1
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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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Boutry S, Helaers R, Lenaerts T, Vikkula M. Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations. Brief Bioinform 2023; 24:bbad412. [PMID: 37974506 DOI: 10.1093/bib/bbad412] [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: 02/14/2023] [Revised: 10/14/2023] [Accepted: 10/28/2023] [Indexed: 11/19/2023] Open
Abstract
Over the past years, progress made in next-generation sequencing technologies and bioinformatics have sparked a surge in association studies. Especially, genome-wide association studies (GWASs) have demonstrated their effectiveness in identifying disease associations with common genetic variants. Yet, rare variants can contribute to additional disease risk or trait heterogeneity. Because GWASs are underpowered for detecting association with such variants, numerous statistical methods have been recently proposed. Aggregation tests collapse multiple rare variants within a genetic region (e.g. gene, gene set, genomic loci) to test for association. An increasing number of studies using such methods successfully identified trait-associated rare variants and led to a better understanding of the underlying disease mechanism. In this review, we compare existing aggregation tests, their statistical features and scope of application, splitting them into the five classical classes: burden, adaptive burden, variance-component, omnibus and other. Finally, we describe some limitations of current aggregation tests, highlighting potential direction for further investigations.
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Affiliation(s)
- Simon Boutry
- Human Molecular Genetics, de Duve Institute, University of Louvain, Avenue Hippocrate 74 (+5) bte B1.74.06, 1200 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussels, 1050 Brussels, Belgium
| | - Raphaël Helaers
- Human Molecular Genetics, de Duve Institute, University of Louvain, Avenue Hippocrate 74 (+5) bte B1.74.06, 1200 Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussels, 1050 Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Artificial Intelligence laboratory, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, University of Louvain, Avenue Hippocrate 74 (+5) bte B1.74.06, 1200 Brussels, Belgium
- WELBIO department, WEL Research Institute, avenue Pasteur, 6, 1300 Wavre, Belgium
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3
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Akçimen F, Lopez ER, Landers JE, Nath A, Chiò A, Chia R, Traynor BJ. Amyotrophic lateral sclerosis: translating genetic discoveries into therapies. Nat Rev Genet 2023; 24:642-658. [PMID: 37024676 PMCID: PMC10611979 DOI: 10.1038/s41576-023-00592-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 04/08/2023]
Abstract
Recent advances in sequencing technologies and collaborative efforts have led to substantial progress in identifying the genetic causes of amyotrophic lateral sclerosis (ALS). This momentum has, in turn, fostered the development of putative molecular therapies. In this Review, we outline the current genetic knowledge, emphasizing recent discoveries and emerging concepts such as the implication of distinct types of mutation, variability in mutated genes in diverse genetic ancestries and gene-environment interactions. We also propose a high-level model to synthesize the interdependent effects of genetics, environmental and lifestyle factors, and ageing into a unified theory of ALS. Furthermore, we summarize the current status of therapies developed on the basis of genetic knowledge established for ALS over the past 30 years, and we discuss how developing treatments for ALS will advance our understanding of targeting other neurological diseases.
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Affiliation(s)
- Fulya Akçimen
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Elia R Lopez
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute for Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Institute of Cognitive Sciences and Technologies, C.N.R, Rome, Italy
- Azienda Ospedaliero Universitaria Citta' della Salute e della Scienza, Turin, Italy
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
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4
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Vasilopoulou C, Duguez S, Duddy W. Genome-Wide Gene-Set Analysis Approaches in Amyotrophic Lateral Sclerosis. J Pers Med 2022; 12:1932. [PMID: 36422108 PMCID: PMC9699154 DOI: 10.3390/jpm12111932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 09/10/2024] Open
Abstract
The rapid increase in the number of genetic variants identified to be associated with Amyotrophic Lateral Sclerosis (ALS) through genome-wide association studies (GWAS) has created an emerging need to understand the functional pathways that are implicated in the pathology of ALS. Gene-set analysis (GSA) is a powerful method that can provide insight into the associated biological pathways, determining the joint effect of multiple genetic markers. The main contribution of this review is the collection of ALS GSA studies that employ GWAS or individual-based genotype data, investigating their methodology and results related to ALS-associated molecular pathways. Furthermore, the limitations in standard single-gene analyses are summarized, highlighting the power of gene-set analysis, and a brief overview of the statistical properties of gene-set analysis and related concepts is provided. The main aims of this review are to investigate the reproducibility of the collected studies and identify their strengths and limitations, in order to enhance the experimental design and therefore the quality of the results of future studies, deepening our understanding of this devastating disease.
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Affiliation(s)
| | | | - William Duddy
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
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5
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Feronato SG, Silva MLM, Izbicki R, Farias TDJ, Shigunov P, Dallagiovanna B, Passetti F, dos Santos HG. Selecting Genetic Variants and Interactions Associated with Amyotrophic Lateral Sclerosis: A Group LASSO Approach. J Pers Med 2022; 12:jpm12081330. [PMID: 36013279 PMCID: PMC9410070 DOI: 10.3390/jpm12081330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a multi-system neurodegenerative disease that affects both upper and lower motor neurons, resulting from a combination of genetic, environmental, and lifestyle factors. Usually, the association between single-nucleotide polymorphisms (SNPs) and this disease is tested individually, which leads to the testing of multiple hypotheses. In addition, this classical approach does not support the detection of interaction-dependent SNPs. We applied a two-step procedure to select SNPs and pairwise interactions associated with ALS. SNP data from 276 ALS patients and 268 controls were analyzed by a two-step group LASSO in 2000 iterations. In the first step, we fitted a group LASSO model to a bootstrap sample and a random subset of predictors (25%) from the original data set aiming to screen for important SNPs and, in the second step, we fitted a hierarchical group LASSO model to evaluate pairwise interactions. An in silico analysis was performed on a set of variables, which were prioritized according to their bootstrap selection frequency. We identified seven SNPs (rs16984239, rs10459680, rs1436918, rs1037666, rs4552942, rs10773543, and rs2241493) and two pairwise interactions (rs16984239:rs2118657 and rs16984239:rs3172469) potentially involved in nervous system conservation and function. These results may contribute to the understanding of ALS pathogenesis, its diagnosis, and therapeutic strategy improvement.
