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Malamon JS, Farrell JJ, Xia LC, Dombroski BA, Das RG, Way J, Kuzma AB, Valladares O, Leung YY, Scanlon AJ, Lopez IAB, Brehony J, Worley KC, Zhang NR, Wang LS, Farrer LA, Schellenberg GD, Lee WP, Vardarajan BN. A comparative study of structural variant calling in WGS from Alzheimer's disease families. Life Sci Alliance 2024; 7:e202302181. [PMID: 38418088 PMCID: PMC10902710 DOI: 10.26508/lsa.202302181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation for generating a high-quality SV call set in whole-genome sequencing from the Alzheimer's Disease Sequencing Project comprising 578 individuals from 111 families. Employing two complementary pipelines, Scalpel and Parliament, for SV/indel calling, we assessed sensitivity through sample replicates (N = 9) with in silico variant spike-ins. We developed a novel metric, D-score, to evaluate caller specificity for deletions. The accuracy of deletions was evaluated by Sanger sequencing. We generated a high-quality call set of 152,301 deletions of diverse sizes. Sanger sequencing validated 114 of 146 detected deletions (78.1%). Scalpel excelled in accuracy for deletions ≤100 bp, whereas Parliament was optimal for deletions >900 bp. Overall, 83.0% and 72.5% of calls by Scalpel and Parliament were validated, respectively, including all 11 deletions called by both Parliament and Scalpel between 101 and 900 bp. Our flexible protocol successfully generated a high-quality deletion call set and a truth set of Sanger sequencing-validated deletions with precise breakpoints spanning 1-17,000 bp.
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Affiliation(s)
- John S Malamon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - John J Farrell
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Li Charlie Xia
- https://ror.org/03mtd9a03 Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rueben G Das
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jessica Way
- Broad Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda B Kuzma
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Otto Valladares
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison J Scanlon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Irving Antonio Barrera Lopez
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jack Brehony
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kim C Worley
- https://ror.org/02pttbw34 Human Genome Sequencing Center, and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lindsay A Farrer
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Epidemiology and Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Badri N Vardarajan
- https://ror.org/01esghr10 Gertrude H. Sergievsky Center and Taub Institute of Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
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2
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Sierra C, Sabariego-Navarro M, Fernández-Blanco Á, Cruciani S, Zamora-Moratalla A, Novoa EM, Dierssen M. The lncRNA Snhg11, a new candidate contributing to neurogenesis, plasticity, and memory deficits in Down syndrome. Mol Psychiatry 2024:10.1038/s41380-024-02440-9. [PMID: 38409595 DOI: 10.1038/s41380-024-02440-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024]
Abstract
Down syndrome (DS) stands as the prevalent genetic cause of intellectual disability, yet comprehensive understanding of its cellular and molecular underpinnings remains limited. In this study, we explore the cellular landscape of the hippocampus in a DS mouse model, the Ts65Dn, through single-nuclei transcriptional profiling. Our findings demonstrate that trisomy manifests as a highly specific modification of the transcriptome within distinct cell types. Remarkably, we observed a significant shift in the transcriptomic profile of granule cells in the dentate gyrus (DG) associated with trisomy. We identified the downregulation of a specific small nucleolar RNA host gene, Snhg11, as the primary driver behind this observed shift in the trisomic DG. Notably, reduced levels of Snhg11 in this region were also observed in a distinct DS mouse model, the Dp(16)1Yey, as well as in human postmortem brain tissue, indicating its relevance in Down syndrome. To elucidate the function of this long non-coding RNA (lncRNA), we knocked down Snhg11 in the DG of wild-type mice. Intriguingly, this intervention alone was sufficient to impair synaptic plasticity and adult neurogenesis, resembling the cognitive phenotypes associated with trisomy in the hippocampus. Our study uncovers the functional role of Snhg11 in the DG and underscores the significance of this lncRNA in intellectual disability. Furthermore, our findings highlight the importance of DG in the memory deficits observed in Down syndrome.
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Affiliation(s)
- Cesar Sierra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Miguel Sabariego-Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, 08003, Spain
| | - Álvaro Fernández-Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sonia Cruciani
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, 08003, Spain
| | - Alfonsa Zamora-Moratalla
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, 08003, Spain
| | - Mara Dierssen
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, 08003, Spain.
- Biomedical Research Networking Center for Rare Diseases (CIBERER), Barcelona, Spain.
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3
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Zhang H, Xia T, Xia Z, Zhou H, Li Z, Wang W, Zhai X, Jin B. KIF18A inactivates hepatic stellate cells and alleviates liver fibrosis through the TTC3/Akt/mTOR pathway. Cell Mol Life Sci 2024; 81:96. [PMID: 38372748 PMCID: PMC10876760 DOI: 10.1007/s00018-024-05114-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/03/2023] [Accepted: 01/04/2024] [Indexed: 02/20/2024]
Abstract
Activation of hepatic stellate cells (HSCs) has been demonstrated to play a pivotal role in the process of liver fibrogenesis. In this study, we observed a decrease in the expression of KIF18A in fibrotic liver tissues compared to healthy liver tissues, which exhibited a negative correlation with the activation of HSCs. To elucidate the molecular mechanisms underlying the involvement of KIF18A, we performed in vitro proliferation experiments and established a CCl4-induced liver fibrosis model. Our results revealed that KIF18A knockdown enhanced HSCs proliferation and reduced HSCs apoptosis in vitro. Mouse liver fibrosis grade was evaluated with Masson's trichrome and alpha-smooth muscle actin (α-SMA) staining. In addition, the expression of fibrosis markers Col1A1, Stat1, and Timp1 were detected. Animal experiments demonstrated that knockdown of KIF18A could promote liver fibrosis, whereas overexpression of KIF18A alleviated liver fibrosis in a CCl4-induced mouse model. Mechanistically, we found that KIF18A suppressed the AKT/mTOR pathway and exhibited direct binding to TTC3. Moreover, TTC3 was found to interact with p-AKT and could promote its ubiquitination and degradation. Our findings provide compelling evidence that KIF18A enhances the protein binding between TTC3 and p-AKT, promoting TTC3-mediated ubiquitination and degradation of p-AKT. These results refine the current understanding of the mechanisms underlying the pathogenesis of liver fibrosis and may offer new targets for treating this patient population.
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Affiliation(s)
- Hao Zhang
- Organ Transplant Department, Qilu Hospital of Shandong University, Jinan, China
- Department of Hepatobiliary Surgery, The Second Hospital of Shandong University, Jinan, China
| | - Tong Xia
- Organ Transplant Department, Qilu Hospital of Shandong University, Jinan, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Huaxin Zhou
- Department of Hepatobiliary Surgery, The Second Hospital of Shandong University, Jinan, China
| | - Zhipeng Li
- Department of Hepatobiliary Surgery, The Second Hospital of Shandong University, Jinan, China
| | - Wei Wang
- Medical Integration and Practice Center, Shandong University, Jinan, China.
| | - Xiangyu Zhai
- Organ Transplant Department, Qilu Hospital of Shandong University, Jinan, China.
- Department of Hepatobiliary Surgery, The Second Hospital of Shandong University, Jinan, China.
| | - Bin Jin
- Organ Transplant Department, Qilu Hospital of Shandong University, Jinan, China.
- Department of Hepatobiliary Surgery, The Second Hospital of Shandong University, Jinan, China.
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4
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Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. Neurobiol Aging 2023; 131:182-195. [PMID: 37677864 PMCID: PMC10538380 DOI: 10.1016/j.neurobiolaging.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 09/09/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 (TTC3) gene (rs377155188, p.S1038C, NM_003316.4:c 0.3113C>G) was found to segregate with disease in a multigenerational family with late-onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing, and the resulting isogenic pair of iPSC lines was differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3-dimensional morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant.
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Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carolina L Duarte
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mayra J Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shaina A Simon
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek J Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Amanda T Miyares
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; JJ Vance Memorial Summer Internship in Biological and Computational Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina M Carney
- Mental Health & Behavioral Science Service, Bruce W. Carter VA Medical Center, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
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5
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Sierra C, Sabariego-Navarro M, Fernández-Blanco Á, Cruciani S, Zamora-Moratalla A, Novoa EM, Dierssen M. The lncRNA Snhg11, a new candidate contributing to neurogenesis, plasticity and memory deficits in Down syndrome. RESEARCH SQUARE 2023:rs.3.rs-3184329. [PMID: 37841843 PMCID: PMC10571621 DOI: 10.21203/rs.3.rs-3184329/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Down syndrome (DS) stands as the prevalent genetic cause of intellectual disability, yet comprehensive understanding of its cellular and molecular underpinnings remains limited. In this study, we explore the cellular landscape of the hippocampus in a DS mouse model through single-nuclei transcriptional profiling. Our findings demonstrate that trisomy manifests as a highly specific modification of the transcriptome within distinct cell types. Remarkably, we observed a significant shift in the transcriptomic profile of granule cells in the dentate gyrus (DG) associated with trisomy. We identified the downregulation of a specific small nucleolar RNA host gene, Snhg11, as the primary driver behind this observed shift in the trisomic DG. Notably, reduced levels of Snhg11 in this region were also observed in a distinct DS mouse model, the Dp(16)1Yey, as well as in human postmortem tissue, indicating its relevance in Down syndrome. To elucidate the function of this long non-coding RNA (lncRNA), we knocked down Snhg11 in the DG of wild-type mice. Intriguingly, this intervention alone was sufficient to impair synaptic plasticity and adult neurogenesis, resembling the cognitive phenotypes associated with trisomy in the hippocampus. Our study uncovers the functional role of Snhg11 in the DG and underscores the significance of this lncRNA in intellectual disability. Furthermore, our findings highlight the importance of the DG in the memory deficits observed in Down syndrome.
