of Neurology, Molecular Neurology Research Program, Biomedicum, University of Helsinki, Helsinki, Finland
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Pentti J Tienari
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Terhi Peuralinna
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Liisa Myllykangas
- Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, and Folkhalsan Institute of Genetics, Helsinki, Finland
| | - Adriano Chiò
- Department of Neuroscience, University of Turin and Azienda Ospedaliera Universitaria San Giovanni Battista, Turin, Italy
| | - Bryan J Traynor
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Michael A Nalls
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Nicole Gurunlian
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Aleksey Shatunov
- Medical Research Council Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, London, UK
| | - Gabriella Restagno
- Molecular Genetics Laboratory, Azienda Ospedaliera OIRM-Sant'Anna, Turin, Italy
| | - Gabriele Mora
- Fondazione Salvatore Mangeri, IRCCS Scientific Institute of Milan, Milan, Italy
| | - P Nigel Leigh
- Brighton and Sussex Medical School, Trafford Centre for Biomedical Research, University of Sussex, Falmer, UK
| | - Chris E Shaw
- Medical Research Council Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, London, UK
| | - Karen E Morrison
- School of Clinical and Experimental Medicine, University of Birmingham and Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Pamela J Shaw
- Department of Neuroscience, The Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Ammar Al-Chalabi
- Medical Research Council Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, London, UK
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Richard W Orrell
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
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47
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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] [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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48
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Goris A, van Setten J, Diekstra F, Ripke S, Patsopoulos NA, Sawcer SJ, van Es M, Andersen PM, Melki J, Meininger V, Hardiman O, Landers JE, Brown RH, Shatunov A, Leigh N, Al-Chalabi A, Shaw CE, Traynor BJ, Chiò A, Restagno G, Mora G, Ophoff RA, Oksenberg JR, Van Damme P, Compston A, Robberecht W, Dubois B, van den Berg LH, De Jager PL, Veldink JH, de Bakker PIW. No evidence for shared genetic basis of common variants in multiple sclerosis and amyotrophic lateral sclerosis. Hum Mol Genet 2013; 23:1916-22. [PMID: 24234648 DOI: 10.1093/hmg/ddt574] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have been successful in identifying common variants that influence the susceptibility to complex diseases. From these studies, it has emerged that there is substantial overlap in susceptibility loci between diseases. In line with those findings, we hypothesized that shared genetic pathways may exist between multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). While both diseases may have inflammatory and neurodegenerative features, epidemiological studies have indicated an increased co-occurrence within individuals and families. To this purpose, we combined genome-wide data from 4088 MS patients, 3762 ALS patients and 12 030 healthy control individuals in whom 5 440 446 single-nucleotide polymorphisms (SNPs) were successfully genotyped or imputed. We tested these SNPs for the excess association shared between MS and ALS and also explored whether polygenic models of SNPs below genome-wide significance could explain some of the observed trait variance between diseases. Genome-wide association meta-analysis of SNPs as well as polygenic analyses fails to provide evidence in favor of an overlap in genetic susceptibility between MS and ALS. Hence, our findings do not support a shared genetic background of common risk variants in MS and ALS.
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Affiliation(s)
- An Goris
- Laboratory for Neuroimmunology, Experimental Neurology, KU Leuven, Leuven, Belgium
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Al-Chalabi A, Kwak S, Mehler M, Rouleau G, Siddique T, Strong M, Leigh PN. Genetic and epigenetic studies of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2013; 14 Suppl 1:44-52. [DOI: 10.3109/21678421.2013.778571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Turner MR, Hardiman O, Benatar M, Brooks BR, Chio A, de Carvalho M, Ince PG, Lin C, Miller RG, Mitsumoto H, Nicholson G, Ravits J, Shaw PJ, Swash M, Talbot K, Traynor BJ, Van den Berg LH, Veldink JH, Vucic S, Kiernan MC. Controversies and priorities in amyotrophic lateral sclerosis. Lancet Neurol 2013; 12:310-22. [PMID: 23415570 DOI: 10.1016/s1474-4422(13)70036-x] [Citation(s) in RCA: 383] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Two decades after the discovery that 20% of familial amyotrophic lateral sclerosis (ALS) cases were linked to mutations in the superoxide dismutase-1 (SOD1) gene, a substantial proportion of the remainder of cases of familial ALS have now been traced to an expansion of the intronic hexanucleotide repeat sequence in C9orf72. This breakthrough provides an opportunity to re-evaluate longstanding concepts regarding the cause and natural history of ALS, coming soon after the pathological unification of ALS with frontotemporal dementia through a shared pathological signature of cytoplasmic inclusions of the ubiquitinated protein TDP-43. However, with profound clinical, prognostic, neuropathological, and now genetic heterogeneity, the concept of ALS as one disease appears increasingly untenable. This background calls for the development of a more sophisticated taxonomy, and an appreciation of ALS as the breakdown of a wider network rather than a discrete vulnerable population of specialised motor neurons. Identification of C9orf72 repeat expansions in patients without a family history of ALS challenges the traditional division between familial and sporadic disease. By contrast, the 90% of apparently sporadic cases and incomplete penetrance of several genes linked to familial cases suggest that at least some forms of ALS arise from the interplay of multiple genes, poorly understood developmental, environmental, and age-related factors, as well as stochastic events.
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Affiliation(s)
- Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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