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Affiliation(s)
| | | | - Rafael Izbicki
- Department of Statistics, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil
| | - Ticiana D. J. Farias
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81310-020, Brazil
- Division of Biomedical Informatics, Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Patrícia Shigunov
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81310-020, Brazil
| | | | - Fabio Passetti
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81310-020, Brazil
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6
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Ruffini N, Klingenberg S, Heese R, Schweiger S, Gerber S. The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Front Aging Neurosci 2022; 14:866886. [PMID: 35832065 PMCID: PMC9271745 DOI: 10.3389/fnagi.2022.866886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.
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Affiliation(s)
- Nicolas Ruffini
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research, Leibniz Association, Mainz, Germany
| | - Susanne Klingenberg
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Raoul Heese
- Fraunhofer Institute for Industrial Mathematics (ITWM), Kaiserslautern, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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7
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Pan S, Liu X, Liu T, Zhao Z, Dai Y, Wang YY, Jia P, Liu F. Causal Inference of Genetic Variants and Genes in Amyotrophic Lateral Sclerosis. Front Genet 2022; 13:917142. [PMID: 35812739 PMCID: PMC9257137 DOI: 10.3389/fgene.2022.917142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal progressive multisystem disorder with limited therapeutic options. Although genome-wide association studies (GWASs) have revealed multiple ALS susceptibility loci, the exact identities of causal variants, genes, cell types, tissues, and their functional roles in the development of ALS remain largely unknown. Here, we reported a comprehensive post-GWAS analysis of the recent large ALS GWAS (n = 80,610), including functional mapping and annotation (FUMA), transcriptome-wide association study (TWAS), colocalization (COLOC), and summary data-based Mendelian randomization analyses (SMR) in extensive multi-omics datasets. Gene property analysis highlighted inhibitory neuron 6, oligodendrocytes, and GABAergic neurons (Gad1/Gad2) as functional cell types of ALS and confirmed cerebellum and cerebellar hemisphere as functional tissues of ALS. Functional annotation detected the presence of multiple deleterious variants at three loci (9p21.2, 12q13.3, and 12q14.2) and highlighted a list of SNPs that are potentially functional. TWAS, COLOC, and SMR identified 43 genes at 24 loci, including 23 novel genes and 10 novel loci, showing significant evidence of causality. Integrating multiple lines of evidence, we further proposed that rs2453555 at 9p21.2 and rs229243 at 14q12 functionally contribute to the development of ALS by regulating the expression of C9orf72 in pituitary and SCFD1 in skeletal muscle, respectively. Together, these results advance our understanding of the biological etiology of ALS, feed into new therapies, and provide a guide for subsequent functional experiments.
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Affiliation(s)
- Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Tianzi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Yin-Ying Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- *Correspondence: Fan Liu, ; Peilin Jia,
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Fan Liu, ; Peilin Jia,
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8
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Sabaie H, Mazaheri Moghaddam M, Mazaheri Moghaddam M, Amirinejad N, Asadi MR, Daneshmandpour Y, Hussen BM, Taheri M, Rezazadeh M. Long non-coding RNA-associated competing endogenous RNA axes in the olfactory epithelium in schizophrenia: a bioinformatics analysis. Sci Rep 2021; 11:24497. [PMID: 34969953 PMCID: PMC8718521 DOI: 10.1038/s41598-021-04326-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
The etiology of schizophrenia (SCZ), as a serious mental illness, is unknown. The significance of genetics in SCZ pathophysiology is yet unknown, and newly identified mechanisms involved in the regulation of gene transcription may be helpful in determining how these changes affect SCZ development and progression. In the current work, we used a bioinformatics approach to describe the role of long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs) in the olfactory epithelium (OE) samples in order to better understand the molecular regulatory processes implicated in SCZ disorders in living individuals. The Gene Expression Omnibus database was used to obtain the OE microarray dataset (GSE73129) from SCZ sufferers and control subjects, which contained information about both lncRNAs and mRNAs. The limma package of R software was used to identify the differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). RNA interaction pairs were discovered using the Human MicroRNA Disease Database, DIANA-LncBase, and miRTarBase databases. In this study, the Pearson correlation coefficient was utilized to find positive correlations between DEmRNAs and DElncRNAs in the ceRNA network. Eventually, lncRNA-associated ceRNA axes were developed based on co-expression relations and DElncRNA-miRNA-DEmRNA interactions. This work found six potential DElncRNA-miRNA-DEmRNA loops in SCZ pathogenesis, including, SNTG2-AS1/hsa-miR-7-5p/SLC7A5, FLG-AS1/hsa-miR-34a-5p/FOSL1, LINC00960/hsa-miR-34a-5p/FOSL1, AQP4-AS1/hsa-miR-335-5p/FMN2, SOX2-OT/hsa-miR-24-3p/NOS3, and CASC2/hsa-miR-24-3p/NOS3. According to the findings, ceRNAs in OE might be promising research targets for studying SCZ molecular mechanisms. This could be a great opportunity to examine different aspects of neurodevelopment that may have been hampered early in SCZ patients.