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Affiliation(s)
- Cesar Sierra
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Miguel Sabariego-Navarro
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Álvaro Fernández-Blanco
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Sonia Cruciani
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Alfonsa Zamora-Moratalla
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Eva Maria Novoa
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain
| | - Mara Dierssen
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain
- Biomedical Research Networking Center for Rare Diseases (CIBERER), 08003 Barcelona, Spain
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6
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Ray NR, Ayodele T, Jean-Francois M, Baez P, Fernandez V, Bradley J, Crane PK, Dalgard CL, Kuzma A, Nicaretta H, Sims R, Williams J, Cuccaro ML, Pericak-Vance MA, Mayeux R, Wang LS, Schellenberg GD, Cruchaga C, Beecham GW, Reitz C. The Early-Onset Alzheimer's Disease Whole-Genome Sequencing Project: Study design and methodology. Alzheimers Dement 2023; 19:4187-4195. [PMID: 37390458 PMCID: PMC10527497 DOI: 10.1002/alz.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/02/2023]
Abstract
INTRODUCTION Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations, resulting in a lack of understanding of its molecular etiology. METHODS Whole-genome sequencing and harmonization of clinical, neuropathological, and biomarker data of over 5000 EOAD cases of diverse ancestries. RESULTS A publicly available genomics resource for EOAD with extensive harmonized phenotypes. Primary analysis will (1) identify novel EOAD risk loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. DISCUSSION This novel resource complements over 50,000 control and late-onset AD samples generated through the Alzheimer's Disease Sequencing Project (ADSP). The harmonized EOAD/ADSP joint call will be available through upcoming ADSP data releases and will allow for additional analyses across the full onset range. HIGHLIGHTS Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations. This results in a significant lack of understanding of the molecular etiology of this devastating form of the disease. The Early-Onset Alzheimer's Disease Whole-genome Sequencing Project is a collaborative initiative to generate a large-scale genomics resource for early-onset Alzheimer's disease with extensive harmonized phenotype data. Primary analyses are designed to (1) identify novel EOAD risk and protective loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. The harmonized genomic and phenotypic data from this initiative will be available through NIAGADS.
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Affiliation(s)
- Nicholas R. Ray
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Temitope Ayodele
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Melissa Jean-Francois
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Penelope Baez
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Victoria Fernandez
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Joseph Bradley
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Paul K. Crane
- Division of General Internal Medicine, University of
Washington, Seattle, WA 98195, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics,
Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- The American Genome Center, Uniformed Services University
of the Health Sciences, Bethesda, MD 20814, USA
| | - Amanda Kuzma
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Heather Nicaretta
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Julie Williams
- UK Dementia Research Institute, Cardiff University,
Cardiff CF10 3AT, UK
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Michael L. Cuccaro
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Richard Mayeux
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Gary W. Beecham
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
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7
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Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542316. [PMID: 37292815 PMCID: PMC10246004 DOI: 10.1101/2023.05.25.542316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 ( TTC3 ) gene (rs377155188, p.S1038C, NM_003316.4:c.3113C>G) was found to segregate with disease in a multigenerational family with late onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing and the resulting isogenic pair of iPSC lines were differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3D morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant. Highlights The AD risk variant TTC3 p.S1038C reduces the expression levels of TTC3 The variant modifies the expression of AD specific genes BACE1 , INPP5F , and UNC5C Neurons with the variant are enriched for genes in the PI3K-Akt pathwayiPSC-derived neurons with the alteration have increased neurite length and branchingThe variant interferes with actin cytoskeleton and is ameliorated by Cytochalasin D.
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8
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Mol MO, van der Lee SJ, Hulsman M, Pijnenburg YAL, Scheltens P, Seelaar H, van Swieten JC, Kaat LD, Holstege H, van Rooij JGJ. Mapping the genetic landscape of early-onset Alzheimer's disease in a cohort of 36 families. Alzheimers Res Ther 2022; 14:77. [PMID: 35650585 PMCID: PMC9158156 DOI: 10.1186/s13195-022-01018-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Many families with clinical early-onset Alzheimer's disease (EOAD) remain genetically unexplained. A combination of genetic factors is not standardly investigated. In addition to monogenic causes, we evaluated the possible polygenic architecture in a large series of families, to assess if genetic testing of familial EOAD could be expanded. METHODS Thirty-six pedigrees (77 patients) were ascertained from a larger cohort of patients, with relationships determined by genetic data (exome sequencing data and/or SNP arrays). All families included at least one AD patient with symptom onset <70 years. We evaluated segregating rare variants in known dementia-related genes, and other genes or variants if shared by multiple families. APOE was genotyped and duplications in APP were assessed by targeted test or using SNP array data. We computed polygenic risk scores (PRS) compared with a reference population-based dataset, by imputing SNP arrays or exome sequencing data. RESULTS In eight families, we identified a pathogenic variant, including the genes APP, PSEN1, SORL1, and an unexpected GRN frameshift variant. APOE-ε4 homozygosity was present in eighteen families, showing full segregation with disease in seven families. Eight families harbored a variant of uncertain significance (VUS), of which six included APOE-ε4 homozygous carriers. PRS was not higher in the families combined compared with the population mean (beta 0.05, P = 0.21), with a maximum increase of 0.61 (OR = 1.84) in the GRN family. Subgroup analyses indicated lower PRS in six APP/PSEN1 families compared with the rest (beta -0.22 vs. 0.10; P = 0.009) and lower APOE burden in all eight families with monogenic cause (beta 0.29 vs. 1.15, P = 0.010). Nine families remained without a genetic cause or risk factor identified. CONCLUSION Besides monogenic causes, we suspect a polygenic disease architecture in multiple families based on APOE and rare VUS. The risk conveyed by PRS is modest across the studied families. Families without any identified risk factor render suitable candidates for further in-depth genetic evaluation.
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Affiliation(s)
- Merel O Mol
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Sven J van der Lee
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Marc Hulsman
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Phillip Scheltens
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Laura Donker Kaat
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henne Holstege
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Jeroen G J van Rooij
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
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9
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Molecular interaction of stress granules with Tau and autophagy in Alzheimer's disease. Neurochem Int 2022; 157:105342. [DOI: 10.1016/j.neuint.2022.105342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/09/2022] [Accepted: 04/10/2022] [Indexed: 11/23/2022]
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10
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Ben-Yosef N, Frampton M, Schiff ER, Daher S, Abu Baker F, Safadi R, Israeli E, Segal AW, Levine AP. Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease. Gastroenterol Rep (Oxf) 2021; 9:521-532. [PMID: 34925849 PMCID: PMC8677555 DOI: 10.1093/gastro/goab007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Family studies support a genetic predisposition to inflammatory bowel diseases (IBD), but known genetic variants only partially explain the disease heritability. Families with multiple affected individuals potentially harbour rare and high-impact causal variants. Long regions of homozygosity due to recent inbreeding may increase the risk of individuals bearing homozygous loss-of-function variants. This study aimed to identify rare and homozygous genetic variants contributing to IBD. METHODS Four families with known consanguinity and multiple cases of IBD were recruited. In a family-specific analysis, we utilised homozygosity mapping complemented by whole-exome sequencing. RESULTS We detected a single region of homozygosity shared by Crohn's disease cases from a family of Druze ancestry, spanning 2.6 Mb containing the NOD2 gene. Whole-exome sequencing did not identify any potentially damaging variants within the region, suggesting that non-coding variation may be involved. In addition, affected individuals in the families harboured several rare and potentially damaging homozygous variants in genes with a role in autophagy and innate immunity including LRRK1, WHAMM, DENND3, and C5. CONCLUSION This study examined the potential contribution of rare, high-impact homozygous variants in consanguineous families with IBD. While the analysis was not designed to achieve statistical significance, our findings highlight genes or loci that warrant further research. Non-coding variants affecting NOD2 may be of importance in Druze patients with Crohn's disease.
