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Xin Y, Sheng J, Miao M, Wang L, Yang Z, Huang H. A review ofimaging genetics in Alzheimer's disease. J Clin Neurosci 2022; 100:155-163. [PMID: 35487021 DOI: 10.1016/j.jocn.2022.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/01/2022] [Accepted: 04/15/2022] [Indexed: 01/18/2023]
Abstract
Determining the association between genetic variation and phenotype is a key step to study the mechanism of Alzheimer's disease (AD), laying the foundation for studying drug therapies and biomarkers. AD is the most common type of dementia in the aged population. At present, three early-onset AD genes (APP, PSEN1, PSEN2) and one late-onset AD susceptibility gene apolipoprotein E (APOE) have been determined. However, the pathogenesis of AD remains unknown. Imaging genetics, an emerging interdisciplinary field, is able to reveal the complex mechanisms from the genetic level to human cognition and mental disorders via macroscopic intermediates. This paper reviews methods of establishing genotype-phenotype to explore correlations, including sparse canonical correlation analysis, sparse reduced rank regression, sparse partial least squares and so on. We found that most research work did poorly in supervised learning and exploring the nonlinear relationship between SNP-QT.
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Affiliation(s)
- Yu Xin
- College of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China; Key Laboratory of Intelligent Image Analysis for Sensory and Cognitive Health, Ministry of Industry and Information Technology of China, Hangzhou, Zhejiang 310018, China
| | - Jinhua Sheng
- College of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China; Key Laboratory of Intelligent Image Analysis for Sensory and Cognitive Health, Ministry of Industry and Information Technology of China, Hangzhou, Zhejiang 310018, China.
| | - Miao Miao
- Beijing Hospital, Beijing 100730, China; National Center of Gerontology, Beijing 100730, China; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Luyun Wang
- College of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China; Key Laboratory of Intelligent Image Analysis for Sensory and Cognitive Health, Ministry of Industry and Information Technology of China, Hangzhou, Zhejiang 310018, China; Hangzhou Vocational & Technical College, Hangzhou, Zhejiang 310018, China
| | - Ze Yang
- College of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China; Key Laboratory of Intelligent Image Analysis for Sensory and Cognitive Health, Ministry of Industry and Information Technology of China, Hangzhou, Zhejiang 310018, China
| | - He Huang
- College of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China; Key Laboratory of Intelligent Image Analysis for Sensory and Cognitive Health, Ministry of Industry and Information Technology of China, Hangzhou, Zhejiang 310018, China
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2
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Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022; 17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Yonejung Yoon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Miranda E. Orr
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
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3
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Wang K, Lu Y, Morrow DF, Xiao D, Xu C. Associations of ARHGAP26 Polymorphisms with Alzheimer's Disease and Cardiovascular Disease. J Mol Neurosci 2022; 72:1085-1097. [PMID: 35171450 DOI: 10.1007/s12031-022-01972-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/10/2022] [Indexed: 02/03/2023]
Abstract
The Rho GTPase activating protein 26 (ARHGAP26) gene has been reported to be associated with neuropsychiatric diseases and neurodegenerative diseases including Parkinson's disease. We examined whether the ARHGAP26 gene is associated with Alzheimer's disease (AD) and/or cardiovascular disease (CVD). Multivariable logistic regression model was used to examine the associations of 154 single nucleotide polymorphisms (SNPs) within the ARHGAP26 gene with AD and CVD using the Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) cohort. Fourteen SNPs were associated with AD (top SNP rs3776362 with p = 3.43 × 10-3), while 37 SNPs revealed associations with CVD (top SNP rs415235 with p = 2.06 × 10-4). Interestingly, 13 SNPs were associated with both AD and CVD. SNP rs3776362 was associated with CVD, Functional Activities Questionnaire (FAQ), and Clinical Dementia Rating Sum of Boxes (CDR-SB). A replication study using a Caribbean Hispanics sample showed that 17 SNPs revealed associations with AD, and 12 SNPs were associated with CVD. The third sample using a family-based study design showed that 9 SNPs were associated with AD, and 3 SNPs were associated with CVD. SNP rs6836509 within the ARHGAP10 gene (an important paralogon of ARHGAP26) was associated with AD and cerebrospinal fluid total tau (t-tau) level in the ADNI sample. Several SNPs were functionally important using the RegulomeDB, while a number of SNPs were associated with significant expression quantitative trait loci (eQTLs) using Genotype-Tissue Expression (GTEx) databases. In conclusion, genetic variants within ARHGAP26 were associated with AD and CVD. These findings add important new insights into the potentially shared pathogenesis of AD and CVD.
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Affiliation(s)
- Kesheng Wang
- Department of Family and Community Health, School of Nursing, Health Sciences Center, West Virginia University, Post Office Box 9600 - Office 6419, Morgantown, WV, 26506, USA.
| | - Yongke Lu
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, 25755, USA
| | - Deana F Morrow
- School of Social Work, West Virginia University, Morgantown, WV, 26506, USA
| | - Danqing Xiao
- Department of STEM, School of Arts and Sciences, Regis College, Weston, MA, 02493, USA
- McLean Imaging Center, McLean Hospital, MA, 02478, Belmont, USA
| | - Chun Xu
- Department of Health and Biomedical Sciences, College of Health Professions, University of Texas Rio Grande Valley, TX, 78520, Brownsville, USA.
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4
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Hoogmartens J, Cacace R, Van Broeckhoven C. Insight into the genetic etiology of Alzheimer's disease: A comprehensive review of the role of rare variants. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12155. [PMID: 33665345 PMCID: PMC7896636 DOI: 10.1002/dad2.12155] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
Early-onset Alzheimer's disease (EOAD) is generally known as a dominant disease due to highly penetrant pathogenic mutations in the amyloid precursor protein, presenilin 1 and 2. However, they explain only a fraction of EOAD patients (5% to 10%). Furthermore, only 10% to 15% of EOAD families present with clear autosomal dominant inheritance. Studies showed that only 35% to 60% of EOAD patients have at least one affected first-degree relative. Parent-offspring concordance in EOAD was estimated to be <10%, indicating that full penetrant dominant alleles are not the sole players in EOAD. We aim to summarize current knowledge of rare variants underlying familial and seemingly sporadic Alzheimer's disease (AD) patients. Genetic findings indicate that in addition to the amyloid beta pathway, other pathways are of importance in AD pathophysiology. We discuss the difficulties in interpreting the influence of rare variants on disease onset and we underline the value of carefully selected ethnicity-matched cohorts in AD genetic research.
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Affiliation(s)
- Julie Hoogmartens
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Rita Cacace
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
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5
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Leszek J, Mikhaylenko EV, Belousov DM, Koutsouraki E, Szczechowiak K, Kobusiak-Prokopowicz M, Mysiak A, Diniz BS, Somasundaram SG, Kirkland CE, Aliev G. The Links between Cardiovascular Diseases and Alzheimer's Disease. Curr Neuropharmacol 2021; 19:152-169. [PMID: 32727331 PMCID: PMC8033981 DOI: 10.2174/1570159x18666200729093724] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/02/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
The root cause of non-inherited Alzheimer's disease (AD) remains unknown despite hundreds of research studies performed to attempt to solve this problem. Since proper prophylaxis remains the best strategy, many scientists have studied the risk factors that may affect AD development. There is robust evidence supporting the hypothesis that cardiovascular diseases (CVD) may contribute to AD progression, as the diseases often coexist. Therefore, a lack of well-defined diagnostic criteria makes studying the relationship between AD and CVD complicated. Additionally, inflammation accompanies the pathogenesis of AD and CVD, and is not only a consequence but also implicated as a significant contributor to the course of the diseases. Of note, АроЕε4 is found to be one of the major risk factors affecting both the cardiovascular and nervous systems. According to genome wide association and epidemiological studies, numerous common risk factors have been associated with the development of AD-related pathology. Furthermore, the risk of developing AD and CVDs appears to be increased by a wide range of conditions and lifestyle factors: hypertension, dyslipidemia, hypercholesterolemia, hyperhomocysteinemia, gut/oral microbiota, physical activity, and diet. This review summarizes the literature and provides possible mechanistic links between CVDs and AD.