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Affiliation(s)
- Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Madiheh Mazaheri Moghaddam
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Nazanin Amirinejad
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Reza Asadi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. .,Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
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9
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Wu P, Ding L, Li X, Liu S, Cheng F, He Q, Xiao M, Wu P, Hou H, Jiang M, Long P, Wang H, Liu L, Qu M, Shi X, Jiang Q, Mo T, Ding W, Fu Y, Han S, Huo X, Zeng Y, Zhou Y, Zhang Q, Ke J, Xu X, Ni W, Shao Z, Wang J, Liu P, Li Z, Jin Y, Zheng F, Wang F, Liu L, Li W, Liu K, Peng R, Xu X, Lin Y, Gao H, Shi L, Geng Z, Mu X, Yan Y, Wang K, Wu D, Hao X, Cheng S, Qiu G, Guo H, Li K, Chen G, Sun Z, Lin X, Jin X, Wang F, Sun C, Wang C. Trans-ethnic genome-wide association study of severe COVID-19. Commun Biol 2021; 4:1034. [PMID: 34465887 PMCID: PMC8408224 DOI: 10.1038/s42003-021-02549-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/12/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 has caused numerous infections with diverse clinical symptoms. To identify human genetic variants contributing to the clinical development of COVID-19, we genotyped 1457 (598/859 with severe/mild symptoms) and sequenced 1141 (severe/mild: 474/667) patients of Chinese ancestry. We further incorporated 1401 genotyped and 948 sequenced ancestry-matched population controls, and tested genome-wide association on 1072 severe cases versus 3875 mild or population controls, followed by trans-ethnic meta-analysis with summary statistics of 3199 hospitalized cases and 897,488 population controls from the COVID-19 Host Genetics Initiative. We identified three significant signals outside the well-established 3p21.31 locus: an intronic variant in FOXP4-AS1 (rs1853837, odds ratio OR = 1.28, P = 2.51 × 10-10, allele frequencies in Chinese/European AF = 0.345/0.105), a frameshift insertion in ABO (rs8176719, OR = 1.19, P = 8.98 × 10-9, AF = 0.422/0.395) and a Chinese-specific intronic variant in MEF2B (rs74490654, OR = 8.73, P = 1.22 × 10-8, AF = 0.004/0). These findings highlight an important role of the adaptive immunity and the ABO blood-group system in protection from developing severe COVID-19.
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Affiliation(s)
- Peng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Ding
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaodong Li
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Siyang Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing He
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Mingzhong Xiao
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Ping Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Hongyan Hou
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minghui Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pinpin Long
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linlin Liu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Minghan Qu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xian Shi
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Jiang
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Mo
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wencheng Ding
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Shi Han
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Xixiang Huo
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Yingchun Zeng
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Yana Zhou
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Qing Zhang
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Jia Ke
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Xi Xu
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Wei Ni
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Zuoyu Shao
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Jingzhi Wang
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Panhong Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zilong Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Jin
- Department of Emergency, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Wang
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Lei Liu
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Wending Li
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Liu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Peng
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuedan Xu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhui Lin
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Gao
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Limei Shi
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziyue Geng
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuanwen Mu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Degang Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingjie Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shanshan Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gaokun Qiu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huan Guo
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kezhen Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Ziyong Sun
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Jin
- School of Medicine, South China University of Technology, Guangzhou, China.
| | - Feng Wang
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China.
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China.
| | - Chaolong Wang
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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10
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Hall MA, Wallace J, Lucas AM, Bradford Y, Verma SS, Müller-Myhsok B, Passero K, Zhou J, McGuigan J, Jiang B, Pendergrass SA, Zhang Y, Peissig P, Brilliant M, Sleiman P, Hakonarson H, Harley JB, Kiryluk K, Van Steen K, Moore JH, Ritchie MD. Novel EDGE encoding method enhances ability to identify genetic interactions. PLoS Genet 2021; 17:e1009534. [PMID: 34086673 PMCID: PMC8208534 DOI: 10.1371/journal.pgen.1009534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/16/2021] [Accepted: 04/06/2021] [Indexed: 11/26/2022] Open
Abstract
Assumptions are made about the genetic model of single nucleotide polymorphisms (SNPs) when choosing a traditional genetic encoding: additive, dominant, and recessive. Furthermore, SNPs across the genome are unlikely to demonstrate identical genetic models. However, running SNP-SNP interaction analyses with every combination of encodings raises the multiple testing burden. Here, we present a novel and flexible encoding for genetic interactions, the elastic data-driven genetic encoding (EDGE), in which SNPs are assigned a heterozygous value based on the genetic model they demonstrate in a dataset prior to interaction testing. We assessed the power of EDGE to detect genetic interactions using 29 combinations of simulated genetic models and found it outperformed the traditional encoding methods across 10%, 30%, and 50% minor allele frequencies (MAFs). Further, EDGE maintained a low false-positive rate, while additive and dominant encodings demonstrated inflation. We evaluated EDGE and the traditional encodings with genetic data from the Electronic Medical Records and Genomics (eMERGE) Network for five phenotypes: age-related macular degeneration (AMD), age-related cataract, glaucoma, type 2 diabetes (T2D), and resistant hypertension. A multi-encoding genome-wide association study (GWAS) for each phenotype was performed using the traditional encodings, and the top results of the multi-encoding GWAS were considered for SNP-SNP interaction using the traditional encodings and EDGE. EDGE identified a novel SNP-SNP interaction for age-related cataract that no other method identified: rs7787286 (MAF: 0.041; intergenic region of chromosome 7)–rs4695885 (MAF: 0.34; intergenic region of chromosome 4) with a Bonferroni LRT p of 0.018. A SNP-SNP interaction was found in data from the UK Biobank within 25 kb of these SNPs using the recessive encoding: rs60374751 (MAF: 0.030) and rs6843594 (MAF: 0.34) (Bonferroni LRT p: 0.026). We recommend using EDGE to flexibly detect interactions between SNPs exhibiting diverse action. Although traditional genetic encodings are widely implemented in genetics research, including in genome-wide association studies (GWAS) and epistasis, each method makes assumptions that may not reflect the underlying etiology. Here, we introduce a novel encoding method that estimates and assigns an individualized data-driven encoding for each single nucleotide polymorphism (SNP): the elastic data-driven genetic encoding (EDGE). With simulations, we demonstrate that this novel method is more accurate and robust than traditional encoding methods in estimating heterozygous genotype values, reducing the type I error, and detecting SNP-SNP interactions. We further applied the traditional encodings and EDGE to biomedical data from the Electronic Medical Records and Genomics (eMERGE) Network for five phenotypes, and EDGE identified a novel interaction for age-related cataract not detected by traditional methods, which replicated in data from the UK Biobank. EDGE provides an alternative approach to understanding and modeling diverse SNP models and is recommended for studying complex genetics in common human phenotypes.