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Affiliation(s)
- Noam Ben-Yosef
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Matthew Frampton
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Elena R Schiff
- Institute of Ophthalmology, Moorfields Eye Hospital, University College London, London, UK
| | - Saleh Daher
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Fadi Abu Baker
- Institue of Gastroenterology and Hepatology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Rifaat Safadi
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Eran Israeli
- Institute of Gastroenterology and Liver disease, E. Wolfson Medical Center, Holon, Israel
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Department of Pathology, University College London, London, UK
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11
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Potjewyd FM, Axtman AD. Exploration of Aberrant E3 Ligases Implicated in Alzheimer's Disease and Development of Chemical Tools to Modulate Their Function. Front Cell Neurosci 2021; 15:768655. [PMID: 34867205 PMCID: PMC8637409 DOI: 10.3389/fncel.2021.768655] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/28/2021] [Indexed: 11/24/2022] Open
Abstract
The Ubiquitin Proteasome System (UPS) is responsible for the degradation of misfolded or aggregated proteins via a multistep ATP-dependent proteolytic mechanism. This process involves a cascade of ubiquitin (Ub) transfer steps from E1 to E2 to E3 ligase. The E3 ligase transfers Ub to a targeted protein that is brought to the proteasome for degradation. The inability of the UPS to remove misfolded or aggregated proteins due to UPS dysfunction is commonly observed in neurodegenerative diseases, such as Alzheimer's disease (AD). UPS dysfunction in AD drives disease pathology and is associated with the common hallmarks such as amyloid-β (Aβ) accumulation and tau hyperphosphorylation, among others. E3 ligases are key members of the UPS machinery and dysfunction or changes in their expression can propagate other aberrant processes that accelerate AD pathology. The upregulation or downregulation of expression or activity of E3 ligases responsible for these processes results in changes in protein levels of E3 ligase substrates, many of which represent key proteins that propagate AD. A powerful way to better characterize UPS dysfunction in AD and the role of individual E3 ligases is via the use of high-quality chemical tools that bind and modulate specific E3 ligases. Furthermore, through combining gene editing with recent advances in 3D cell culture, in vitro modeling of AD in a dish has become more relevant and possible. These cell-based models of AD allow for study of specific pathways and mechanisms as well as characterization of the role E3 ligases play in driving AD. In this review, we outline the key mechanisms of UPS dysregulation linked to E3 ligases in AD and highlight the currently available chemical modulators. We present several key approaches for E3 ligase ligand discovery being employed with respect to distinct classes of E3 ligases. Where possible, specific examples of the use of cultured neurons to delineate E3 ligase biology have been captured. Finally, utilizing the available ligands for E3 ligases in the design of proteolysis targeting chimeras (PROTACs) to degrade aberrant proteins is a novel strategy for AD, and we explore the prospects of PROTACs as AD therapeutics.
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12
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Zhang D, Zhou S, Zhou Z, Jiang X, Chen D, Sun HX, Huang J, Qu S, Yang S, Gu Y, Zhang X, Jin X, Gao Y, Shen Y, Chen F. BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data. BMC Med Genomics 2021; 14:260. [PMID: 34736471 PMCID: PMC8570004 DOI: 10.1186/s12920-021-01110-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Birth defects pose a major challenge to infant health. Thus far, however, the causes of most birth defects remain cryptic. Over the past few decades, considerable effort has been expended on disclosing the underlying mechanisms related to birth defects, yielding myriad treatises and data. To meet the increasing requirements for data resources, we developed a freely accessible birth defect multi-omics database (BDdb, http://t21omics.cngb.org) consisting of multi-omics data and potential disease biomarkers. Results In total, omics datasets from 136 Gene Expression Omnibus (GEO) Series records, including 5245 samples, as well as 869 biomarkers of 22 birth defects in six different species, were integrated into the BDdb. The database provides a user-friendly interface for searching, browsing, and downloading data of interest. The BDdb also enables users to explore the correlations among different sequencing methods, such as chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) from different studies, to obtain the information on gene expression patterns from diverse aspects. Conclusion To the best of our knowledge, the BDdb is the first comprehensive database associated with birth defects, which should benefit the diagnosis and prevention of birth defects. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01110-x.
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Affiliation(s)
- Dengwei Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Si Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Ziheng Zhou
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Xiaosen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Dongsheng Chen
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Hai-Xi Sun
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China
| | - Jie Huang
- National Institutes for Food and Drug Control (NIFDC), Beijing, 100050, People's Republic of China
| | - Shoufang Qu
- National Institutes for Food and Drug Control (NIFDC), Beijing, 100050, People's Republic of China
| | - Songchen Yang
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Xiuqing Zhang
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,Guangdong Provincial Key Laboratory of Human Disease GenomicsShenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China. .,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,MGI, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.
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13
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Zhou X, Chen X, Hong T, Zhang M, Cai Y, Cui L. TTC3-Mediated Protein Quality Control, A Potential Mechanism for Cognitive Impairment. Cell Mol Neurobiol 2021; 42:1659-1669. [PMID: 33638766 PMCID: PMC9239942 DOI: 10.1007/s10571-021-01060-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/11/2021] [Indexed: 01/14/2023]
Abstract
The tetrapeptide repeat domain 3 (TTC3) gene falls within Down's syndrome (DS) critical region. Cognitive impairment is a common phenotype of DS and Alzheimer’s disease (AD), and overexpression of TTC3 can accelerate cognitive decline, but the specific mechanism is unknown. The TTC3-mediated protein quality control (PQC) mechanism, similar to the PQC system, is divided into three parts: it acts as a cochaperone to assist proteins in folding correctly; it acts as an E3 ubiquitin ligase (E3s) involved in protein degradation processes through the ubiquitin–proteasome system (UPS); and it may also eventually cause autophagy by affecting mitochondrial function. Thus, this article reviews the research progress on the structure, function, and metabolism of TTC3, including the recent research progress on TTC3 in DS and AD; the role of TTC3 in cognitive impairment through PQC in combination with the abovementioned attributes of TTC3; and the potential targets of TTC3 in the treatment of such diseases.
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Affiliation(s)
- Xu Zhou
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Xiongjin Chen
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Tingting Hong
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Miaoping Zhang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Yujie Cai
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China.
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14
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Laverde-Paz MJ, Nuytemans K, Wang L, Vance JM, Pericak-Vance MA, Dykxhoorn DM, Cukier HN. Derivation of stem cell line UMi028-A-2 containing a CRISPR/Cas9 induced Alzheimer's disease risk variant p.S1038C in the TTC3 gene. Stem Cell Res 2021; 52:102258. [PMID: 33626494 DOI: 10.1016/j.scr.2021.102258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/28/2022] Open
Abstract
The UMi028-A-2 human induced pluripotent stem cell line carries a homozygous mutation (rs377155188, C>G, p.S1038C) in the tetratricopeptide repeat domain 3 (TTC3) gene that was introduced via CRISPR/Cas9 genome editing. The line was originally derived from a neurologically normal male and has been thoroughly characterized following editing. The p.S1038C variant has been shown to potentially contribute to the risk of late onset Alzheimer's disease and is a resource to further investigate the consequences of TTC3 and this alteration in disease pathology.
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Affiliation(s)
- Mayra Juliana Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136.
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15
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Schmidt MF, Gan ZY, Komander D, Dewson G. Ubiquitin signalling in neurodegeneration: mechanisms and therapeutic opportunities. Cell Death Differ 2021; 28:570-590. [PMID: 33414510 PMCID: PMC7862249 DOI: 10.1038/s41418-020-00706-7] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases are characterised by progressive damage to the nervous system including the selective loss of vulnerable populations of neurons leading to motor symptoms and cognitive decline. Despite millions of people being affected worldwide, there are still no drugs that block the neurodegenerative process to stop or slow disease progression. Neuronal death in these diseases is often linked to the misfolded proteins that aggregate within the brain (proteinopathies) as a result of disease-related gene mutations or abnormal protein homoeostasis. There are two major degradation pathways to rid a cell of unwanted or misfolded proteins to prevent their accumulation and to maintain the health of a cell: the ubiquitin–proteasome system and the autophagy–lysosomal pathway. Both of these degradative pathways depend on the modification of targets with ubiquitin. Aging is the primary risk factor of most neurodegenerative diseases including Alzheimer’s disease, Parkinson’s disease and amyotrophic lateral sclerosis. With aging there is a general reduction in proteasomal degradation and autophagy, and a consequent increase of potentially neurotoxic protein aggregates of β-amyloid, tau, α-synuclein, SOD1 and TDP-43. An often over-looked yet major component of these aggregates is ubiquitin, implicating these protein aggregates as either an adaptive response to toxic misfolded proteins or as evidence of dysregulated ubiquitin-mediated degradation driving toxic aggregation. In addition, non-degradative ubiquitin signalling is critical for homoeostatic mechanisms fundamental for neuronal function and survival, including mitochondrial homoeostasis, receptor trafficking and DNA damage responses, whilst also playing a role in inflammatory processes. This review will discuss the current understanding of the role of ubiquitin-dependent processes in the progressive loss of neurons and the emergence of ubiquitin signalling as a target for the development of much needed new drugs to treat neurodegenerative disease. ![]()
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Affiliation(s)
- Marlene F Schmidt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, 3052, Australia
| | - Zhong Yan Gan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, 3052, Australia
| | - David Komander
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, 3052, Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, 3052, Australia.