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Affiliation(s)
- Jerzy Leszek
- Address correspondence to these authors at the Department of Psychiatry, Wrocław Medical University, Ul. Pasteura 10, 50-367, Wroclaw, Poland;, E-mail: and GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX 78229, USA; Tel: +1-210-442-8625 or +1-440-263-7461; E-mails: ,
| | | | | | | | | | | | | | | | | | | | - Gjumrakch Aliev
- Address correspondence to these authors at the Department of Psychiatry, Wrocław Medical University, Ul. Pasteura 10, 50-367, Wroclaw, Poland;, E-mail: and GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX 78229, USA; Tel: +1-210-442-8625 or +1-440-263-7461; E-mails: ,
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6
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D’Argenio V, Sarnataro D. New Insights into the Molecular Bases of Familial Alzheimer's Disease. J Pers Med 2020; 10:jpm10020026. [PMID: 32325882 PMCID: PMC7354425 DOI: 10.3390/jpm10020026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Like several neurodegenerative disorders, such as Prion and Parkinson diseases, Alzheimer's disease (AD) is characterized by spreading mechanism of aggregated proteins in the brain in a typical "prion-like" manner. Recent genetic studies have identified in four genes associated with inherited AD (amyloid precursor protein-APP, Presenilin-1, Presenilin-2 and Apolipoprotein E), rare mutations which cause dysregulation of APP processing and alterations of folding of the derived amyloid beta peptide (A). Accumulation and aggregation of A in the brain can trigger a series of intracellular events, including hyperphosphorylation of tau protein, leading to the pathological features of AD. However, mutations in these four genes account for a small of the total genetic risk for familial AD (FAD). Genome-wide association studies have recently led to the identification of additional AD candidate genes. Here, we review an update of well-established, highly penetrant FAD-causing genes with correlation to the protein misfolding pathway, and novel emerging candidate FAD genes, as well as inherited risk factors. Knowledge of these genes and of their correlated biochemical cascade will provide several potential targets for treatment of AD and aging-related disorders.
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Affiliation(s)
- Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate scarl, via G. Salvatore 486, 80145 Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, via di val Cannuta 247, 00166 Rome, Italy
- Correspondence: (V.D.); (D.S.); Tel.: +39-081-3737909 (V.D.); +39-081-7464575 (D.S.)
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, via S. Pansini 5, 80131 Naples, Italy
- Correspondence: (V.D.); (D.S.); Tel.: +39-081-3737909 (V.D.); +39-081-7464575 (D.S.)
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7
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Foster EM, Dangla-Valls A, Lovestone S, Ribe EM, Buckley NJ. Clusterin in Alzheimer's Disease: Mechanisms, Genetics, and Lessons From Other Pathologies. Front Neurosci 2019; 13:164. [PMID: 30872998 PMCID: PMC6403191 DOI: 10.3389/fnins.2019.00164] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/12/2019] [Indexed: 01/10/2023] Open
Abstract
Clusterin (CLU) or APOJ is a multifunctional glycoprotein that has been implicated in several physiological and pathological states, including Alzheimer's disease (AD). With a prominent extracellular chaperone function, additional roles have been discussed for clusterin, including lipid transport and immune modulation, and it is involved in pathways common to several diseases such as cell death and survival, oxidative stress, and proteotoxic stress. Although clusterin is normally a secreted protein, it has also been found intracellularly under certain stress conditions. Multiple hypotheses have been proposed regarding the origin of intracellular clusterin, including specific biogenic processes leading to alternative transcripts and protein isoforms, but these lines of research are incomplete and contradictory. Current consensus is that intracellular clusterin is most likely to have exited the secretory pathway at some point or to have re-entered the cell after secretion. Clusterin's relationship with amyloid beta (Aβ) has been of great interest to the AD field, including clusterin's apparent role in altering Aβ aggregation and/or clearance. Additionally, clusterin has been more recently identified as a mediator of Aβ toxicity, as evidenced by the neuroprotective effect of CLU knockdown and knockout in rodent and human iPSC-derived neurons. CLU is also the third most significant genetic risk factor for late onset AD and several variants have been identified in CLU. Although the exact contribution of these variants to altered AD risk is unclear, some have been linked to altered CLU expression at both mRNA and protein levels, altered cognitive and memory function, and altered brain structure. The apparent complexity of clusterin's biogenesis, the lack of clarity over the origin of the intracellular clusterin species, and the number of pathophysiological functions attributed to clusterin have all contributed to the challenge of understanding the role of clusterin in AD pathophysiology. Here, we highlight clusterin's relevance to AD by discussing the evidence linking clusterin to AD, as well as drawing parallels on how the role of clusterin in other diseases and pathways may help us understand its biological function(s) in association with AD.
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Affiliation(s)
| | | | | | | | - Noel J. Buckley
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
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8
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Nikolac Perkovic M, Pivac N. Genetic Markers of Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1192:27-52. [PMID: 31705489 DOI: 10.1007/978-981-32-9721-0_3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease is a complex and heterogeneous, severe neurodegenerative disorder and the predominant form of dementia, characterized by cognitive disturbances, behavioral and psychotic symptoms, progressive cognitive decline, disorientation, behavioral changes, and death. Genetic background of Alzheimer's disease differs between early-onset familial Alzheimer's disease, other cases of early-onset Alzheimer's disease, and late-onset Alzheimer's disease. Rare cases of early-onset familial Alzheimer's diseases are caused by high-penetrant mutations in genes coding for amyloid precursor protein, presenilin 1, and presenilin 2. Late-onset Alzheimer's disease is multifactorial and associated with many different genetic risk loci (>20), with the apolipoprotein E ε4 allele being a major genetic risk factor for late-onset Alzheimer's disease. Genetic and genomic studies offer insight into many additional genetic risk loci involved in the genetically complex nature of late-onset Alzheimer's disease. This review highlights the contributions of individual loci to the pathogenesis of Alzheimer's disease and suggests that their exact contribution is still not clear. Therefore, the use of genetic markers of Alzheimer's disease, for monitoring development, time course, treatment response, and prognosis of Alzheimer's disease, is still far away from the clinical application, because the contribution of genetic variations to the relative risk of developing Alzheimer's disease is limited. In the light of prediction and prevention of Alzheimer's disease, a novel approach could be found in the form of additive genetic risk scores, which combine additive effects of numerous susceptibility loci.
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Affiliation(s)
- Matea Nikolac Perkovic
- Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, 10000, Croatia
| | - Nela Pivac
- Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, 10000, Croatia.
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9
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Robbins JP, Perfect L, Ribe EM, Maresca M, Dangla-Valls A, Foster EM, Killick R, Nowosiad P, Reid MJ, Polit LD, Nevado AJ, Ebner D, Bohlooly-Y M, Buckley N, Pangalos MN, Price J, Lovestone S. Clusterin Is Required for β-Amyloid Toxicity in Human iPSC-Derived Neurons. Front Neurosci 2018; 12:504. [PMID: 30090055 PMCID: PMC6068261 DOI: 10.3389/fnins.2018.00504] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/04/2018] [Indexed: 02/01/2023] Open
Abstract
Our understanding of the molecular processes underlying Alzheimer's disease (AD) is still limited, hindering the development of effective treatments, and highlighting the need for human-specific models. Advances in identifying components of the amyloid cascade are progressing, including the role of the protein clusterin in mediating β-amyloid (Aβ) toxicity. Mutations in the clusterin gene (CLU), a major genetic AD risk factor, are known to have important roles in Aβ processing. Here we investigate how CLU mediates Aβ-driven neurodegeneration in human induced pluripotent stem cell (iPSC)-derived neurons. We generated a novel CLU-knockout iPSC line by CRISPR/Cas9-mediated gene editing to investigate Aβ-mediated neurodegeneration in cortical neurons differentiated from wild type and CLU knockout iPSCs. We measured response to Aβ using an imaging assay and measured changes in gene expression using qPCR and RNA sequencing. In wild type neurons imaging indicated that neuronal processes degenerate following treatment with Aβ25-35 peptides and Aβ1-42 oligomers, in a dose dependent manner, and that intracellular levels of clusterin are increased following Aβ treatment. However, in CLU knockout neurons Aβ exposure did not affect neurite length, suggesting that clusterin is an important component of the amyloid cascade. Transcriptomic data were analyzed to elucidate the pathways responsible for the altered response to Aβ in neurons with the CLU deletion. Four of the five genes previously identified as downstream to Aβ and Dickkopf-1 (DKK1) proteins in an Aβ-driven neurotoxic pathway in rodent cells were also dysregulated in human neurons with the CLU deletion. AD and lysosome pathways were the most significantly dysregulated pathways in the CLU knockout neurons, and pathways relating to cytoskeletal processes were most dysregulated in Aβ treated neurons. The absence of neurodegeneration in the CLU knockout neurons in response to Aβ compared to the wild type neurons supports the role of clusterin in Aβ-mediated AD pathogenesis.