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Affiliation(s)
- Molly A. Hall
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Penn State Cancer Institute, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| | - John Wallace
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Anastasia M. Lucas
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yuki Bradford
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shefali S. Verma
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Kristin Passero
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jiayan Zhou
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - John McGuigan
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Beibei Jiang
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, United States of America
| | - Peggy Peissig
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
| | - Murray Brilliant
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
| | - Patrick Sleiman
- Department of Pediatrics, Center for Applied Genomics, Children’s Hospital of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hakon Hakonarson
- Department of Pediatrics, Center for Applied Genomics, Children’s Hospital of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- United States Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Kristel Van Steen
- WELBIO, GIGA-R Medical Genomics-BIO3, University of Liège, Liège, Belgium
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Jason H. Moore
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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11
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Ruffini N, Klingenberg S, Schweiger S, Gerber S. Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale. Cells 2020; 9:E2642. [PMID: 33302607 PMCID: PMC7764447 DOI: 10.3390/cells9122642] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/24/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS) are heterogeneous, progressive diseases with frequently overlapping symptoms characterized by a loss of neurons. Studies have suggested relations between neurodegenerative diseases for many years (e.g., regarding the aggregation of toxic proteins or triggering endogenous cell death pathways). We gathered publicly available genomic, transcriptomic, and proteomic data from 177 studies and more than one million patients to detect shared genetic patterns between the neurodegenerative diseases on three analyzed omics-layers. The results show a remarkably high number of shared differentially expressed genes between the transcriptomic and proteomic levels for all conditions, while showing a significant relation between genomic and proteomic data between AD and PD and AD and ALS. We identified a set of 139 genes being differentially expressed in several transcriptomic experiments of all four diseases. These 139 genes showed overrepresented gene ontology (GO) Terms involved in the development of neurodegeneration, such as response to heat and hypoxia, positive regulation of cytokines and angiogenesis, and RNA catabolic process. Furthermore, the four analyzed neurodegenerative diseases (NDDs) were clustered by their mean direction of regulation throughout all transcriptomic studies for this set of 139 genes, with the closest relation regarding this common gene set seen between AD and HD. GO-Term and pathway analysis of the proteomic overlap led to biological processes (BPs), related to protein folding and humoral immune response. Taken together, we could confirm the existence of many relations between Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis on transcriptomic and proteomic levels by analyzing the pathways and GO-Terms arising in these intersections. The significance of the connection and the striking relation of the results to processes leading to neurodegeneration between the transcriptomic and proteomic data for all four analyzed neurodegenerative diseases showed that exploring many studies simultaneously, including multiple omics-layers of different neurodegenerative diseases simultaneously, holds new relevant insights that do not emerge from analyzing these data separately. Furthermore, the results shed light on processes like the humoral immune response that have previously been described only for certain diseases. Our data therefore suggest human patients with neurodegenerative diseases should be addressed as complex biological systems by integrating multiple underlying data sources.
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Affiliation(s)
- Nicolas Ruffini
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
- Leibniz Institute for Resilience Research, Leibniz Association, Wallstraße 7, 55122 Mainz, Germany
| | - Susanne Klingenberg
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susann Schweiger
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
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12
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Vasilopoulou C, Morris AP, Giannakopoulos G, Duguez S, Duddy W. What Can Machine Learning Approaches in Genomics Tell Us about the Molecular Basis of Amyotrophic Lateral Sclerosis? J Pers Med 2020; 10:E247. [PMID: 33256133 PMCID: PMC7712791 DOI: 10.3390/jpm10040247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is the most common late-onset motor neuron disorder, but our current knowledge of the molecular mechanisms and pathways underlying this disease remain elusive. This review (1) systematically identifies machine learning studies aimed at the understanding of the genetic architecture of ALS, (2) outlines the main challenges faced and compares the different approaches that have been used to confront them, and (3) compares the experimental designs and results produced by those approaches and describes their reproducibility in terms of biological results and the performances of the machine learning models. The majority of the collected studies incorporated prior knowledge of ALS into their feature selection approaches, and trained their machine learning models using genomic data combined with other types of mined knowledge including functional associations, protein-protein interactions, disease/tissue-specific information, epigenetic data, and known ALS phenotype-genotype associations. The importance of incorporating gene-gene interactions and cis-regulatory elements into the experimental design of future ALS machine learning studies is highlighted. Lastly, it is suggested that future advances in the genomic and machine learning fields will bring about a better understanding of ALS genetic architecture, and enable improved personalized approaches to this and other devastating and complex diseases.
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Affiliation(s)
- Christina Vasilopoulou
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK; (C.V.); (S.D.)
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK;
| | - George Giannakopoulos
- Institute of Informatics and Telecommunications, NCSR Demokritos, 153 10 Aghia Paraskevi, Greece;
- Science For You (SciFY) PNPC, TEPA Lefkippos-NCSR Demokritos, 27, Neapoleos, 153 41 Ag. Paraskevi, Greece
| | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK; (C.V.); (S.D.)
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK; (C.V.); (S.D.)
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13
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Xiao L, Yuan Z, Jin S, Wang T, Huang S, Zeng P. Multiple-Tissue Integrative Transcriptome-Wide Association Studies Discovered New Genes Associated With Amyotrophic Lateral Sclerosis. Front Genet 2020; 11:587243. [PMID: 33329728 PMCID: PMC7714931 DOI: 10.3389/fgene.2020.587243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple causal genes associated with amyotrophic lateral sclerosis (ALS); however, the genetic architecture of ALS remains completely unknown and a large number of causal genes have yet been discovered. To full such gap in part, we implemented an integrative analysis of transcriptome-wide association study (TWAS) for ALS to prioritize causal genes with summary statistics from 80,610 European individuals and employed 13 GTEx brain tissues as reference transcriptome panels. The summary-level TWAS analysis with single brain tissue was first undertaken and then a flexible p-value combination strategy, called summary data-based Cauchy Aggregation TWAS (SCAT), was proposed to pool association signals from single-tissue TWAS analysis while protecting against highly positive correlation among tests. Extensive simulations demonstrated SCAT can produce well-calibrated p-value for the control of type I error and was often much more powerful to identify association signals across various scenarios compared with single-tissue TWAS analysis. Using SCAT, we replicated three ALS-associated genes (i.e., ATXN3, SCFD1, and C9orf72) identified in previous GWASs and discovered additional five genes (i.e., SLC9A8, FAM66D, TRIP11, JUP, and RP11-529H20.6) which were not reported before. Furthermore, we discovered the five associations were largely driven by genes themselves and thus might be new genes which were likely related to the risk of ALS. However, further investigations are warranted to verify these results and untangle the pathophysiological function of the genes in developing ALS.