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16
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Mishra R, Li B. The Application of Artificial Intelligence in the Genetic Study of Alzheimer's Disease. Aging Dis 2020; 11:1567-1584. [PMID: 33269107 PMCID: PMC7673858 DOI: 10.14336/ad.2020.0312] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease in which genetic factors contribute approximately 70% of etiological effects. Studies have found many significant genetic and environmental factors, but the pathogenesis of AD is still unclear. With the application of microarray and next-generation sequencing technologies, research using genetic data has shown explosive growth. In addition to conventional statistical methods for the processing of these data, artificial intelligence (AI) technology shows obvious advantages in analyzing such complex projects. This article first briefly reviews the application of AI technology in medicine and the current status of genetic research in AD. Then, a comprehensive review is focused on the application of AI in the genetic research of AD, including the diagnosis and prognosis of AD based on genetic data, the analysis of genetic variation, gene expression profile, gene-gene interaction in AD, and genetic analysis of AD based on a knowledge base. Although many studies have yielded some meaningful results, they are still in a preliminary stage. The main shortcomings include the limitations of the databases, failing to take advantage of AI to conduct a systematic biology analysis of multilevel databases, and lack of a theoretical framework for the analysis results. Finally, we outlook the direction of future development. It is crucial to develop high quality, comprehensive, large sample size, data sharing resources; a multi-level system biology AI analysis strategy is one of the development directions, and computational creativity may play a role in theory model building, verification, and designing new intervention protocols for AD.
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Affiliation(s)
- Rohan Mishra
- Washington Institute for Health Sciences, Arlington, VA 22203, USA
| | - Bin Li
- Washington Institute for Health Sciences, Arlington, VA 22203, USA
- Georgetown University Medical Center, Washington D.C. 20057, USA
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17
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Grenn FP, Kim JJ, Makarious MB, Iwaki H, Illarionova A, Brolin K, Kluss JH, Schumacher‐Schuh AF, Leonard H, Faghri F, Billingsley K, Krohn L, Hall A, Diez‐Fairen M, Periñán MT, Foo JN, Sandor C, Webber C, Fiske BK, Gibbs JR, Nalls MA, Singleton AB, Bandres‐Ciga S, Reed X, Blauwendraat C. The Parkinson's Disease Genome-Wide Association Study Locus Browser. Mov Disord 2020; 35:2056-2067. [PMID: 32864809 PMCID: PMC7754106 DOI: 10.1002/mds.28197] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/27/2020] [Accepted: 06/10/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a neurodegenerative disease with an often complex component identifiable by genome-wide association studies. The most recent large-scale PD genome-wide association studies have identified more than 90 independent risk variants for PD risk and progression across more than 80 genomic regions. One major challenge in current genomics is the identification of the causal gene(s) and variant(s) at each genome-wide association study locus. The objective of the current study was to create a tool that would display data for relevant PD risk loci and provide guidance with the prioritization of causal genes and potential mechanisms at each locus. METHODS We included all significant genome-wide signals from multiple recent PD genome-wide association studies including themost recent PD risk genome-wide association study, age-at-onset genome-wide association study, progression genome-wide association study, and Asian population PD risk genome-wide association study. We gathered data for all genes 1 Mb up and downstream of each variant to allow users to assess which gene(s) are most associated with the variant of interest based on a set of self-ranked criteria. Multiple databases were queried for each gene to collect additional causal data. RESULTS We created a PD genome-wide association study browser tool (https://pdgenetics.shinyapps.io/GWASBrowser/) to assist the PD research community with the prioritization of genes for follow-up functional studies to identify potential therapeutic targets. CONCLUSIONS Our PD genome-wide association study browser tool provides users with a useful method of identifying potential causal genes at all known PD risk loci from large-scale PD genome-wide association studies. We plan to update this tool with new relevant data as sample sizes increase and new PD risk loci are discovered. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Francis P. Grenn
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Jonggeol J. Kim
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Mary B. Makarious
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Hirotaka Iwaki
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | | | - Kajsa Brolin
- Lund UniversityTranslational Neurogenetics Unit, Department of Experimental Medical ScienceLundSweden
| | - Jillian H. Kluss
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | | | - Hampton Leonard
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | - Faraz Faghri
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | - Kimberley Billingsley
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Lynne Krohn
- Department of Human GeneticsMcGill UniversityMontrealQuebecCanada
| | - Ashley Hall
- Department of Molecular and Clinical PharmacologyInstitute of Translational Medicine, University of LiverpoolLiverpoolUK
| | - Monica Diez‐Fairen
- Fundació Docència i Recerca Mútua Terrassa and Movement Disorders Unit, Department of NeurologyUniversity Hospital Mútua TerrassaBarcelonaSpain
| | - Maria Teresa Periñán
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de SevillaHospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Jia Nee Foo
- Lee Kong Chian School of MedicineNanyang Technological University SingaporeSingaporeSingapore
- Human GeneticsGenome Institute of Singapore, A*STARSingaporeSingapore
| | - Cynthia Sandor
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Caleb Webber
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Brian K. Fiske
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central StationNew YorkNYUSA
| | - J. Raphael Gibbs
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Mike A. Nalls
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | - Andrew B. Singleton
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Sara Bandres‐Ciga
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Xylena Reed
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Cornelis Blauwendraat
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
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18
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Kong D, Zhang Z, Chen L, Huang W, Zhang F, Wang L, Wang Y, Cao P, Zheng S. Curcumin blunts epithelial-mesenchymal transition of hepatocytes to alleviate hepatic fibrosis through regulating oxidative stress and autophagy. Redox Biol 2020; 36:101600. [PMID: 32526690 PMCID: PMC7287144 DOI: 10.1016/j.redox.2020.101600] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/08/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
The massive production and activation of myofibroblasts (MFB) is key to the development of liver fibrosis. In many studies, it has been proven that hepatocytes are an important part of MFB, and can be transformed into MFB through epithelial-mesenchymal transition (EMT) during hepatic fibrogenesis. In our previous study, we confirmed that curcumin inhibited EMT procession and differentiation of hepatocytes into MFB. In addition, in previous studies, it has been shown that autophagy plays an important role in the regulation of cellular EMT procession. In the current study, we showed that curcumin inhibited TGF-β/Smad signaling transmission by activating autophagy, thereby inhibiting EMT. The mechanism of degradative polyubiquitylation of Smad2 and Smad3 is likely through inhibiting tetratricopeptide repeat domain 3 (TTC3) and by inducing ubiquitylation and proteasomal degradation of Smad ubiquitination regulatory factor 2 (SMURF2), which on account of the increase of autophagy in hepatocytes. Curcumin inhibits levels of reactive oxygen species (ROS) and oxidative stress in hepatocytes by activating PPAR-α, and regulates upstream signaling pathways of autophagy AMPK and PI3K/AKT/mTOR, leading to an increase of the autophagic flow in hepatocytes. In this study, we confirm that curcumin effectively reduced the occurrence of EMT in hepatocytes and inhibited production of the extracellular matrix (ECM) by activating autophagy, which provides a potential novel therapeutic strategy for hepatic fibrosis.
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Affiliation(s)
- Desong Kong
- Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, 210022, China; Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zili Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Liping Chen
- Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, 210022, China
| | - Weifang Huang
- Department of Pharmacology, School of Integral Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Feng Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ling Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yu Wang
- Department of Oncology, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, 210022, China
| | - Peng Cao
- Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China.
| | - Shizhong Zheng
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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19
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Rasheed A, Gumus E, Zaki M, Johnson K, Manzoor H, LaForce G, Ross D, McEvoy-Venneri J, Stanley V, Lee S, Virani A, Ben-Omran T, Gleeson JG, Naz S, Schaffer A. Bi-allelic TTC5 variants cause delayed developmental milestones and intellectual disability. J Med Genet 2020; 58:237-246. [PMID: 32439809 DOI: 10.1136/jmedgenet-2020-106849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/01/2020] [Accepted: 04/17/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Intellectual disability syndromes (IDSs) with or without developmental delays affect up to 3% of the world population. We sought to clinically and genetically characterise a novel IDS segregating in five unrelated consanguineous families. METHODS Clinical analyses were performed for eight patients with intellectual disability (ID). Whole-exome sequencing for selected participants followed by Sanger sequencing for all available family members was completed. Identity-by-descent (IBD) mapping was carried out for patients in two Egyptian families harbouring an identical variant. RNA was extracted from blood cells of Turkish participants, followed by cDNA synthesis and real-time PCR for TTC5. RESULTS Phenotype comparisons of patients revealed shared clinical features of moderate-to-severe ID, corpus callosum agenesis, mild ventriculomegaly, simplified gyral pattern, cerebral atrophy, delayed motor and verbal milestones and hypotonia, presenting with an IDS. Four novel homozygous variants in TTC5: c.629A>G;p.(Tyr210Cys), c.692C>T;p.(Ala231Val), c.787C>T;p.(Arg263Ter) and c.1883C>T;p.(Arg395Ter) were identified in the eight patients from participating families. IBD mapping revealed that c.787C>T;p.(Arg263Ter) is a founder variant in Egypt. Missense variants c.629A>G;p.(Tyr210Cys) and c.692C>T;p.(Ala231Val) disrupt highly conserved residues of TTC5 within the fifth and sixth tetratricopeptide repeat motifs which are required for p300 interaction, while the nonsense variants are predicted to decrease TTC5 expression. Functional analysis of variant c.1883C>T;p.(Arg395Ter) showed reduced TTC5 transcript levels in accordance with nonsense-mediated decay. CONCLUSION Combining our clinical and molecular data with a recent case report, we identify the core and variable clinical features associated with TTC5 loss-of-function variants and reveal the requirement for TTC5 in human brain development and health.