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Affiliation(s)
| | - Leo Perfect
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom
| | - Elena M Ribe
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Marcello Maresca
- Translational Genomics, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | | | | | - Richard Killick
- Department of Old Age Psychiatry, King's College London, London, United Kingdom
| | - Paulina Nowosiad
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom
| | - Matthew J Reid
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom
| | - Lucia Dutan Polit
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom
| | - Alejo J Nevado
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Daniel Ebner
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Noel Buckley
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Menelas N Pangalos
- Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Jack Price
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
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10
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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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11
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Pimenova AA, Raj T, Goate AM. Untangling Genetic Risk for Alzheimer's Disease. Biol Psychiatry 2018; 83:300-310. [PMID: 28666525 PMCID: PMC5699970 DOI: 10.1016/j.biopsych.2017.05.014] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/15/2017] [Accepted: 05/15/2017] [Indexed: 01/01/2023]
Abstract
Alzheimer's disease (AD) is a genetically heterogeneous neurodegenerative disorder caused by fully penetrant single gene mutations in a minority of cases, while the majority of cases are sporadic or show modest familial clustering. These cases are of late onset and likely result from the interaction of many genes and the environment. More than 30 loci have been implicated in AD by a combination of linkage, genome-wide association, and whole genome/exome sequencing. We have learned from these studies that perturbations in endolysosomal, lipid metabolism, and immune response pathways substantially contribute to sporadic AD pathogenesis. We review here current knowledge about functions of AD susceptibility genes, highlighting cells of the myeloid lineage as drivers of at least part of the genetic component in late-onset AD. Although targeted resequencing utilized for the identification of causal variants has discovered coding mutations in some AD-associated genes, a lot of risk variants lie in noncoding regions. Here we discuss the use of functional genomics approaches that integrate transcriptomic, epigenetic, and endophenotype traits with systems biology to annotate genetic variants, and to facilitate discovery of AD risk genes. Further validation in cell culture and mouse models will be necessary to establish causality for these genes. This knowledge will allow mechanism-based design of novel therapeutic interventions in AD and promises coherent implementation of treatment in a personalized manner.
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Affiliation(s)
- Anna A Pimenova
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York.
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12
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Seripa D, Panza F, Paroni G, D'Onofrio G, Bisceglia P, Gravina C, Urbano M, Lozupone M, Solfrizzi V, Bizzarro A, Boccardi V, Piccininni C, Daniele A, Logroscino G, Mecocci P, Masullo C, Greco A. Role of CLU, PICALM, and TNK1 Genotypes in Aging With and Without Alzheimer's Disease. Mol Neurobiol 2017. [PMID: 28631188 DOI: 10.1007/s12035-017-0547-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Healthy and impaired cognitive aging may be associated to different prevalences of single-nucleotide polymorphisms (SNPs). In a multicenter case-control association study, we studied the SNPs rs11136000 (clusterin, CLU), rs541458 (phosphatidylinositol binding clatrin assembly protein, PICALM), and rs1554948 (transcription factor A, and tyrosine kinase, non-receptor, 1, TNK1) according to the three age groups 50-65 years (group 1), 66-80 years (group 2), and 80+ years (group 3) in 569 older subjects without cognitive impairment (NoCI) and 520 Alzheimer's disease (AD) patients. In NoCI subjects, a regression analysis suggested a relationship between age and TNK1 genotypes, with the TNK1-A/A genotype frequency that increased with higher age, and resulting in a different distribution of the TNK1-A allele. In AD patients, a regression analysis suggested a relationship between age and PICALM genotypes and TNK1 genotypes, with the PICALM-T/C and TNK1-A/A genotype frequencies that decreased with increasing age. A resulting difference in the distribution of PICALM-C allele and TNK1-A allele was also observed. The TNK1-A allele was overrepresented in NoCI subjects than in AD patients in age groups 2 and 3. These results confirmed after adjustment for apolipoprotein E polymorphism, which suggested a different role of PICALM and TNK1 in healthy and impaired cognitive aging. More studies, however, are needed to confirm the observed associations.
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Affiliation(s)
- Davide Seripa
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy.
| | - Francesco Panza
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy. .,Unit of Neurodegenerative Disease, Department of Basic Medicine Sciences, Neuroscience, and Sense Organs, University of "BariAldo Moro", Bari, Italy. .,Unit of Neurodegenerative Disease, Department of Clinical Research in Neurology, University of Bari "Aldo Moro" at "Pia Fondazione Card. G. Panico", Tricase, Lecce, Italy. .,Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy.
| | - Giulia Paroni
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Grazia D'Onofrio
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Paola Bisceglia
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Carolina Gravina
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Maria Urbano
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Madia Lozupone
- Unit of Neurodegenerative Disease, Department of Basic Medicine Sciences, Neuroscience, and Sense Organs, University of "BariAldo Moro", Bari, Italy
| | - Vincenzo Solfrizzi
- Geriatric Medicine-Memory Unit and Rare Disease Centre, University of Bari Aldo Moro, Bari, Italy
| | | | - Virginia Boccardi
- Institute of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | - Chiara Piccininni
- Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Antonio Daniele
- Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Giancarlo Logroscino
- Unit of Neurodegenerative Disease, Department of Basic Medicine Sciences, Neuroscience, and Sense Organs, University of "BariAldo Moro", Bari, Italy.,Unit of Neurodegenerative Disease, Department of Clinical Research in Neurology, University of Bari "Aldo Moro" at "Pia Fondazione Card. G. Panico", Tricase, Lecce, Italy
| | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | - Carlo Masullo
- Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Antonio Greco
- Complex Structure of Geriatrics, Research Laboratory, Department of Medical Sciences, I.R.C.C.S. Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
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13
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Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ. Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Front Aging Neurosci 2016; 8:183. [PMID: 27536236 PMCID: PMC4971101 DOI: 10.3389/fnagi.2016.00183] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/15/2016] [Indexed: 11/13/2022] Open
Abstract
Human aging is associated with cognitive decline and an increased risk of neurodegenerative disease. Our objective for this study was to evaluate potential relationships between age and variation in gene expression across different regions of the brain. We analyzed the Genotype-Tissue Expression (GTEx) data from 54 to 101 tissue samples across 13 brain regions in post-mortem donors of European descent aged between 20 and 70 years at death. After accounting for the effects of covariates and hidden confounding factors, we identified 1446 protein-coding genes whose expression in one or more brain regions is correlated with chronological age at a false discovery rate of 5%. These genes are involved in various biological processes including apoptosis, mRNA splicing, amino acid biosynthesis, and neurotransmitter transport. The distribution of these genes among brain regions is uneven, suggesting variable regional responses to aging. We also found that the aging response of many genes, e.g., TP37 and C1QA, depends on individuals' genotypic backgrounds. Finally, using dispersion-specific analysis, we identified genes such as IL7R, MS4A4E, and TERF1/TERF2 whose expressions are differentially dispersed by aging, i.e., variances differ between age groups. Our results demonstrate that age-related gene expression is brain region-specific, genotype-dependent, and associated with both mean and dispersion changes. Our findings provide a foundation for more sophisticated gene expression modeling in the studies of age-related neurodegenerative diseases.
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Affiliation(s)
| | - Jinting Guan
- Department of Automation, Xiamen UniversityXiamen, China
| | - Guoli Ji
- Department of Automation, Xiamen UniversityXiamen, China
- Innovation Center for Cell Signaling Network, Xiamen UniversityXiamen, China
| | - James J. Cai
- Department of Veterinary Integrative Biosciences, Texas A&M UniversityCollege Station, TX, USA
- Interdisciplinary Program in Genetics, Texas A&M UniversityCollege Station, TX, USA
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14
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Tan L, Wang HF, Tan MS, Tan CC, Zhu XC, Miao D, Yu WJ, Jiang T, Tan L, Yu JT. Effect of CLU genetic variants on cerebrospinal fluid and neuroimaging markers in healthy, mild cognitive impairment and Alzheimer's disease cohorts. Sci Rep 2016; 6:26027. [PMID: 27229352 PMCID: PMC4882617 DOI: 10.1038/srep26027] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 04/25/2016] [Indexed: 01/18/2023] Open
Abstract
The Clusterin (CLU) gene, also known as apolipoprotein J (ApoJ), is currently the third most associated late-onset Alzheimer's disease (LOAD) risk gene. However, little was known about the possible effect of CLU genetic variants on AD pathology in brain. Here, we evaluated the interaction between 7 CLU SNPs (covering 95% of genetic variations) and the role of CLU in β-amyloid (Aβ) deposition, AD-related structure atrophy, abnormal glucose metabolism on neuroimaging and CSF markers to clarify the possible approach by that CLU impacts AD. Finally, four loci (rs11136000, rs1532278, rs2279590, rs7982) showed significant associations with the Aβ deposition at the baseline level while genotypes of rs9331888 (P = 0.042) increased Aβ deposition. Besides, rs9331888 was significantly associated with baseline volume of left hippocampus (P = 0.014). We then further validated the association with Aβ deposition in the AD, mild cognitive impairment (MCI), normal control (NC) sub-groups. The results in sub-groups confirmed the association between CLU genotypes and Aβ deposition further. Our findings revealed that CLU genotypes could probably modulate the cerebral the Aβ loads on imaging and volume of hippocampus. These findings raise the possibility that the biological effects of CLU may be relatively confined to neuroimaging trait and hence may offer clues to AD.