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Affiliation(s)
- Lishun Xiao
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Siyi Jin
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China
| | - Ting Wang
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China
| | - Shuiping Huang
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ping Zeng
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
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14
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Abstract
Abstract
Purpose of Review
Amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) spectrum disorder is a rare fatal disease with strong genetic influences. The implementation of short-read sequencing methodologies in increasingly large patient cohorts has rapidly expanded our knowledge of the complex genetic architecture of the disease. We aim to convey the broad history of ALS gene discovery as context for a focused review of 11 ALS gene associations reported over the last 5 years. We also summarize the current level of genetic evidence for all previously reported genes.
Recent Findings
The history of ALS gene discovery has occurred in at least four identifiable phases, each powered by different technologies and scale of investigation. The most recent epoch, benefitting from population-scale genome data, large international consortia, and low-cost sequencing, has yielded 11 new gene associations. We summarize the current level of genetic evidence supporting these ALS genes, highlighting any genotype-phenotype or genotype-pathology correlations, and discussing preliminary understanding of molecular pathogenesis. This era has also raised uncertainty around prior ALS-associated genes and clarified the role of others.
Summary
Our understanding of the genetic underpinning of ALS has expanded rapidly over the last 25 years and has led directly to the clinical application of molecularly driven therapies. Ongoing sequencing efforts in ALS will identify new causative and risk factor genes while clarifying the status of genes reported in prior eras of research.
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15
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Shatunov A, Al-Chalabi A. The genetic architecture of ALS. Neurobiol Dis 2020; 147:105156. [PMID: 33130222 DOI: 10.1016/j.nbd.2020.105156] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Aleksey Shatunov
- Department of Basic & Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9RX, UK
| | - Ammar Al-Chalabi
- Department of Basic & Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9RX, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK.
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16
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Zhang Z, Chen G. A logical relationship for schizophrenia, bipolar, and major depressive disorder. Part 1: Evidence from chromosome 1 high density association screen. J Comp Neurol 2020; 528:2620-2635. [PMID: 32266715 DOI: 10.1002/cne.24921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022]
Abstract
Familial clustering of schizophrenia (SCZ), bipolar disorder (BPD), and major depressive disorder (MDD) was investigated systematically (Aukes et al., Genetics in Medicine, 2012, 14, 338-341) and any two or even three of these disorders could coexist in some families. Furthermore, evidence from symptomatology and psychopharmacology also imply the existence of intrinsic connections between these three major psychiatric disorders. A total of 71,445 SNPs on chromosome 1 were genotyped on 119 SCZ, 253 BPD (type-I), 177 MDD cases and 1000 controls and further validated in 986 SCZ patients in the population of Shandong province of China. Outstanding psychosis genes are systematically revealed( ATP1A4, ELTD1, FAM5C, HHAT, KIF26B, LMX1A, NEGR1, NFIA, NR5A2, NTNG1, PAPPA2, PDE4B, PEX14, RYR2, SYT6, TGFBR3, TTLL7, and USH2A). Unexpectedly, flanking genes for up to 97.09% of the associated SNPs were also replicated in an enlarged cohort of 986 SCZ patients. From the perspective of etiological rather than clinical psychiatry, bipolar, and major depressive disorder could be subtypes of schizophrenia. Meanwhile, the varied clinical feature and prognosis might be the result of interaction of genetics and epigenetics, for example, irreversible or reversible shut down, and over or insufficient expression of certain genes, which may gives other aspects of these severe mental disorders.
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Affiliation(s)
- Zhihua Zhang
- Shandong Mental Health Center, Jinan, Shandong, China
| | - Gang Chen
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, China
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17
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Ravnik-Glavač M, Glavač D. Circulating RNAs as Potential Biomarkers in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2020; 21:ijms21051714. [PMID: 32138249 PMCID: PMC7084402 DOI: 10.3390/ijms21051714] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex multi-system neurodegenerative disorder with currently limited diagnostic and no therapeutic options. Despite the intense efforts no clinically applicable biomarkers for ALS are yet established. Most current research is thus focused, in particular, in identifying potential non-invasive circulating biomarkers for more rapid and accurate diagnosis and monitoring of the disease. In this review, we have focused on messenger RNA (mRNA), non-coding RNAs (lncRNAs), micro RNAs (miRNAs) and circular RNA (circRNAs) as potential biomarkers for ALS in peripheral blood serum, plasma and cells. The most promising miRNAs include miR-206, miR-133b, miR-27a, mi-338-3p, miR-183, miR-451, let-7 and miR-125b. To test clinical potential of this miRNA panel, a useful approach may be to perform such analysis on larger multi-center scale using similar experimental design. However, other types of RNAs (lncRNAs, circRNAs and mRNAs) that, together with miRNAs, represent RNA networks, have not been yet extensively studied in blood samples of patients with ALS. Additional research has to be done in order to find robust circulating biomarkers and therapeutic targets that will distinguish key RNA interactions in specific ALS-types to facilitate diagnosis, predict progression and design therapy.
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Affiliation(s)
- Metka Ravnik-Glavač
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
- Correspondence: (M.R.-G.); (D.G.)
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
- Correspondence: (M.R.-G.); (D.G.)
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18
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Diaz-Ortiz ME, Chen-Plotkin AS. Omics in Neurodegenerative Disease: Hope or Hype? Trends Genet 2020; 36:152-159. [PMID: 31932096 PMCID: PMC7065657 DOI: 10.1016/j.tig.2019.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/22/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022]
Abstract
The past 15 years have seen a boom in the use and integration of 'omic' approaches (limited here to genomic, transcriptomic, and epigenomic techniques) to study neurodegenerative disease in an unprecedented way. We first highlight advances in and the limitations of using such approaches in the neurodegenerative disease literature, with a focus on Alzheimer's disease (AD), Parkinson's disease (PD), frontotemporal lobar degeneration (FTLD), and amyotrophic lateral sclerosis (ALS). We next discuss how these studies can advance human health in the form of generating leads for downstream mechanistic investigation or yielding polygenic risk scores (PRSs) for prognostication. However, we argue that these approaches constitute a new form of molecular description, analogous to clinical or pathological description, that alone does not hold the key to solving these complex diseases.