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Affiliation(s)
- Arisha Rasheed
- School of Biological Sciences, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Evren Gumus
- Medical Genetics, Mugla Sitki Kocman University Faculty of Medicine, Mugla, Turkey.,Medical Genetics, Harran University Faculty of Medicine, Sanliurfa, Turkey
| | - Maha Zaki
- Clinical Genetic Department, National Research Centre, Cairo, Egypt
| | - Katherine Johnson
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Humera Manzoor
- School of Biological Sciences, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Geneva LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Danica Ross
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer McEvoy-Venneri
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, USA
| | - Valentina Stanley
- Department of Neuroscience, University of California, San Diego, La Jolla, CA, USA
| | - Sangmoon Lee
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, USA
| | - Abbir Virani
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, USA
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics Division, Department of Pediatrics, Weill-Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Neuroscience and Pediatrics, Howard Hughes Medical Insistute, University of California, San Diego, La Jolla, CA, USA
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Ashleigh Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
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20
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Kottyan LC, Parameswaran S, Weirauch MT, Rothenberg ME, Martin LJ. The genetic etiology of eosinophilic esophagitis. J Allergy Clin Immunol 2020; 145:9-15. [PMID: 31910986 PMCID: PMC6984394 DOI: 10.1016/j.jaci.2019.11.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Eosinophilic esophagitis (EoE) is a chronic allergic disease associated with marked mucosal eosinophil accumulation. Multiple studies have reported a strong familial component to EoE, with the presence of EoE increasing the risk for other family members with EoE. Epidemiologic studies support an important role for environmental risk factors as modulators of genetic risk. In a small percentage of cases, including patients who have Mendelian diseases with co-occurrent EoE, rare genetic variation with large effect sizes could mediate EoE and explain multigenerational incidence in families. Common genetic risk variants mediate genetic risk for the majority of patients with EoE. Across the 31 reported independent EoE risk loci (P < 10-5), most of the EoE risk variants are located in between genes (36.7%) or within the introns of genes (42.4%). Although some variants do change the amino acid sequence of genes (2.2%), only 3 of the 31 EoE risk loci harbor an amino acid-changing variant. Thus most EoE risk loci are outside of the coding regions of genes, suggesting a key role for gene regulation in patients with EoE, which is consistent with most other complex diseases.
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Affiliation(s)
- Leah C Kottyan
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Marc E Rothenberg
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lisa J Martin
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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21
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Apicco DJ, Zhang C, Maziuk B, Jiang L, Ballance HI, Boudeau S, Ung C, Li H, Wolozin B. Dysregulation of RNA Splicing in Tauopathies. Cell Rep 2019; 29:4377-4388.e4. [PMID: 31875547 PMCID: PMC6941411 DOI: 10.1016/j.celrep.2019.11.093] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/28/2019] [Accepted: 11/22/2019] [Indexed: 12/13/2022] Open
Abstract
Pathological aggregation of RNA binding proteins (RBPs) is associated with dysregulation of RNA splicing in PS19 P301S tau transgenic mice and in Alzheimer's disease brain tissues. The dysregulated splicing particularly affects genes involved in synaptic transmission. The effects of neuroprotective TIA1 reduction on PS19 mice are also examined. TIA1 reduction reduces disease-linked alternative splicing events for the major synaptic mRNA transcripts examined, suggesting that normalization of RBP functions is associated with the neuroprotection. Use of the NetDecoder informatics algorithm identifies key upstream biological targets, including MYC and EGFR, underlying the transcriptional and splicing changes in the protected compared to tauopathy mice. Pharmacological inhibition of MYC and EGFR activity in neuronal cultures tau recapitulates the neuroprotective effects of TIA1 reduction. These results demonstrate that dysfunction of RBPs and RNA splicing processes are major elements of the pathophysiology of tauopathies, as well as potential therapeutic targets for tauopathies.
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Affiliation(s)
- Daniel J Apicco
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | | | - Brandon Maziuk
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Lulu Jiang
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Heather I Ballance
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Samantha Boudeau
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | | | - Hu Li
- Mayo Clinic, Rochester, MN, USA.
| | - Benjamin Wolozin
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA; Boston University School of Medicine, Department of Neurology, Boston, MA, USA.
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22
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Escrig A, Canal C, Sanchis P, Fernández-Gayol O, Montilla A, Comes G, Molinero A, Giralt M, Giménez-Llort L, Becker-Pauly C, Rose-John S, Hidalgo J. IL-6 trans-signaling in the brain influences the behavioral and physio-pathological phenotype of the Tg2576 and 3xTgAD mouse models of Alzheimer's disease. Brain Behav Immun 2019; 82:145-159. [PMID: 31401302 DOI: 10.1016/j.bbi.2019.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/09/2019] [Accepted: 08/07/2019] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease (AD) is the most commonly diagnosed dementia but its underlying pathological mechanisms still unclear. Neuroinflammation and secretion of cytokines such as interleukin-6 (IL-6) accompany the main hallmarks of the disease: amyloid plaques and neurofibrillary tangles. In this study, we analyzed the role of IL-6 trans-signaling in two mouse models of AD, Tg2576 and 3xTg-AD mice. The inhibition of IL-6 trans-signaling partially rescued the AD-induced mortality in females of both models. Before amyloid plaques deposition, it reversed AD-induced changes in exploration and anxiety (but did not affect locomotion) in Tg2576 female mice. However, after plaque deposition the only behavioral trait affected by the inhibition of IL-6 trans-signaling was locomotion. Results in the Morris water maze suggest that cognitive flexibility was reduced by the blocking of the IL-6 trans-signaling in young and old Tg2576 female mice. The inhibition of IL-6 trans-signaling also decreased amyloid plaque burden in cortex and hippocampus, and Aβ40 and Aβ42 levels in the cortex, of Tg2576 female mice. The aforementioned changes might be correlated with changes in blood vessels and matrix structure and organization rather than changes in neuroinflammation. 3xTgAD mice showed a very mild phenotype regarding amyloid cascade, but results were in accordance with those of Tg2576 mice. These results strongly suggest that the inhibition of the IL-6 trans-signaling could represent a powerful therapeutic target in AD.
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Affiliation(s)
- Anna Escrig
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Carla Canal
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Paula Sanchis
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Olaya Fernández-Gayol
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Alejandro Montilla
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Gemma Comes
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Amalia Molinero
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Mercedes Giralt
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain
| | - Lydia Giménez-Llort
- Institute of Neurosciences and Department of Psychiatry and Forensic Medicine, Faculty of Medicine, Universitat Autònoma de Barcelona, 08193, Spain
| | - Christoph Becker-Pauly
- Department of Biochemistry, Medical Faculty, Christian-Albrechts-Universität zu Kiel, 24098, Germany
| | - Stefan Rose-John
- Department of Biochemistry, Medical Faculty, Christian-Albrechts-Universität zu Kiel, 24098, Germany
| | - Juan Hidalgo
- Institute of Neurosciences and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Spain.
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23
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Zhao X, Liu X, Zhang A, Chen H, Huo Q, Li W, Ye R, Chen Z, Liang L, Liu QA, Shen J, Jin X, Li W, Nygaard M, Liu X, Hou Y, Ni T, Bolund L, Gottschalk W, Tao W, Gu J, Tian XL, Yang H, Wang J, Xu X, Lutz MW, Min J, Zeng Y, Nie C. The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese. Aging (Albany NY) 2019; 10:1206-1222. [PMID: 29883365 PMCID: PMC6046244 DOI: 10.18632/aging.101461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/30/2018] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) have been shown to cause numerous diseases, however, their roles in human lifespan remain elusive. In this study, we investigate the association of CNVs with longevity by comparing the Han Chinese genomes of long-lived individuals from 90 to 117 years of age and the middle-aged from 30 to 65. Our data demonstrate that the numbers of CNVs, especially deletions, increase significantly in a direct correlation with longevity. We identify eleven CNVs that strongly associate with longevity; four of them locate in the chromosome bands, 7p11.2, 20q13.33, 19p12 and 8p23.3 and overlap partially with the CNVs identified in long-lived Danish or U.S. populations, while the other seven have not been reported previously. These CNV regions encode nineteen known genes, and some of which have been shown to affect aging-related phenotypes such as the shortening of telomere length (ZNF208), the risk of cancer (FOXA1, LAMA5, ZNF716), and vascular and immune-related diseases (ARHGEF10, TOR2A, SH2D3C). In addition, we found several pathways enriched in long-lived genomes, including FOXA1 and FOXA transcription factor networks involved in regulating aging or age-dependent diseases such as cancer. Thus, our study has identified longevity-associated CNV regions and their affected genes and pathways. Our results suggest that the human genome structures such as CNVs might play an important role in determining a long life in human.