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Affiliation(s)
- Lin Tan
- College of Medicine and Pharmaceutics, Ocean University of China, China
| | - Hui-Fu Wang
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao, China
| | - Meng-Shan Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Chen-Chen Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Xi-Chen Zhu
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao, China
| | - Dan Miao
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Wan-Jiang Yu
- Department of Radiology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Teng Jiang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lan Tan
- College of Medicine and Pharmaceutics, Ocean University of China, China.,Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao, China.,Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Jin-Tai Yu
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao, China
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15
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Ebbert MTW, Boehme KL, Wadsworth ME, Staley LA, Mukherjee S, Crane PK, Ridge PG, Kauwe JSK. Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk. Alzheimers Dement 2016; 12:121-129. [PMID: 26449541 PMCID: PMC4744542 DOI: 10.1016/j.jalz.2015.08.163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/17/2015] [Accepted: 08/17/2015] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Ebbert et al. reported gene-gene interactions between rs11136000-rs670139 (CLU-MS4A4E) and rs3865444-rs670139 (CD33-MS4A4E). We evaluate these interactions in the largest data set for an epistasis study. METHODS We tested interactions using 3837 cases and 4145 controls from Alzheimer's Disease Genetics Consortium using meta-analyses and permutation analyses. We repeated meta-analyses stratified by apolipoprotein E (APOE) ε4 status, estimated combined odds ratio (OR) and population attributable fraction (cPAF), and explored causal variants. RESULTS Results support the CLU-MS4A4E interaction and a dominant effect. An association between CLU-MS4A4E and APOE ε4 negative status exists. The estimated synergy factor, OR, and cPAF for rs11136000-rs670139 are 2.23, 2.45, and 8.0, respectively. We identified potential causal variants. DISCUSSION We replicated the CLU-MS4A4E interaction in a large case-control series and observed APOE ε4 and possible dominant effect. The CLU-MS4A4E OR is higher than any Alzheimer's disease locus except APOE ε4, APP, and TREM2. We estimated an 8% decrease in Alzheimer's disease incidence without CLU-MS4A4E risk alleles and identified potential causal variants.
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Affiliation(s)
- Mark T W Ebbert
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Kevin L Boehme
- Department of Biology, Brigham Young University, Provo, UT, USA
| | | | | | | | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA.
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16
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Abstract
For the first time in the history of human genetics research, it is now both technically feasible and economically affordable to screen individual genomes for novel disease-causing mutations at base-pair resolution using "next-generation sequencing" (NGS). One popular aim in many of today's NGS studies is genome resequencing (in part or whole) to identify DNA variants potentially accounting for the "missing heritability" problem observed in many genetically complex traits. Thus far, only relatively few projects have applied these powerful new technologies to search for novel Alzheimer's disease (AD) related sequence variants. In this review, I summarize the findings from the first NGS-based resequencing studies in AD and discuss their potential implications and limitations. Notable recent discoveries using NGS include the identification of rare susceptibility modifying alleles in APP, TREM2, and PLD3. Several other large-scale NGS projects are currently underway so that additional discoveries can be expected over the coming years.
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17
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Li K, Wang J, Ma ZB, Guo GH. Association between clusterin polymorphisms and esophageal squamous cell carcinoma risk in Han Chinese population. Int J Clin Exp Med 2015; 8:14004-10. [PMID: 26550359 PMCID: PMC4613044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/22/2015] [Indexed: 06/05/2023]
Abstract
Genetic susceptibility plays an essential role in an individual's risk of esophageal squamous cell carcinoma (ESCC). The aim of this study is to investigate the associations between clusterin (CLU) gene polymorphisms and ESCC risk. We undertook a case-control study to analyze three CLU polymorphisms (gene rs9331888 C>G, rs17466684 A>G and rs1532278 T>C) in an Han Chinese population, by extraction of genomic DNA from the peripheral blood of 642 patients with ESCC and 658 control participants, and performed CLU genotyping using DNA sequencing. The obtained results indicated that overall, no statistically significant association was observed in rs17466684 and rs1532278. However, gene rs9331888 C>G genotype was at increased risk of ESCCs (P=0.037; odds ratio (OR)=1.089, 95% CI: 1.006-1.175). Moreover, rs9331888 G/G genotype ESCCs were more significantly common in patients with tumor size of >5 cm than T allele ESCC and in cases of poor differentiation and lower advanced pathological stage. In conclusion, polymorphism in rs9331888 C>G was observed to be associated with susceptibility of ESCC. Nevertheless, further investigation with a larger sample size is needed to support our results.
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Affiliation(s)
- Kun Li
- Department of Gastroenterology, Affiliated Hospital of Binzhou Medical CollegeBinzhou 256600, China
| | - Jian Wang
- Department of Gastroenterology, Affiliated Hospital of Binzhou Medical CollegeBinzhou 256600, China
| | - Zhen-Bin Ma
- Department of Gastroenterology, Affiliated Hospital of Binzhou Medical CollegeBinzhou 256600, China
| | - Guang-Hong Guo
- Department of Gynaecology, Affiliated Hospital of Binzhou Medical CollegeBinzhou 256600, China
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18
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Optimization of specific multiplex DNA primers to detect variable CLU genomic lesions in patients with Alzheimer’s disease. BIOCHIP JOURNAL 2015. [DOI: 10.1007/s13206-015-9306-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
Alzheimer's disease (AD) represents the main form of dementia, and is a major public health problem. Despite intensive research efforts, current treatments have only marginal symptomatic benefits and there are no effective disease-modifying or preventive interventions. AD has a strong genetic component, so much research in AD has focused on identifying genetic causes and risk factors. This chapter will cover genetic discoveries in AD and their consequences in terms of improved knowledge regarding the disease and the identification of biomarkers and drug targets. First, we will discuss the study of the rare early-onset, autosomal dominant forms of AD that led to the discovery of mutations in three major genes, APP, PSEN1, and PSEN2. These discoveries have shaped our current understanding of the pathophysiology and natural history of AD as well as the development of therapeutic targets and the design of clinical trials. Then, we will explore linkage analysis and candidate gene approaches, which identified variants in Apolipoprotein E (APOE) as the major genetic risk factor for late-onset, "sporadic" forms of AD (LOAD), but failed to robustly identify other genetic risk factors, with the exception of variants in SORL1. The main focus of this chapter will be on recent genome-wide association studies that have successfully identified common genetic variations at over 20 loci associated with LOAD outside of the APOE locus. These loci are in or near-novel AD genes including BIN1, CR1, CLU, phosphatidylinositol-binding clathrin assembly protein (PICALM), CD33, EPHA1, MS4A4/MS4A6, ABCA7, CD2AP, SORL1, HLA-DRB5/DRB1, PTK2B, SLC24A4-RIN3, INPP5D, MEF2C, NME8, ZCWPW1, CELF1, FERMT2, CASS4, and TRIP4 and each has small effects on risk of AD (relative risks of 1.1-1.3). Finally, we will touch upon the ongoing effort to identify less frequent and rare variants through whole exome and whole genome sequencing. This effort has identified two novel genes, TREM2 and PLD3, and shown a role for APP in LOAD. The identification of these recently identified genes has implicated previously unsuspected biological pathways in the pathophysiology of AD.
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Affiliation(s)
- Vincent Chouraki
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Framingham Heart Study, Framingham, MA, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Framingham Heart Study, Framingham, MA, USA
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20
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Lord J, Lu AJ, Cruchaga C. Identification of rare variants in Alzheimer's disease. Front Genet 2014; 5:369. [PMID: 25389433 PMCID: PMC4211559 DOI: 10.3389/fgene.2014.00369] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 10/03/2014] [Indexed: 12/21/2022] Open
Abstract
Much progress has been made in recent years in identifying genes involved in the risk of developing Alzheimer's disease (AD), the most common form of dementia. Yet despite the identification of over 20 disease associated loci, mainly through genome wide association studies (GWAS), a large proportion of the genetic component of the disorder remains unexplained. Recent evidence from the AD field, as with other complex diseases, suggests a large proportion of this "missing heritability" may be due to rare variants of moderate to large effect size, but the methodologies to detect such variants are still in their infancy. The latest studies in the field have been focused on the identification of coding variation associated with AD risk, through whole-exome or whole-genome sequencing. Such variants are expected to have larger effect sizes than GWAS loci, and are easier to functionally characterize, and develop cellular and animal models for. This review explores the issues involved in detecting rare variant associations in the context of AD, highlighting some successful approaches utilized to date.