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Affiliation(s)
- Maria E Diaz-Ortiz
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Alice S Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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19
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Dolinar A, Koritnik B, Glavač D, Ravnik-Glavač M. Circular RNAs as Potential Blood Biomarkers in Amyotrophic Lateral Sclerosis. Mol Neurobiol 2019; 56:8052-8062. [PMID: 31175544 PMCID: PMC6834740 DOI: 10.1007/s12035-019-1627-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are emerging as a novel, yet powerful player in many human diseases. They are involved in several cellular processes and are becoming a noteworthy type of biomarkers. Among other functions, circRNAs can serve as RNA sponges or as scaffolds for RNA-binding proteins. Here, we investigated a microarray expression profile of circRNAs in leukocyte samples from ALS patients and age- and sex-matched healthy controls to identify differentially expressed circRNAs. We selected 10 of them for a qPCR validation of expression on a larger set of samples, identification of their associations with clinical parameters, and evaluation of their diagnostic potential. In total, expression of 7/10 circRNAs was significant in a larger cohort of ALS patients, compared with age- and sex-matched healthy controls. Three of them (hsa_circ_0023919, hsa_circ_0063411, and hsa_circ_0088036) showed the same regulation as in microarray results. These three circRNAs also had AUC > 0.95, and sensitivity and specificity for the optimal threshold point > 90%, showing their potential for using them as diagnostic biomarkers.
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Affiliation(s)
- Ana Dolinar
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Blaž Koritnik
- Institute of Clinical Neurophysiology, Division of Neurology, University Medical Centre Ljubljana, Zaloška cesta 7, 1000, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Metka Ravnik-Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia.
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20
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Multiple roles of the actin and microtubule-regulating formins in the developing brain. Neurosci Res 2019; 138:59-69. [DOI: 10.1016/j.neures.2018.09.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 01/08/2023]
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21
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Kumar S, Yadav N, Pandey S, Thelma BK. Advances in the discovery of genetic risk factors for complex forms of neurodegenerative disorders: contemporary approaches, success, challenges and prospects. J Genet 2018. [DOI: 10.1007/s12041-018-0953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Putilov AA, Dorokhov VB, Puchkova AN, Arsenyev GN, Sveshnikov DS. Genetic-based signatures of the latitudinal differences in chronotype. BIOL RHYTHM RES 2018. [DOI: 10.1080/09291016.2018.1465249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Arcady A. Putilov
- Research Group for Math-Modeling of Biomedical Systems, The Research Institute for Molecular Biology and Biophysics, Novosibirsk, Russia
| | - Vladimir B. Dorokhov
- Laboratory of Sleep/Wake Neurobiology, the Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexandra N. Puchkova
- Laboratory of Sleep/Wake Neurobiology, the Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, Moscow, Russia
- Center for Cognition and Communication, Pushkin State Russian Language Institute, Moscow, Russia
| | - Gleb N. Arsenyev
- Laboratory of Sleep/Wake Neurobiology, the Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry S. Sveshnikov
- Department of Normal Physiology, Medical Institute, Peoples’ Friendship University of Russia, Moscow, Russia
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23
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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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24
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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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25
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Copy Number Variations in Amyotrophic Lateral Sclerosis: Piecing the Mosaic Tiles Together through a Systems Biology Approach. Mol Neurobiol 2017; 55:1299-1322. [PMID: 28120152 PMCID: PMC5820374 DOI: 10.1007/s12035-017-0393-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/06/2017] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and still untreatable motor neuron disease. Despite the molecular mechanisms underlying ALS pathogenesis that are still far from being understood, several studies have suggested the importance of a genetic contribution in both familial and sporadic forms of the disease. In addition to single-nucleotide polymorphisms (SNPs), which account for only a limited number of ALS cases, a consistent number of common and rare copy number variations (CNVs) have been associated to ALS. Most of the CNV-based association studies use a traditional candidate-gene approach that is inadequate for uncovering the genetic architectures of complex traits like ALS. The emergent paradigm of “systems biology” may offer a new perspective to better interpret the wide spectrum of CNVs in ALS, enabling the characterization of the complex network of gene products underlying ALS pathogenesis. In this review, we will explore the landscape of CNVs in ALS, putting specific emphasis on the functional impact of common CNV regions and genes consistently associated with increased risk of developing disease. In addition, we will discuss the potential contribution of multiple rare CNVs in ALS pathogenesis, focusing our attention on the complex mechanisms by which these proteins might impact, individually or in combination, the genetic susceptibility of ALS. The comprehensive detection and functional characterization of common and rare candidate risk CNVs in ALS susceptibility may bring new pieces into the intricate mosaic of ALS pathogenesis, providing interesting and important implications for a more precise molecular biomarker-assisted diagnosis and more effective and personalized treatments.
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26
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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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27
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Zhao H, Fan D, Nyholt DR, Yang Y. Enrichment of SNPs in Functional Categories Reveals Genes Affecting Complex Traits. Hum Mutat 2016; 37:820-6. [PMID: 27113629 DOI: 10.1002/humu.23007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 04/03/2016] [Indexed: 02/03/2023]
Abstract
Genome-wide association studies (GWAS) have indicated potential to identify heritability of common complex phenotypes, but traditional approaches have limited ability to detect hiding signals because single SNP has weak effect size accounting for only a small fraction of overall phenotypic variations. To improve the power of GWAS, methods have been developed to identify truly associated genes by jointly testing effects of all SNPs. However, equally considering all SNPs within a gene might dilute strong signals of SNPs in real functional categories. Here, we observed a consistent pattern on enrichment of significant SNPs in eight functional categories across six phenotypes, with the highest enrichment in coding and both UTR regions while the lowest enrichment in the intron. Based on the pattern of SNP enrichment in functional categories, we developed a new approach for detecting gene associations on traits (DGAT) by selecting the most significant functional category and then using SNPs within it to assess gene associations. The method was found to be robust in type I error rate on simulated data, and to have mostly higher power in detecting associated genes for three different diseases than other methods. Further analysis indicated ability of the DGAT to detect novel genes. The DGAT is available by http://sparks-lab.org/server/DGAT.