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Affiliation(s)
- Xin Zhao
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Liu
- BGI Shenzhen, Shenzhen 518083, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | - Huashuai Chen
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China.,Business School of Xiangtan University, Xiangtan 411105, China
| | - Qing Huo
- BGI Shenzhen, Shenzhen 518083, China
| | | | - Rui Ye
- BGI Shenzhen, Shenzhen 518083, China
| | | | | | | | - Juan Shen
- BGI Shenzhen, Shenzhen 518083, China
| | - Xin Jin
- BGI Shenzhen, Shenzhen 518083, China
| | - Wenwen Li
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Marianne Nygaard
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C 5000, Denmark
| | - Xiao Liu
- BGI Shenzhen, Shenzhen 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen 518083, China
| | - Ting Ni
- State Key Laboratory of Genetics Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Lars Bolund
- BGI Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - William Gottschalk
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Wei Tao
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Jun Gu
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Xiao-Li Tian
- Department of Human Population Genetics, Human Aging Research Institute and School of Life Science Nanchang University, Nanchang 330000, China
| | | | - Jian Wang
- BGI Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI Shenzhen, Shenzhen 518083, China
| | - Michael W Lutz
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yi Zeng
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China
| | - Chao Nie
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
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24
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Alkelai A, Greenbaum L, Heinzen EL, Baugh EH, Teitelbaum A, Zhu X, Strous RD, Tatarskyy P, Zai CC, Tiwari AK, Tampakeras M, Freeman N, Müller DJ, Voineskos AN, Lieberman JA, Delaney SL, Meltzer HY, Remington G, Kennedy JL, Pulver AE, Peabody EP, Levy DL, Lerer B. New insights into tardive dyskinesia genetics: Implementation of whole-exome sequencing approach. Prog Neuropsychopharmacol Biol Psychiatry 2019; 94:109659. [PMID: 31153890 DOI: 10.1016/j.pnpbp.2019.109659] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023]
Abstract
Tardive dyskinesia (TD) is an adverse movement disorder induced by chronic treatment with antipsychotics drugs. The contribution of common genetic variants to TD susceptibility has been investigated in recent years, but with limited success. The aim of the current study was to investigate the potential contribution of rare variants to TD vulnerability. In order to identify TD risk genes, we performed whole-exome sequencing (WES) and gene-based collapsing analysis focusing on rare (allele frequency < 1%) and putatively deleterious variants (qualifying variants). 82 Jewish schizophrenia patients chronically treated with antipsychotics were included and classified as having severe TD or lack of any abnormal movements based on a rigorous definition of the TD phenotype. First, we performed a case-control, exome-wide collapsing analysis comparing 39 schizophrenia patients with severe TD to 3118 unrelated population controls. Then, we checked the potential top candidate genes among 43 patients without any TD manifestations. All the genes that were found to harbor one or more qualifying variants in patients without any TD features were excluded from the final list of candidate genes. Only one gene, regulating synaptic membrane exocytosis 2 (RIMS2), showed significant enrichment of qualifying variants in TD patients compared with unrelated population controls after correcting for multiple testing (Fisher's exact test p = 5.32E-08, logistic regression p = 2.50E-08). Enrichment was caused by a single variant (rs567070433) due to a frameshift in an alternative transcript of RIMS2. None of the TD negative patients had qualifying variants in this gene. In a validation cohort of 140 schizophrenia patients assessed for TD, the variant was also not detected in any individual. Some potentially suggestive TD genes were detected in the TD cohort and warrant follow-up in future studies. No significant enrichment in previously reported TD candidate genes was identified. To the best of our knowledge, this is the first WES study of TD, demonstrating the potential role of rare loss-of-function variant enrichment in this pharmacogenetic phenotype.
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Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Alexander Teitelbaum
- Jerusalem Mental Health Center, Kfar Shaul Psychiatric Hospital, Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
| | - Xiaolin Zhu
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Rael D Strous
- Maayenei Hayeshua Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pavel Tatarskyy
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clement C Zai
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Arun K Tiwari
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Maria Tampakeras
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Natalie Freeman
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Daniel J Müller
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Aristotle N Voineskos
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Jeffrey A Lieberman
- Columbia University, New York State Psychiatric Institute, New York City, NY, USA
| | - Shannon L Delaney
- Columbia University, New York State Psychiatric Institute, New York City, NY, USA
| | - Herbert Y Meltzer
- Psychiatry and Behavioral Sciences, Pharmacology and Physiology, Chemistry of Life Processes Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gary Remington
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - James L Kennedy
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emma P Peabody
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Deborah L Levy
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Bernard Lerer
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Gong Y, Wang K, Xiao SP, Mi P, Li W, Shang Y, Dou F. Overexpressed TTC3 Protein Tends to be Cleaved into Fragments and Form Aggregates in the Nucleus. Neuromolecular Med 2019; 21:85-96. [PMID: 30203323 DOI: 10.1007/s12017-018-8509-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/31/2018] [Indexed: 12/01/2022]
Abstract
Human tetratricopeptide repeat domain 3 (TTC3) is a gene on 21q22.2 within the Down syndrome critical region (DSCR). Earlier studies suggest that TTC3 may be an important regulator in individual development, especially in neural development. As an E3 ligase, TTC3 binds to phosphorylated Akt and silence its activity via proteasomal cascade. Several groups also reported the involvement of TTC3 in familial Alzheimer's disease recently. In addition, our previous work shows that TTC3 also regulates the degradation of DNA polymerase gamma and over-expressed TTC3 protein tends to form insoluble aggregates in cells. In this study, we focus on the solubility and intracellular localization of TTC3 protein. Over-expressed TTC3 tends to form insoluble aggregates over time. The proteasome inhibitor MG132 treatment resulted in more TTC3 aggregates in a short period of time. We fused the fluorescent protein to either terminus of the TTC3 protein and found that the intracellular localization of fluorescent signals are different between the N-terminal tagged and C-terminal tagged proteins. Western blotting revealed that the TTC3 protein is cleaved into fragments of different sizes at multiple sites. The N-terminal sub-fragments of TTC3 are prone to from nuclear aggregates and the TTC3 nuclear import is mediated by signals within the N-terminal 1 to 650 residues. Moreover, over-expressed TTC3 induced a considerable degree of cytotoxicity, and its N-terminal sub-fragments are more potent inhibitors of cell proliferation than full-length protein. Considering the prevalent proteostasis dysregulation in neurodegenerative diseases, these findings may relate to the pathology of such diseases.
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Affiliation(s)
- Yueqing Gong
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, College of Life Sciences, Beijing Normal University, Beijing, China
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- Center for Collaboration and Innovation in Brain and Learning Sciences, Beijing Normal University, Beijing, China
| | - Kun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, College of Life Sciences, Beijing Normal University, Beijing, China
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- Center for Collaboration and Innovation in Brain and Learning Sciences, Beijing Normal University, Beijing, China
| | - Sheng-Ping Xiao
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, College of Life Sciences, Beijing Normal University, Beijing, China
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- Center for Collaboration and Innovation in Brain and Learning Sciences, Beijing Normal University, Beijing, China
| | - Panying Mi
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, College of Life Sciences, Beijing Normal University, Beijing, China
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- Center for Collaboration and Innovation in Brain and Learning Sciences, Beijing Normal University, Beijing, China
| | - Wanjie Li
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yu Shang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Fei Dou
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, College of Life Sciences, Beijing Normal University, Beijing, China.
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China.
- Center for Collaboration and Innovation in Brain and Learning Sciences, Beijing Normal University, Beijing, China.
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26
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Beecham GW, Vardarajan B, Blue E, Bush W, Jaworski J, Barral S, DeStefano A, Hamilton-Nelson K, Kunkle B, Martin ER, Naj A, Rajabli F, Reitz C, Thornton T, van Duijn C, Goate A, Seshadri S, Farrer LA, Boerwinkle E, Schellenberg G, Haines JL, Wijsman E, Mayeux R, Pericak-Vance MA. Rare genetic variation implicated in non-Hispanic white families with Alzheimer disease. Neurol Genet 2018; 4:e286. [PMID: 30569016 PMCID: PMC6278241 DOI: 10.1212/nxg.0000000000000286] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To identify genetic variation influencing late-onset Alzheimer disease (LOAD), we used a large data set of non-Hispanic white (NHW) extended families multiply-affected by LOAD by performing whole genome sequencing (WGS). METHODS As part of the Alzheimer Disease Sequencing Project, WGS data were generated for 197 NHW participants from 42 families (affected individuals and unaffected, elderly relatives). A two-pronged approach was taken. First, variants were prioritized using heterogeneity logarithm of the odds (HLOD) and family-specific LOD scores as well as annotations based on function, frequency, and segregation with disease. Second, known Alzheimer disease (AD) candidate genes were assessed for rare variation using a family-based association test. RESULTS We identified 41 rare, predicted-damaging variants that segregated with disease in the families that contributed to the HLOD or family-specific LOD regions. These included a variant in nitric oxide synthase 1 adaptor protein that segregates with disease in a family with 7 individuals with AD, as well as variants in RP11-433J8, ABCA1, and FISP2. Rare-variant association identified 2 LOAD candidate genes associated with disease in these families: FERMT2 (p-values = 0.001) and SLC24A4 (p-value = 0.009). These genes still showed association while controlling for common index variants, indicating the rare-variant signal is distinct from common variation that initially identified the genes as candidates. CONCLUSIONS We identified multiple genes with putative damaging rare variants that segregate with disease in multiplex AD families and showed that rare variation may influence AD risk at AD candidate genes. These results identify novel AD candidate genes and show a role for rare variation in LOAD etiology, even at genes previously identified by common variation.