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Affiliation(s)
- Jenny Lord
- Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
| | - Alexander J. Lu
- Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of MedicineSt. Louis, MO, USA
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21
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Mengel-From J, Thinggaard M, Lindahl-Jacobsen R, McGue M, Christensen K, Christiansen L. CLU genetic variants and cognitive decline among elderly and oldest old. PLoS One 2013; 8:e79105. [PMID: 24244428 PMCID: PMC3828341 DOI: 10.1371/journal.pone.0079105] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/18/2013] [Indexed: 01/18/2023] Open
Abstract
The CLU gene is one of the prime genetic candidates associated with Alzheimers disease. In the present study CLU genotypes and haplotypes were associated with baseline cognition and the rate of cognitive decline in two cohorts, the Danish 1905 birth cohort (93 years of age in 1998) and the Longitudinal Study of Aging Danish twins (LSADT) (73-83 year old twins in 1997). Both Mini Mental State Examination (MMSE) and a cognitive composite score was attained up to six times for up to 10 years and analysed using random effects models and vital status. The rs11136000 T allele was associated with better baseline cognitive performance both in the LSADT (effect on intercept: 0.41 95% CI [-0.04; 0.87]) and the 1905 birth cohort (effect on intercept: 0.28 95% CI [0.01; 0.55]), although it did not reach significance in the LSADT cohort. However, the rs11136000 T allele was significantly associated with a steeper decline (effect on slope: -0.06 95% CI [-0.11; -0.01]) in the LSADT cohort, but not in the 1905 birth cohort. Haplotype analyses revealed that carriers of the common rs11136000, rs1532278 and rs9331888 TTC haplotype (36%) in the CLU gene performed cognitively better than non-carriers in the 1905 birth cohort (effect on intercept: 0.50 95% CI [0.12; 0.91]) and carriers of a rare TCC haplotype (1%) performed worse on the cognitive composite score (effect on intercept: -1.51 95% CI [-2.92; -0.06]). The association between the TTC haplotype and better cognitive composite score was higher among those surviving past the age of 98 (p = 0.014), and among these the TTC haplotype was borderline associated with a steep decline (effect on slope: -0.13 95% CI [-0.27; 0.00]). In summery CLU genetic variants associate with cognition in two cohorts, but the genetic effect of CLU seems to regress toward the mean when aging.
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Affiliation(s)
- Jonas Mengel-From
- The Danish Aging Research Center and The Danish Twin Registry, Epidemiology Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- * E-mail:
| | - Mikael Thinggaard
- The Danish Aging Research Center and The Danish Twin Registry, Epidemiology Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Rune Lindahl-Jacobsen
- The Danish Aging Research Center and The Danish Twin Registry, Epidemiology Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Matt McGue
- The Danish Aging Research Center and The Danish Twin Registry, Epidemiology Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kaare Christensen
- The Danish Aging Research Center and The Danish Twin Registry, Epidemiology Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Lene Christiansen
- The Danish Aging Research Center and The Danish Twin Registry, Epidemiology Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
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22
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Abstract
Genome-wide association studies are identifying novel Alzheimer's disease (AD) risk factors. Elucidating the mechanism underlying these polymorphisms is critical to the validation process and, by identifying rate-limiting steps in AD risk, may yield novel therapeutic targets. Here, we elucidate the mechanism of action of the AD-associated polymorphism rs3865444 in the promoter of CD33, a member of the sialic acid-binding Ig-superfamily of lectins (SIGLECs). Immunostaining established that CD33 is expressed in microglia in human brain. Consistent with this finding, CD33 mRNA expression correlated well with expression of the microglial genes CD11b and AIF-1 and was modestly increased with AD status and the rs3865444C AD-risk allele. Analysis of CD33 isoforms identified a common isoform lacking exon 2 (D2-CD33). The proportion of CD33 expressed as D2-CD33 correlated robustly with rs3865444 genotype. Because rs3865444 is in the CD33 promoter region, we sought the functional polymorphism by sequencing CD33 from the promoter through exon 4. We identified a single polymorphism that is coinherited with rs3865444, i.e., rs12459419 in exon 2. Minigene RNA splicing studies in BV2 microglial cells established that rs12459419 is a functional single nucleotide polymorphism (SNP) that modulates exon 2 splicing efficiency. Thus, our primary findings are that CD33 is a microglial mRNA and that rs3865444 is a proxy SNP for rs12459419 that modulates CD33 exon 2 splicing. Exon 2 encodes the CD33 IgV domain that typically mediates sialic acid binding in SIGLEC family members. In summary, these results suggest a novel model wherein SNP-modulated RNA splicing modulates CD33 function and, thereby, AD risk.
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Genetics of Alzheimer's disease. BIOMED RESEARCH INTERNATIONAL 2013; 2013:254954. [PMID: 23984328 PMCID: PMC3741956 DOI: 10.1155/2013/254954] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 01/18/2023]
Abstract
Alzheimer's disease is the most common form of dementia and is the only top 10 cause of death in the United States that lacks disease-altering treatments. It is a complex disorder with environmental and genetic components. There are two major types of Alzheimer's disease, early onset and the more common late onset. The genetics of early-onset Alzheimer's disease are largely understood with variants in three different genes leading to disease. In contrast, while several common alleles associated with late-onset Alzheimer's disease, including APOE, have been identified using association studies, the genetics of late-onset Alzheimer's disease are not fully understood. Here we review the known genetics of early- and late-onset Alzheimer's disease.
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Holton P, Ryten M, Nalls M, Trabzuni D, Weale ME, Hernandez D, Crehan H, Gibbs JR, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Schellenberg GD, Ramirez-Restrepo M, Engel A, Myers AJ, Corneveaux JJ, Huentelman MJ, Dillman A, Cookson MR, Reiman EM, Singleton A, Hardy J, Guerreiro R. Initial assessment of the pathogenic mechanisms of the recently identified Alzheimer risk Loci. Ann Hum Genet 2013; 77:85-105. [PMID: 23360175 PMCID: PMC3578142 DOI: 10.1111/ahg.12000] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 03/05/2012] [Indexed: 12/27/2022]
Abstract
Recent genome wide association studies have identified CLU, CR1, ABCA7 BIN1, PICALM and MS4A6A/MS4A6E in addition to the long established APOE, as loci for Alzheimer's disease. We have systematically examined each of these loci to assess whether common coding variability contributes to the risk of disease. We have also assessed the regional expression of all the genes in the brain and whether there is evidence of an eQTL explaining the risk. In agreement with other studies we find that coding variability may explain the ABCA7 association, but common coding variability does not explain any of the other loci. We were not able to show that any of the loci had eQTLs within the power of this study. Furthermore the regional expression of each of the loci did not match the pattern of brain regional distribution in Alzheimer pathology. Although these results are mainly negative, they allow us to start defining more realistic alternative approaches to determine the role of all the genetic loci involved in Alzheimer's disease.