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Affiliation(s)
- Huiying Zhao
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
| | - Dale R Nyholt
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Yuedong Yang
- Institute for Glycomics, Griffith University, Queensland, Australia
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28
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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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29
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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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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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31
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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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Schachtner LT, Sola IE, Forand D, Antonacci S, Postovit AJ, Mortimer NT, Killian DJ, Olesnicky EC. Drosophila Shep and C. elegans SUP-26 are RNA-binding proteins that play diverse roles in nervous system development. Dev Genes Evol 2015; 225:319-30. [PMID: 26271810 DOI: 10.1007/s00427-015-0514-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/03/2015] [Indexed: 12/14/2022]
Abstract
The Caenorhabditis elegans gene sup-26 encodes a well-conserved RNA-recognition motif-containing RNA-binding protein (RBP) that functions in dendrite morphogenesis of the PVD sensory neuron. The Drosophila ortholog of sup-26, alan shepard (shep), is expressed throughout the nervous system and has been shown to regulate neuronal remodeling during metamorphosis. Here, we extend these studies to show that sup-26 and shep are required for the development of diverse cell types within the nematode and fly nervous systems during embryonic and larval stages. We ascribe roles for sup-26 in regulating dendrite number and the expression of genes involved in mechanosensation within the nematode peripheral nervous system. We also find that in Drosophila, shep regulates dendrite length and branch order of nociceptive neurons, regulates the organization of neuronal clusters of the peripheral nervous system and the organization of axons within the ventral nerve cord. Taken together, our results suggest that shep/sup-26 orthologs play diverse roles in neural development across animal species. Moreover, we discuss potential roles for shep/sup-26 orthologs in the human nervous system.
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Affiliation(s)
- Logan T Schachtner
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Ismail E Sola
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Daniel Forand
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Simona Antonacci
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903, USA
| | - Adam J Postovit
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Nathan T Mortimer
- Department of Biological Sciences, University of Denver, Denver, CO, 80208, USA.,School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903, USA.
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA.
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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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34
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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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35
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Rosenfeld J, Strong MJ. Challenges in the Understanding and Treatment of Amyotrophic Lateral Sclerosis/Motor Neuron Disease. Neurotherapeutics 2015; 12:317-25. [PMID: 25572957 PMCID: PMC4404444 DOI: 10.1007/s13311-014-0332-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
With the acceleration in our understanding of ALS and the related motor neuron disease has come even greater challenges in reconciling all of the proposed pathogenic mechanisms and how this will translate into impactful treatments. Fundamental issues such as diagnostic definition(s) of the disease spectrum, relevant biomarkers, the impact of multiple novel genetic mutations and the significant effect of symptomatic treatments on disease progression are all areas of active investigation. In this review, we will focus on these key issues and highlight the challenges that confront both clinicians and basic science researchers.
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Affiliation(s)
- Jeffrey Rosenfeld
- Central California Neuroscience Institute, UCSF Fresno, Division of Neurology, Fresno, CA, USA,
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36
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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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Khankhanian P, Din L, Caillier SJ, Gourraud PA, Baranzini SE. SNP imputation bias reduces effect size determination. Front Genet 2015; 6:30. [PMID: 25709616 PMCID: PMC4321633 DOI: 10.3389/fgene.2015.00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
Imputation is a commonly used technique that exploits linkage disequilibrium to infer missing genotypes in genetic datasets, using a well-characterized reference population. While there is agreement that the reference population has to match the ethnicity of the query dataset, it is common practice to use the same reference to impute genotypes for a wide variety of phenotypes. We hypothesized that using a reference composed of samples with a different phenotype than the query dataset would introduce imputation bias. To test this hypothesis we used GWAS datasets from Amyotrophic Lateral Sclerosis (ALS), Parkinson Disease (PD), and Crohn's Disease (CD). First, we masked and then performed imputation of 100 disease-associated markers and 100 non-associated markers from each study. Two references for imputation were used in parallel: one consisting of healthy controls and another consisting of patients with the same disease. We assessed the discordance (imprecision) and bias (inaccuracy) of imputation by comparing predicted genotypes to those assayed by SNP-chip. We also assessed the bias on the observed effect size when the predicted genotypes were used in a GWAS study. When healthy controls were used as reference for imputation, a significant bias was observed, particularly in the disease-associated markers. Using cases as reference significantly attenuated this bias. For nearly all markers, the direction of the bias favored the non-risk allele. In GWAS studies of the three diseases (with healthy reference controls from the 1000 genomes as reference), the mean OR for disease-associated markers obtained by imputation was lower than that obtained using original assayed genotypes. We found that the bias is inherent to imputation as using different methods did not alter the results. In conclusion, imputation is a powerful method to predict genotypes and estimate genetic risk for GWAS. However, a careful choice of reference population is needed to minimize biases inherent to this approach.
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Affiliation(s)
- Pouya Khankhanian
- Department of Neurology, University of California San Francisco San Francisco, CA, USA
| | - Lennox Din
- Department of Neurology, University of California San Francisco San Francisco, CA, USA
| | - Stacy J Caillier
- Department of Neurology, University of California San Francisco San Francisco, CA, USA
| | | | - Sergio E Baranzini
- Department of Neurology, University of California San Francisco San Francisco, CA, USA
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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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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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Sher RB, Heiman-Patterson TD, Blankenhorn EA, Jiang J, Alexander G, Deitch JS, Cox GA. A major QTL on mouse chromosome 17 resulting in lifespan variability in SOD1-G93A transgenic mouse models of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:588-600. [PMID: 25008789 DOI: 10.3109/21678421.2014.932381] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis is a late-onset degenerative disease affecting motor neurons in the spinal cord, brainstem, and motor cortex. There is great variation in the expression of ALS symptoms even between siblings who both carry the same Cu/Zn superoxide dismutase (SOD1) mutations. One important use of transgenic mouse models of SOD1-ALS is the study of genetic influences on ALS severity. We utilized multiple inbred mouse strains containing the SOD1-G93A transgene to demonstrate a major quantitative trait locus (QTL) on mouse chromosome 17 resulting in a significant shift in lifespan. Reciprocal crosses between long- and short-lived strains identified critical regions, and we have narrowed the area for potential genetic modifier(s) to < 2Mb of the genome. Results showed that resequencing of this region resulted in 28 candidate genes with potentially functional differences between strains. In conclusion, these studies provide the first major modifier locus affecting lifespan in this model of FALS and, once identified, these candidate modifier genes may provide insight into modifiers of human disease and, most importantly, define new targets for the development of therapies.