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Affiliation(s)
- Gary W Beecham
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Badri Vardarajan
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Elizabeth Blue
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - William Bush
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - James Jaworski
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Sandra Barral
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Anita DeStefano
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Brian Kunkle
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Adam Naj
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Christiane Reitz
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Timothy Thornton
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Cornelia van Duijn
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Allison Goate
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Sudha Seshadri
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Lindsay A Farrer
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Eric Boerwinkle
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Gerard Schellenberg
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Jonathan L Haines
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Ellen Wijsman
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Richard Mayeux
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics (G.W.B., J.J., K.H.-N., B.K., E.R.M., F.R., M.A.P.-V.), University of Miami, Miller School of Medicine; Dr. John T. Macdonald Foundation Department of Human Genetics (G.W.B., E.R.M., M.A.P.-V.), University of Miami, Miller School of Medicine, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.V., S.B., C.R., R.M.), Columbia University; The Gertrude H. Segievsky Center (B.V., S.B., C.R., R.M.), Columbia University, New York Presbyterian Hospital; Division of Medical Genetics (E. Blue, E.W.), Department of Medicine, University of Washington, Seattle; Institute for Computational Biology (W.B., J.L.H.), Case Western Reserve University, Cleveland, OH; Department of Neurology (A.D., S.S., L.A.F.), Boston University School of Medicine; Department of Biostatistics (A.D., S.S., L.A.F.), Boston University School of Medicine, MA; School of Medicine (A.N., G.S.), University of Pennsylvania, Philadelphia; Department of Biostatistics (T.T., E.W.), University of Washington, Seattle; Erasmus Medical University (C.D.), Rotterdam, The Netherlands; Icahn School of Medicine at Mount Sinai (A.G.), New York, NY; Department of Medicine (L.A.F.), Boston University School of Medicine, MA; and University of Texas (E. Boerwinkle), Houston
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Zhu X, Yu H, Xiao Q, Ke J, Li H, Chen Z, Ding H, Leng S, Huang Y, Zhan J, Lei J, Fan W, Luo H. Genetic variations in chromodomain helicase DNA-binding protein 5, gene-environment interactions and risk of sporadic Alzheimer's disease in Chinese population. Oncotarget 2018; 9:24872-24881. [PMID: 29861839 PMCID: PMC5982770 DOI: 10.18632/oncotarget.23791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/05/2017] [Indexed: 11/25/2022] Open
Abstract
CHD5 is an essential factor for neuronal differentiation and neurodegenerative diseases. Here, the targeted next generation sequencing and TaqMan genotyping technologies were carried out for CHD5 gene in a two-staged case-control study in Chinese population. The genetic statistics and gene-environment interactions were analyzed to find certain risk factors of Alzheimer's disease. We found intronic rs11121295 was associated with the risk of Alzheimer's disease at both stages including combined cohorts. This risk effect presented consistently significant associations with the alcoholic subgroups at both all stages in the stratified analysis. The gene-environment interactions further supported the above findings. Our study highlighted the potential role of CHD5 variants in conferring susceptibility to sporadic Alzheimer's disease, especially modified its risk by alcoholic intake.
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Affiliation(s)
- Xiao Zhu
- Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Haibing Yu
- Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Qin Xiao
- Department of Blood Transfusion, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jianhao Ke
- Tropical Crops Department, Guangdong AIB Polytechnic, Guangzhou, China
| | - Hongmei Li
- Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Zhihong Chen
- Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Hongrong Ding
- Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Shuilong Leng
- Department of Human Anatomy, Guangzhou Medical University, Guangzhou, China
| | - Yongmei Huang
- Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Jingting Zhan
- Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Jinli Lei
- Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Wenguo Fan
- Department of Anatomy and Physiology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Hui Luo
- Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
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Pasanen P, Myllykangas L, Pöyhönen M, Kiviharju A, Siitonen M, Hardy J, Bras J, Paetau A, Tienari PJ, Guerreiro R, Verkkoniemi-Ahola A. Genetics of dementia in a Finnish cohort. Eur J Hum Genet 2018; 26:827-837. [PMID: 29476165 DOI: 10.1038/s41431-018-0117-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 12/03/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) and frontotemporal dementia (FTD) are the two most common neurodegenerative dementias. Variants in APP, PSEN1 and PSEN2 are typically linked to early-onset AD, and several genetic risk loci are associated with late-onset AD. Inherited FTD can be caused by hexanucleotide expansions in C9orf72, or variants in GRN, MAPT or CHMP2B. Several other genes have also been linked to FTD or FTD with motor neuron disease. Here we describe a cohort of 60 Finnish families with possible inherited dementia. Our aim was to clarify the genetic background of dementia in this cohort by analysing both known dementia-associated genes (APOE, APP, C9ORF72, GRN, PSEN1 and PSEN2) and searching for rare or novel segregating variants with exome sequencing. C9orf72 repeat expansions were detected in 12 (20%) of the 60 families, including, in addition to FTD, a family with neuropathologically verified AD. Twelve families (10 with AD and 2 with FTD) with representative samples from affected and unaffected subjects and without C9orf72 expansions were selected for whole-exome sequencing. Exome sequencing did not reveal any variants that could be regarded unequivocally causative, but revealed potentially damaging variants in UNC13C and MARCH4.
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Affiliation(s)
- Petra Pasanen
- Department of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Turku, Finland. .,Tyks Genetics and Saske, Department of Medical Genetics, Turku University Hospital, Turku, Finland.
| | - Liisa Myllykangas
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Minna Pöyhönen
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Anna Kiviharju
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Maija Siitonen
- Department of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Turku, Finland
| | - John Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Jose Bras
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute at UCL, London, UK.,Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Anders Paetau
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pentti J Tienari
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Rita Guerreiro
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute at UCL, London, UK.,Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Auli Verkkoniemi-Ahola
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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29
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Fenoglio C. Genetics and Epigenetics in the Neurodegenerative Disorders of the Central Nervous System. NEURODEGENER DIS 2018. [DOI: 10.1007/978-3-319-72938-1_1] [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] Open
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30
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Fenoglio C, Scarpini E, Serpente M, Galimberti D. Role of Genetics and Epigenetics in the Pathogenesis of Alzheimer's Disease and Frontotemporal Dementia. J Alzheimers Dis 2018; 62:913-932. [PMID: 29562532 PMCID: PMC5870004 DOI: 10.3233/jad-170702] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2017] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) and frontotemporal dementia (FTD) represent the first cause of dementia in senile and pre-senile population, respectively. A percentage of cases have a genetic cause, inherited with an autosomal dominant pattern of transmission. The majority of cases, however, derive from complex interactions between a number of genetic and environmental factors. Gene variants may act as risk or protective factors. Their combination with a variety of environmental exposures may result in increased susceptibility to these diseases or may influence their course. The scenario is even more complicated considering the effect of epigenetics, which encompasses mechanisms able to alter the expression of genes without altering the DNA sequence. In this review, an overview of the current genetic and epigenetic progresses in AD and FTD will be provided, with particular focus on 1) causative genes, 2) genetic risk factors and disease modifiers, and 3) epigenetics, including methylation, non-coding RNAs and chromatin remodeling.
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Affiliation(s)
- Chiara Fenoglio
- Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Fondazione Cá Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Elio Scarpini
- Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Fondazione Cá Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria Serpente
- Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Fondazione Cá Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniela Galimberti
- Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Fondazione Cá Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
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31
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Hansen RD, Christensen AF, Olesen J. Family studies to find rare high risk variants in migraine. J Headache Pain 2017; 18:32. [PMID: 28255817 PMCID: PMC5334193 DOI: 10.1186/s10194-017-0729-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Migraine has long been known as a common complex disease caused by genetic and environmental factors. The pathophysiology and the specific genetic susceptibility are poorly understood. Common variants only explain a small part of the heritability of migraine. It is thought that rare genetic variants with bigger effect size may be involved in the disease. Since migraine has a tendency to cluster in families, a family approach might be the way to find these variants. This is also indicated by identification of migraine-associated loci in classical linkage-analyses in migraine families. A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides an affordable tool to investigate the genetic variation in the entire exome or genome. The family-based study design using NGS is described in this paper. We also review family studies using NGS that have been successful in finding rare variants in other common complex diseases in order to argue the promising application of a family approach to migraine. METHOD PubMed was searched to find studies that looked for rare genetic variants in common complex diseases through a family-based design using NGS, excluding studies looking for de-novo mutations, or using a candidate-gene approach and studies on cancer. All issues from Nature Genetics and PLOS genetics 2014, 2015 and 2016 (UTAI June) were screened for relevant papers. Reference lists from included and other relevant papers were also searched. For the description of the family-based study design using NGS an in-house protocol was used. RESULTS Thirty-two successful studies, which covered 16 different common complex diseases, were included in this paper. We also found a single migraine study. Twenty-three studies found one or a few family specific variants (less than five), while other studies found several possible variants. Not all of them were genome wide significant. Four studies performed follow-up analyses in unrelated cases and controls and calculated odds ratios that supported an association between detected variants and risk of disease. Studies of 11 diseases identified rare variants that segregated fully or to a large degree with the disease in the pedigrees. CONCLUSION It is possible to find rare high risk variants for common complex diseases through a family-based approach. One study using a family approach and NGS to find rare variants in migraine has already been published but with strong limitations. More studies are under way.