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Affiliation(s)
- Patrick Holton
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Michael Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Daniah Trabzuni
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Michael E. Weale
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
| | - Dena Hernandez
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Helen Crehan
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - J. Raphael Gibbs
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Richard Mayeux
- Gertrude H. Sergievsky Center and Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY
| | - Jonathan L. Haines
- Department of Molecular Physiology and Biophysics and Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Biostatistics, Ophthalmology, Epidemiology, and Neurology, Boston University Schools of Medicine and Public Health, Boston, MA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA
| | | | - Manuel Ramirez-Restrepo
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL
- Johnnie B. Byrd Sr. Alzheimer's Center and Research Institute, Tampa, FL
| | - Anzhelika Engel
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL
- Johnnie B. Byrd Sr. Alzheimer's Center and Research Institute, Tampa, FL
| | - Amanda J. Myers
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL
- Johnnie B. Byrd Sr. Alzheimer's Center and Research Institute, Tampa, FL
| | - Jason J. Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute and Arizona Alzheimer's Consortium, Phoenix, AZ
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute and Arizona Alzheimer's Consortium, Phoenix, AZ
| | - Allissa Dillman
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Eric M. Reiman
- Neurogenomics Division, Translational Genomics Research Institute and Arizona Alzheimer's Consortium, Phoenix, AZ
- Banner Alzheimer's Institute and Department of Psychiatry, University of Arizona, Phoenix, AZ
- Department of Psychiatry, University of Arizona, Tucson, AZ
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Reta Lila Weston Laboratories and Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Rita Guerreiro
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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Yu JT, Ma XY, Wang YL, Sun L, Tan L, Hu N, Tan L. Genetic variation in clusterin gene and Alzheimer's disease risk in Han Chinese. Neurobiol Aging 2013; 34:1921.e17-23. [PMID: 23411014 DOI: 10.1016/j.neurobiolaging.2013.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/18/2013] [Accepted: 01/20/2013] [Indexed: 10/27/2022]
Abstract
Clusterin gene (CLU), also known as apolipoprotein J (ApoJ), is a strong candidate gene for late-onset Alzheimer's disease (LOAD) according to the Alzgene database. To further characterize this association and to isolate the variants contributing to the pathogenesis of LOAD in Han Chinese, we first sequenced a small sample (n = 100) to discover variants in the promoter, exons, the 5' and 3' untranslated regions, and exon-intron boundaries of CLU. Follow-up genotyping of identified variants in a larger sample (n = 1592). Sequencing analysis identified 18 variants. Analysis in the larger population revealed that only the rs9331949 C allele was significantly associated with an increased risk of LOAD, even after adjusting for multiple testing (p = 0.026). Logistic analysis identified the rs9331949 polymorphism was still strongly associated with LOAD (additive model: p = 0.004, odds ratio = 1.274; dominant model: p = 0.039, odds ratio = 1.239; recessive model: p = 0.002, OR = 1.975) after adjusting for sex, age, and APOE ε4 status. Our findings implicate CLU as a susceptibility gene for LOAD in Han Chinese.
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Affiliation(s)
- Jin-Tai Yu
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao, China.
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26
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Abstract
In the search for new genes in Alzheimer's disease, classic linkage-based and candidate-gene-based association studies have been supplanted by exome sequencing, genome-wide sequencing (for mendelian forms of Alzheimer's disease), and genome-wide association studies (for non-mendelian forms). The identification of new susceptibility genes has opened new avenues for exploration of the underlying disease mechanisms. In addition to detecting novel risk factors in large samples, next-generation sequencing approaches can deliver novel insights with even small numbers of patients. The shift in focus towards translational studies and sequencing of individual patients places each patient's biomaterials as the central unit of genetic studies. The notional shift needed to make the patient central to genetic studies will necessitate strong collaboration and input from clinical neurologists.
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Affiliation(s)
- Karolien Bettens
- Neurodegenerative Brain Diseases Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
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27
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Ferrari R, Moreno JH, Minhajuddin AT, O'Bryant SE, Reisch JS, Barber RC, Momeni P. Implication of common and disease specific variants in CLU, CR1, and PICALM. Neurobiol Aging 2012; 33:1846.e7-18. [DOI: 10.1016/j.neurobiolaging.2012.01.110] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 01/25/2012] [Accepted: 01/30/2012] [Indexed: 11/30/2022]
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Abstract
In addition to apolipoprotein E (APOE), recent large genome-wide association studies (GWASs) have identified nine other genes/loci (CR1, BIN1, CLU, PICALM, MS4A4/MS4A6E, CD2AP, CD33, EPHA1 and ABCA7) for late-onset Alzheimer's disease (LOAD). However, the genetic effect attributable to known loci is about 50%, indicating that additional risk genes for LOAD remain to be identified. In this study, we have used a new GWAS data set from the University of Pittsburgh (1291 cases and 938 controls) to examine in detail the recently implicated nine new regions with Alzheimer's disease (AD) risk, and also performed a meta-analysis utilizing the top 1% GWAS single-nucleotide polymorphisms (SNPs) with P<0.01 along with four independent data sets (2727 cases and 3336 controls) for these SNPs in an effort to identify new AD loci. The new GWAS data were generated on the Illumina Omni1-Quad chip and imputed at ~2.5 million markers. As expected, several markers in the APOE regions showed genome-wide significant associations in the Pittsburg sample. While we observed nominal significant associations (P<0.05) either within or adjacent to five genes (PICALM, BIN1, ABCA7, MS4A4/MS4A6E and EPHA1), significant signals were observed 69-180 kb outside of the remaining four genes (CD33, CLU, CD2AP and CR1). Meta-analysis on the top 1% SNPs revealed a suggestive novel association in the PPP1R3B gene (top SNP rs3848140 with P = 3.05E-07). The association of this SNP with AD risk was consistent in all five samples with a meta-analysis odds ratio of 2.43. This is a potential candidate gene for AD as this is expressed in the brain and is involved in lipid metabolism. These findings need to be confirmed in additional samples.
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29
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Ling IF, Bhongsatiern J, Simpson JF, Fardo DW, Estus S. Genetics of clusterin isoform expression and Alzheimer's disease risk. PLoS One 2012; 7:e33923. [PMID: 22506010 PMCID: PMC3323613 DOI: 10.1371/journal.pone.0033923] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 02/21/2012] [Indexed: 01/13/2023] Open
Abstract
The minor allele of rs11136000 within CLU is strongly associated with reduced Alzheimer's disease (AD) risk. The mechanism underlying this association is unclear. Here, we report that CLU1 and CLU2 are the two primary CLU isoforms in human brain; CLU1 and CLU2 share exons 2-9 but differ in exon 1 and proximal promoters. The expression of both CLU1 and CLU2 was increased in individuals with significant AD neuropathology. However, only CLU1 was associated with the rs11136000 genotype, with the minor "protective" rs11136000T allele being associated with increased CLU1 expression. Since CLU1 and CLU2 are predicted to encode intracellular and secreted proteins, respectively, we compared their expression; for both CLU1 and CLU2 transfected cells, clusterin is present in the secretory pathway, accumulates in the extracellular media, and is similar in size to clusterin in human brain. Overall, we interpret these results as indicating that the AD-protective minor rs11136000T allele is associated with increased CLU1 expression. Since CLU1 and CLU2 appear to produce similar proteins and are increased in AD, the AD-protection afforded by the rs11136000T allele may reflect increased soluble clusterin throughout life.
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Affiliation(s)
- I-Fang Ling
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jiraganya Bhongsatiern
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - James F. Simpson
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - David W. Fardo
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Steven Estus
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
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30
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Guerreiro RJ, Gustafson DR, Hardy J. The genetic architecture of Alzheimer's disease: beyond APP, PSENs and APOE. Neurobiol Aging 2012; 33:437-56. [PMID: 20594621 PMCID: PMC2980860 DOI: 10.1016/j.neurobiolaging.2010.03.025] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 03/01/2010] [Accepted: 03/11/2010] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is a complex disorder with a clear genetic component. Three genes have been identified as the cause of early onset familial AD (EOAD). The most common form of the disease, late onset Alzheimer's disease (LOAD), is, however, a sporadic one presenting itself in later stages of life. The genetic component of this late onset form of AD has been the target of a large number of studies, because only one genetic risk factor (APOE4) has been consistently associated with the disease. However, technological advances allow new approaches in the study of complex disorders. In this review, we discuss the new results produced by genome wide association studies, in light of the current knowledge of the complexity of AD genetics.
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Affiliation(s)
- Rita J Guerreiro
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, MD, USA.
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31
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Moraes CF, Lins TC, Carmargos EF, Naves JOS, Pereira RW, Nóbrega OT. Lessons from genome-wide association studies findings in Alzheimer's disease. Psychogeriatrics 2012; 12:62-73. [PMID: 22416831 DOI: 10.1111/j.1479-8301.2011.00378.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder with a complex genetic background. Recent genome-wide association studies (GWAS) have placed important new contributors into the genetic framework of early- and late-onset forms of this dementia. Besides confirming the major role of classic allelic variants (e.g. apolipoprotein E) in the development of AD, GWAS have thus far implicated over 20 single nucleotide polymorphisms in AD. In this review, we summarize the findings of 16 AD-based GWAS performed to date whose public registries are available at the National Human Genome Research Institute, with an emphasis on understanding whether the polymorphic markers under consideration support functional implications to the pathophysiological role of the major genetic risk factors unraveled by GWAS.