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Shang H, Liu G, Jiang Y, Fu J, Zhang B, Song R, Wang W. Pathway Analysis of Two Amyotrophic Lateral Sclerosis GWAS Highlights Shared Genetic Signals with Alzheimer’s Disease and Parkinson’s Disease. Mol Neurobiol 2014; 51:361-9. [DOI: 10.1007/s12035-014-8673-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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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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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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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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Blasco H, Bernard-Marissal N, Vourc'h P, Guettard YO, Sunyach C, Augereau O, Khederchah J, Mouzat K, Antar C, Gordon PH, Veyrat-Durebex C, Besson G, Andersen PM, Salachas F, Meininger V, Camu W, Pettmann B, Andres CR, Corcia P. A rare motor neuron deleterious missense mutation in the DPYSL3 (CRMP4) gene is associated with ALS. Hum Mutat 2013; 34:953-60. [PMID: 23568759 DOI: 10.1002/humu.22329] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/01/2013] [Indexed: 12/17/2022]
Abstract
The dihydropyrimidinase-like 3 (DPYSL3) or Collapsin Response Mediator Protein 4a (CRMP4a) expression is modified in neurodegeneration and is involved in several ALS-associated pathways including axonal transport, glutamate excitotoxicity, and oxidative stress. The objective of the study was to analyze CRMP4 as a risk factor for ALS. We analyzed the DPYSL3/CRMP4 gene in French ALS patients (n = 468) and matched-controls (n = 394). We subsequently examined a variant in a Swedish population (184 SALS, 186 controls), and evaluated its functional effects on axonal growth and survival in motor neuron cell culture. The rs147541241:A>G missense mutation occurred in higher frequency among French ALS patients (odds ratio = 2.99) but the association was not confirmed in the Swedish population. In vitro expression of mutated DPYSL3 in motor neurons reduced axonal growth and accelerated cell death compared with wild type protein. Thus, the association between the rs147541241 variant and ALS was limited to the French population, highlighting the geographic particularities of genetic influences (risks, contributors). The identified variant appears to shorten motor neuron survival through a detrimental effect on axonal growth and CRMP4 could act as a key unifier in transduction pathways leading to neurodegeneration through effects on early axon development.
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Affiliation(s)
- Hélène Blasco
- UMR INSERM U930, Université François-Rabelais de Tours, Tours, France.
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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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Fareed M, Afzal M. Single nucleotide polymorphism in genome-wide association of human population: A tool for broad spectrum service. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2013. [DOI: 10.1016/j.ejmhg.2012.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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50
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Ahmeti KB, Ajroud-Driss S, Al-Chalabi A, Andersen PM, Armstrong J, Birve A, Blauw HM, Brown RH, Bruijn L, Chen W, Chio A, Comeau MC, Cronin S, Diekstra FP, Soraya Gkazi A, Glass JD, Grab JD, Groen EJ, Haines JL, Hardiman O, Heller S, Huang J, Hung WY, Jaworski JM, Jones A, Khan H, Landers JE, Langefeld CD, Leigh PN, Marion MC, McLaughlin RL, Meininger V, Melki J, Miller JW, Mora G, Pericak-Vance MA, Rampersaud E, Robberecht W, Russell LP, Salachas F, Saris CG, Shatunov A, Shaw CE, Siddique N, Siddique T, Smith BN, Sufit R, Topp S, Traynor BJ, Vance C, van Damme P, van den Berg LH, van Es MA, van Vught PW, Veldink JH, Yang Y, Zheng JG. Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1. Neurobiol Aging 2013; 34:357.e7-19. [PMID: 22959728 PMCID: PMC3839234 DOI: 10.1016/j.neurobiolaging.2012.07.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 07/26/2012] [Accepted: 07/29/2012] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is the third most common adult-onset neurodegenerative disease. Individuals with ALS rapidly progress to paralysis and die from respiratory failure within 3 to 5 years after symptom onset. Epidemiological factors explain only a modest amount of the risk for ALS. However, there is growing evidence of a strong genetic component to both familial and sporadic ALS risk. The International Consortium on Amyotrophic Lateral Sclerosis Genetics was established to bring together existing genome-wide association cohorts and identify sporadic ALS susceptibility and age at symptom onset loci. Here, we report the results of a meta-analysis of the International Consortium on Amyotrophic Lateral Sclerosis Genetics genome-wide association samples, consisting of 4243 ALS cases and 5112 controls from 13 European ancestry cohorts from across the United States and Europe. Eight genomic regions provided evidence of association with ALS, including 9p21.2 (rs3849942, odds ratio [OR] = 1.21; p = 4.41 × 10(-7)), 17p11.2 (rs7477, OR = 1.30; p = 2.89 × 10(-7)), and 19p13 (rs12608932, OR = 1.37, p = 1.29 × 10(-7)). Six genomic regions were associated with age at onset of ALS. The strongest evidence for an age of onset locus was observed at 1p34.1, with comparable evidence at rs3011225 (R(2)(partial) = 0.0061; p = 6.59 × 10(-8)) and rs803675 (R(2)(partial) = 0.0060; p = 6.96 × 10(-8)). These associations were consistent across all 13 cohorts. For rs3011225, individuals with at least 1 copy of the minor allele had an earlier average age of onset of over 2 years. Identifying the underlying pathways influencing susceptibility to and age at onset of ALS may provide insight into the pathogenic mechanisms and motivate new pharmacologic targets for this fatal neurodegenerative disease.
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