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Affiliation(s)
- Rikke Dyhr Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Anne Francke Christensen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
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Tang M, Reitz C. Genetics of Alzheimer's disease: an update. FUTURE NEUROLOGY 2017. [DOI: 10.2217/fnl-2017-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is clear that late-onset Alzheimer's disease (AD), the most common form of dementia in western societies, has a significant genetic component. The recent technological advances in high-throughput genome technologies have enabled the identification of more than 20 novel susceptibility loci. These findings have significantly advanced the understanding of the molecular mechanisms potentially underlying AD etiology, and have therefore provided valuable information for the development of targets for genetic testing, prevention and treatment. This article reviews these recent findings in AD genomics and discusses their implications for understanding the molecular underpinnings of the disease.
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Affiliation(s)
- Min Tang
- The Gertrude H Sergievsky Center, Columbia University, 630 West 168th Street, NY 10032, USA
| | - Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, 630 West 168th Street, NY 10032, USA
- The Gertrude H Sergievsky Center, Columbia University, 630 West 168th Street, NY 10032, USA
- The Department of Neurology, Columbia University, NY 10032, USA
- The Department of Epidemiology, Columbia University, NY 10032, USA
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Genetics of Alzheimer's disease: From pathogenesis to clinical usage. J Clin Neurosci 2017; 45:1-8. [PMID: 28869135 DOI: 10.1016/j.jocn.2017.06.074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/19/2017] [Indexed: 01/27/2023]
Abstract
Alzheimer's disease (AD) is the most common type of dementia and has caused a major global health concern. Understanding the etiology of AD can be beneficial for the diagnosis and intervention of this disease. Genetics plays a vital role in the pathogenesis of AD. Research methods in genetics such as the linkage analysis, study of candidate genes, genome-wide association study (GWAS), and next-generation sequencing (NGS) technology help us map the genetic information in AD, which can not only provide a new insight into the pathogenesis of AD but also be beneficial for early targeted intervention of AD. This review summarizes the pathogenesis as well as the diagnostic and therapeutic value of genetics in AD.
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Raghavan N, Tosto G. Genetics of Alzheimer's Disease: the Importance of Polygenic and Epistatic Components. Curr Neurol Neurosci Rep 2017; 17:78. [PMID: 28825204 PMCID: PMC5699909 DOI: 10.1007/s11910-017-0787-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PURPOSE OF REVIEW We aimed to summarize the recent advances in genetic findings of Alzheimer's disease (AD), focusing on traditional single-marker and gene approaches and non-traditional ones, i.e., polygenic and epistatic components. RECENT FINDINGS Genetic studies have progressed over the last few decades from linkage to genome-wide association studies (GWAS), and most recently studies utilizing high-throughput sequencing. So far, GWASs have identified several common variants characterized by small effect sizes (besides APOE-ε4). Sequencing has facilitated the study of rare variants with larger effects. Nevertheless, missing heritability for AD remains extensive; a possible explanation might lie in the existence of polygenic and epistatic components. We review findings achieved by single-marker approaches, but also polygenic and epistatic associations. The latter two are critical, yet-underexplored mechanisms. Genes involved in complex diseases are likely regulated by mechanisms and pathways involving many other genes, an aspect potentially missed by traditional approaches.
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Affiliation(s)
- Neha Raghavan
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 622 W. 168th Street PH 19-314, New York, NY, 10032, USA
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York, NY, 10032, USA
- Institute for Genomic Medicine, Columbia University, New York, NY, 10032, USA
| | - Giuseppe Tosto
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 622 W. 168th Street PH 19-314, New York, NY, 10032, USA.
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York, NY, 10032, USA.
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 622 W. 168th Street PH 19-314, New York, NY, 10032, USA.
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Cukier HN, Kunkle BK, Hamilton KL, Rolati S, Kohli MA, Whitehead PL, Jaworski J, Vance JM, Cuccaro ML, Carney RM, Gilbert JR, Farrer LA, Martin ER, Beecham GW, Haines JL, Pericak-Vance MA. Exome Sequencing of Extended Families with Alzheimer's Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function. ACTA ACUST UNITED AC 2017; 7. [PMID: 29177109 PMCID: PMC5698805 DOI: 10.4172/2161-0460.1000355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objective Alzheimer’s disease (AD) is a neurodegenerative disorder for which more than 20 genetic loci have been implicated to date. However, studies demonstrate not all genetic factors have been identified. Therefore, in this study we seek to identify additional rare variants and novel genes potentially contributing to AD. Methods Whole exome sequencing was performed on 23 multi-generational families with an average of eight affected subjects. Exome sequencing was filtered for rare, nonsynonymous and loss-of-function variants. Alterations predicted to have a functional consequence and located within either a previously reported AD gene, a linkage peak (LOD>2), or clustering in the same gene across multiple families, were prioritized. Results Rare variants were found in known AD risk genes including AKAP9, CD33, CR1, EPHA1, INPP5D, NME8, PSEN1, SORL1, TREM2 and UNC5C. Three families had five variants of interest in linkage regions with LOD>2. Genes with segregating alterations in these peaks include CD163L1 and CLECL1, two genes that have both been implicated in immunity, CTNNA1, which encodes a catenin in the cerebral cortex and MIEF1, a gene that may induce mitochondrial dysfunction and has the potential to damage neurons. Four genes were identified with alterations in more than one family include PLEKHG5, a gene that causes Charcot-Marie-Tooth disease and THBS2, which promotes synaptogenesis. Conclusion Utilizing large families with a heavy burden of disease allowed for the identification of rare variants co-segregating with disease. Variants were identified in both known AD risk genes and in novel genes.
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Affiliation(s)
- H N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - B K Kunkle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - K L Hamilton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - S Rolati
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M A Kohli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - P L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J Jaworski
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - R M Carney
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Mental Health and Behavioral Sciences Service, Miami Veterans Affairs, Miami, FL, USA
| | - J R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - L A Farrer
- Departments of Medicine, Neurology, Ophthalmology, Genetics and Genomics, Epidemiology and Biostatistics, Boston University, Boston, MA, USA
| | - E R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - G W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - M A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA.,John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
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Pottier C, Ravenscroft TA, Brown PH, Finch NA, Baker M, Parsons M, Asmann YW, Ren Y, Christopher E, Levitch D, van Blitterswijk M, Cruchaga C, Campion D, Nicolas G, Richard AC, Guerreiro R, Bras JT, Zuchner S, Gonzalez MA, Bu G, Younkin S, Knopman DS, Josephs KA, Parisi JE, Petersen RC, Ertekin-Taner N, Graff-Radford NR, Boeve BF, Dickson DW, Rademakers R. TYROBP genetic variants in early-onset Alzheimer's disease. Neurobiol Aging 2016; 48:222.e9-222.e15. [PMID: 27658901 DOI: 10.1016/j.neurobiolaging.2016.07.028] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/01/2016] [Accepted: 07/30/2016] [Indexed: 12/30/2022]
Abstract
We aimed to identify new candidate genes potentially involved in early-onset Alzheimer's disease (EOAD). Exome sequencing was conducted on 45 EOAD patients with either a family history of Alzheimer's disease (AD, <65 years) or an extremely early age at the onset (≤55 years) followed by multiple variant filtering according to different modes of inheritance. We identified 29 candidate genes potentially involved in EOAD, of which the gene TYROBP, previously implicated in AD, was selected for genetic and functional follow-up. Using 3 patient cohorts, we observed rare coding TYROBP variants in 9 out of 1110 EOAD patients, whereas no such variants were detected in 1826 controls (p = 0.0001), suggesting that at least some rare TYROBP variants might contribute to EOAD risk. Overexpression of the p.D50_L51ins14 TYROBP mutant led to a profound reduction of TREM2 expression, a well-established risk factor for AD. This is the first study supporting a role for genetic variation in TYROBP in EOAD, with in vitro support for a functional effect of the p.D50_L51ins14 TYROBP mutation on TREM2 expression.
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Affiliation(s)
- Cyril Pottier
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Matt Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Meeia Parsons
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yan W Asmann
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Yingxue Ren
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Denise Levitch
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Dominique Campion
- Inserm U1079, Rouen University, Normandy Center for Genomic Medicine and Personalized Medicine, Normandy University, Rouen, France; CNR-MAJ, Rouen University Hospital, Rouen, France; Department of Research, Rouvray Psychiatric Hospital, Rouen, France
| | - Gaël Nicolas
- Inserm U1079, Rouen University, Normandy Center for Genomic Medicine and Personalized Medicine, Normandy University, Rouen, France; CNR-MAJ, Rouen University Hospital, Rouen, France; Department of Genetics, Rouen University Hospital, Rouen, France
| | - Anne-Claire Richard
- Inserm U1079, Rouen University, Normandy Center for Genomic Medicine and Personalized Medicine, Normandy University, Rouen, France; CNR-MAJ, Rouen University Hospital, Rouen, France
| | - Rita Guerreiro
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Jose T Bras
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Stephan Zuchner
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | | | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Steven Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
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Affiliation(s)
- Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City
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