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Affiliation(s)
- Clayton F Moraes
- Geriatric Service, Hospital of the Catholic University of Brasília, Graduate Program in Medical Sciences, University of Brasília, Brasília - DF, Brazil
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32
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Lin YL, Chen SY, Lai LC, Chen JH, Yang SY, Huang YL, Chen TF, Sun Y, Wen LL, Yip PK, Chu YM, Chen WJ, Chen YC. Genetic polymorphisms of clusterin gene are associated with a decreased risk of Alzheimer's disease. Eur J Epidemiol 2012; 27:73-75. [PMID: 22286716 DOI: 10.1007/s10654-012-9650-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Accepted: 01/10/2012] [Indexed: 10/14/2022]
Affiliation(s)
- Yen-Ling Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
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33
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The role of clusterin in Alzheimer's disease: pathways, pathogenesis, and therapy. Mol Neurobiol 2012; 45:314-26. [PMID: 22274961 DOI: 10.1007/s12035-012-8237-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
Abstract
Genetic variation in clusterin gene, also known as apolipoprotein J, has been associated with Alzheimer's disease (AD) through replicated genome-wide studies, and plasma clusterin levels are associated with brain atrophy, baseline prevalence and severity, and rapid clinical progression in patients with AD, highlighting the importance of clusterin in AD pathogenesis. Emerging data suggest that clusterin contributes to AD through various pathways, including amyloid-β aggregation and clearance, lipid metabolism, neuroinflammation, and neuronal cell cycle control and apoptosis. Moreover, epigenetic regulation of the clusterin expression also seems to play an important role in the pathogenesis of AD. Emerging knowledge of the contribution of clusterin to the pathogenesis of AD presents new opportunities for AD therapy.
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34
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Bettens K, Brouwers N, Engelborghs S, Lambert JC, Rogaeva E, Vandenberghe R, Le Bastard N, Pasquier F, Vermeulen S, Van Dongen J, Mattheijssens M, Peeters K, Mayeux R, St George-Hyslop P, Amouyel P, De Deyn PP, Sleegers K, Van Broeckhoven C. Both common variations and rare non-synonymous substitutions and small insertion/deletions in CLU are associated with increased Alzheimer risk. Mol Neurodegener 2012; 7:3. [PMID: 22248099 PMCID: PMC3296573 DOI: 10.1186/1750-1326-7-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Accepted: 01/16/2012] [Indexed: 11/23/2022] Open
Abstract
Background We have followed-up on the recent genome-wide association (GWA) of the clusterin gene (CLU) with increased risk for Alzheimer disease (AD), by performing an unbiased resequencing of all CLU coding exons and regulatory regions in an extended Flanders-Belgian cohort of Caucasian AD patients and control individuals (n = 1930). Moreover, we have replicated genetic findings by targeted resequencing in independent Caucasian cohorts of French (n = 2182) and Canadian (n = 573) origin and by performing meta-analysis combining our data with previous genetic CLU screenings. Results In the Flanders-Belgian cohort, we identified significant clustering in exons 5-8 of rare genetic variations leading to non-synonymous substitutions and a 9-bp insertion/deletion affecting the CLU β-chain (p = 0.02). Replicating this observation by targeted resequencing of CLU exons 5-8 in 2 independent Caucasian cohorts of French and Canadian origin identified identical as well as novel non-synonymous substitutions and small insertion/deletions. A meta-analysis, combining the datasets of the 3 cohorts with published CLU sequencing data, confirmed that rare coding variations in the CLU β-chain were significantly enriched in AD patients (ORMH = 1.96 [95% CI = 1.18-3.25]; p = 0.009). Single nucleotide polymorphisms (SNPs) association analysis indicated the common AD risk association (GWA SNP rs11136000, p = 0.013) in the 3 combined datasets could not be explained by the presence of the rare coding variations we identified. Further, high-density SNP mapping in the CLU locus mapped the common association signal to a more 5' CLU region. Conclusions We identified a new genetic risk association of AD with rare coding CLU variations that is independent of the 5' common association signal identified in the GWA studies. At this stage the role of these coding variations and their likely effect on the β-chain domain and CLU protein functioning remains unclear and requires further studies.
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Affiliation(s)
- Karolien Bettens
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, 2610 Antwerpen, Belgium.
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Olgiati P, Politis AM, Papadimitriou GN, De Ronchi D, Serretti A. Genetics of late-onset Alzheimer's disease: update from the alzgene database and analysis of shared pathways. Int J Alzheimers Dis 2011; 2011:832379. [PMID: 22191060 PMCID: PMC3235576 DOI: 10.4061/2011/832379] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 09/21/2011] [Indexed: 12/13/2022] Open
Abstract
The genetics of late-onset Alzheimer's disease (LOAD) has taken impressive steps forwards in the last few years. To date, more than six-hundred genes have been linked to the disorder. However, only a minority of them are supported by a sufficient level of evidence. This review focused on such genes and analyzed shared biological pathways. Genetic markers were selected from a web-based collection (Alzgene). For each SNP in the database, it was possible to perform a meta-analysis. The quality of studies was assessed using criteria such as size of research samples, heterogeneity across studies, and protection from publication bias. This produced a list of 15 top-rated genes: APOE, CLU, PICALM, EXOC3L2, BIN1, CR1, SORL1, TNK1, IL8, LDLR, CST3, CHRNB2, SORCS1, TNF, and CCR2. A systematic analysis of gene ontology terms associated with each marker showed that most genes were implicated in cholesterol metabolism, intracellular transport of beta-amyloid precursor, and autophagy of damaged organelles. Moreover, the impact of these genes on complement cascade and cytokine production highlights the role of inflammatory response in AD pathogenesis. Gene-gene and gene-environment interactions are prominent issues in AD genetics, but they are not specifically featured in the Alzgene database.
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Affiliation(s)
- Paolo Olgiati
- Institute of Psychiatry, University of Bologna, Viale Carlo Pepoli 5, 40123 Bologna, Italy
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36
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Hernandez DG, Singleton AB. Using DNA methylation to understand biological consequences of genetic variability. NEURODEGENER DIS 2011; 9:53-9. [PMID: 22123027 DOI: 10.1159/000333097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 09/13/2011] [Indexed: 12/14/2022] Open
Abstract
The advent of high-content genomic mapping technologies has provided numerous clues about the genetic architecture of complex disease and the tools with which to understand the biological framework resulting from this architecture. We believe that understanding and mapping epigenetic marks, in particular DNA methylation, which is suited to such assays, offers a timely opportunity in this context. Here, we make an argument for this work, describing this opportunity, the likely path ahead, and the problems and pitfalls associated with such work.
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Affiliation(s)
- Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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37
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Shi H, Bevier M, Johansson R, Enquist-Olsson K, Henriksson R, Hemminki K, Lenner P, Försti A. Prognostic impact of polymorphisms in the MYBL2 interacting genes in breast cancer. Breast Cancer Res Treat 2011; 131:1039-47. [PMID: 22037783 DOI: 10.1007/s10549-011-1826-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 10/07/2011] [Indexed: 11/25/2022]
Abstract
MYBL2 is a transcription factor, which regulates the expression of genes involved in cancer progression. In this study, we investigated whether putative functional variants in genes regulating MYBL2 (E2F1, E2F3 and E2F4) or in genes, which are regulated by MYBL2 (BCL2, BIRC5, COL1A1, COL1A2, COL5A2, ERBB2, CLU, LIN9 and TOP2A) affect breast cancer (BC) susceptibility and clinical outcome. Twenty-eight SNPs were genotyped in a population-based series of 782 Swedish BC cases and 1,559 matched controls. BC-specific survival analysis of BIRC5 suggested that carriers of the minor allele of rs8073069 and rs1042489 have a worse survival compared with the major homozygotes (HR 2.46, 95% CI 1.39-4.36 and HR 1.81, 95% CI 1.01-3.25, respectively). The poor survival was observed especially in women with aggressive tumours. Multivariate analysis supported the role of rs8073069 as an independent prognostic marker. For BCL2, minor allele carriers of rs1564483 were more likely to have hormone receptor-positive tumours than the major homozygotes. Another SNP in BCL2, rs4987852, was associated with tumour stages II-IV and histologic grade 3. In CLU, the minor allele carriers of rs9331888 were more likely to have tumours with regional lymph node metastasis and stages II-IV than the major homozygotes. In conclusion, our study suggests a role of genetic variation in BIRC5, BCL2 and CLU as progression and prognostic markers for BC, supporting previous studies based on the expression of the genes.
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Affiliation(s)
- Hong Shi
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
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38
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Complement activation as a biomarker for Alzheimer's disease. Immunobiology 2011; 217:204-15. [PMID: 21856034 DOI: 10.1016/j.imbio.2011.07.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 06/22/2011] [Accepted: 07/18/2011] [Indexed: 01/31/2023]
Abstract
There is increasing evidence from genetic, immunohistochemical, proteomic and epidemiological studies as well as in model systems that complement activation has an important role in the pathogenesis of Alzheimer's disease (AD). The complement cascade is an essential element of the innate immune response. In the brain complement proteins are integral components of amyloid plaques and complement activation occurs at the earliest stage of the disease. The complement cascade has been implicated as a protective mechanism in the clearance of amyloid, and in a causal role through chronic activation of the inflammatory response. In this review we discuss the potential for complement activation to act as a biomarker for AD at several stages in the disease process. An accurate biomarker that has sufficient predictive, diagnostic and prognostic value would provide a significant opportunity to develop and test for effective novel therapies in the treatment of AD.
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Abstract
Genetic variation in CLU encoding clusterin has been associated with Alzheimer's disease (AD) through replicated genome-wide studies, but the underlying mechanisms remain unknown. Following earlier reports that tightly regulated CLU alternative transcripts have different functions, we tested CLU single nucleotide polymorphisms (SNPs) including those associated with AD for quantitative effects on individual alternative transcripts. In 190 temporal lobe samples without pathology we found that the risk allele of the AD associated SNP rs9331888 increases the relative abundance of transcript NM_203339 (P=4.3×10(-12)). Using an independent set of 115 AD and control samples, we replicated this result (p=0.0014) and further observed that multiple CLU transcripts are at higher levels in AD compared to controls. The AD SNP rs9331888 is located in the first exon of NM_203339 and therefore, it is a functional candidate for the observed effects. We tested this hypothesis by in vitro dual luciferase assays using SK-N-SH cells and mouse primary cortical neurons and found allelic effects on enhancer function, consistent with our results on post-mortem human brain. These results suggest a biological mechanism for the genetic association of CLU with AD risk and indicate that rs9331888 is one of the functional DNA variants underlying this association.
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Augustin R, Lichtenthaler SF, Greeff M, Hansen J, Wurst W, Trümbach D. Bioinformatics identification of modules of transcription factor binding sites in Alzheimer's disease-related genes by in silico promoter analysis and microarrays. Int J Alzheimers Dis 2011; 2011:154325. [PMID: 21559189 PMCID: PMC3090009 DOI: 10.4061/2011/154325] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 02/15/2011] [Indexed: 11/21/2022] Open
Abstract
The molecular mechanisms and genetic risk factors underlying Alzheimer's disease (AD) pathogenesis are only partly understood. To identify new factors, which may contribute to AD, different approaches are taken including proteomics, genetics, and functional genomics. Here, we used a bioinformatics approach and found that distinct AD-related genes share modules of transcription factor binding sites, suggesting a transcriptional coregulation. To detect additional coregulated genes, which may potentially contribute to AD, we established a new bioinformatics workflow with known multivariate methods like support vector machines, biclustering, and predicted transcription factor binding site modules by using in silico analysis and over 400 expression arrays from human and mouse. Two significant modules are composed of three transcription factor families: CTCF, SP1F, and EGRF/ZBPF, which are conserved between human and mouse APP promoter sequences. The specific combination of in silico promoter and multivariate analysis can identify regulation mechanisms of genes involved in multifactorial diseases.
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Affiliation(s)
- Regina Augustin
- Institute of Developmental Genetics, Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), Technical University Munich, Ingolstädter Landstraße 1, Munich 85764, Neuherberg, Germany
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Chibnik LB, Shulman JM, Leurgans SE, Schneider JA, Wilson RS, Tran D, Aubin C, Buchman AS, Heward CB, Myers AJ, Hardy JA, Huentelman MJ, Corneveaux JJ, Reiman EM, Evans DA, Bennett DA, De Jager PL. CR1 is associated with amyloid plaque burden and age-related cognitive decline. Ann Neurol 2011; 69:560-9. [PMID: 21391232 DOI: 10.1002/ana.22277] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 09/03/2010] [Accepted: 09/17/2010] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Recently, genome-wide association studies have identified 3 new susceptibility loci for Alzheimer's disease (AD), CLU, CR1, and PICALM. We leveraged available neuropsychological and autopsy data from 2 cohort studies to investigate whether these loci are associated with cognitive decline and AD neuropathology. METHODS The Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP) are longitudinal studies that enroll nondemented subjects and include annual clinical evaluations and brain donation at death. We evaluated CR1 (rs6656401), CLU (rs11136000), and PICALM (rs7110631) in 1,666 subjects. We evaluated associations between genotypes and rate of change in cognitive function as well as AD-related pathology. Lastly, we used pathway analysis to determine whether relationships between single nucleotide polymorphisms and cognitive decline are mediated through AD pathology. RESULTS Among our study cohort, the mean years of follow-up were 7.8 for ROS and 4.3 for MAP. Only the CR1 locus was associated with both global cognitive decline (p = 0.011) and global AD pathology (p = 0.025). More specifically, the locus affects the deposition of neuritic amyloid plaque (p = 0.009). In a mediation analysis, controlling for amyloid pathology strongly attenuated the effect of the CR1 locus on cognitive decline. INTERPRETATION We found that common variation at the CR1 locus has a broad impact on cognition and that this effect is largely mediated by an individual's amyloid plaque burden. We therefore highlight 1 functional consequence of the CR1 susceptibility allele and generalize the role of this locus to cognitive aging in the general population.
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Affiliation(s)
- Lori B Chibnik
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
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Komatsu M, Shibata N, Kuerban B, Ohnuma T, Baba H, Arai H. Genetic association between clusterin polymorphisms and Alzheimer's disease in a Japanese population. Psychogeriatrics 2011; 11:14-8. [PMID: 21447104 DOI: 10.1111/j.1479-8301.2010.00346.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Previous papers have reported that clusterin (CLU, also called apolipoprotein J) maintains amyloid β-peptide (Aβ) solubility and protects against Aβ neurotoxicity. Recently, two large genome-wide association studies (GWAS) identified that a specific single nucleotide polymorphism (SNP) on the gene has been reported to modify the risk for Alzheimer's disease (AD). The present study aimed to investigate whether common single nucleotide polymorphisms (SNP) of the CLU gene are associated with AD. METHODS Six SNP, genotyped using TaqMan technology, were analyzed using a case-control study design. Furthermore, an analysis of the cases divided according to apolipoprotein E (APO E) status was also carried out. Our case-control dataset consisted of 180 AD patients and 130 age-matched controls. RESULTS The present study failed to detect any association between the SNP of the CLU gene and AD. Although rs7982 and rs1532277 showed marginal association in the APO E4 negative group, the linkage disequilibrium analysis results suggest this to be a false positive. CONCLUSION The negative associations were mainly the result of our small sample size. Larger genetic studies in different ethnics and future meta-analysis are needed to clarify the relationship between the CLU gene and AD.
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Affiliation(s)
- Miwa Komatsu
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan.
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Ma SL, Tang NLS, Tam CWC, Lui VWC, Lam LCW, Chiu HFK, Driver JA, Pastorino L, Lu KP. A PIN1 polymorphism that prevents its suppression by AP4 associates with delayed onset of Alzheimer's disease. Neurobiol Aging 2010; 33:804-13. [PMID: 20580132 DOI: 10.1016/j.neurobiolaging.2010.05.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 05/12/2010] [Accepted: 05/16/2010] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD), the most common form of dementia, is characterized by the presence of neurofibrillary tangles composed of tau and senile plaques of amyloid-beta peptides (Aβ) derived from amyloid precursor protein (APP). Pin1 is a unique prolyl isomerase that has been shown to protect against age-dependent neurodegeneration by acting on phosphorylated tau and APP to suppress tangle formation and amyloidogenic APP processing. Here we report a functional polymorphism, rs2287839, in the Pin1 promoter that is significantly associated with a 3-year delay in the average age at onset (AAO) of late-onset AD in a Chinese population. More significantly, the Pin1 polymorphism rs2287839 is located within the consensus binding motif for the brain-selective transcription factor, AP4 (CAGCTG) and almost completely abolishes the ability of AP4 to bind and suppress the Pin1 promoter, as shown by chromatin immunoprecipitation, electrophoretic mobility shift assay, and promoter luciferase assay. Moreover, overexpression or knockdown of AP4 resulted in an 80% reduction or 2-fold increase in endogenous Pin1 levels, respectively. Thus, AP4 is a novel transcriptional repressor of Pin1 expression and the Pin1 promoter single nucleotide polymorphism (SNP) identified in this study that prevents such suppression is associated with delayed onset of AD. These results indicate that regulation of Pin1 by AP4 plays a critical role in determining age at onset of AD and might be a novel therapeutic target to delay the onset of AD.
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Affiliation(s)
- Suk Ling Ma
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
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Implication of CLU gene polymorphisms in Chinese patients with Alzheimer's disease. Clin Chim Acta 2010; 411:1516-9. [PMID: 20599866 DOI: 10.1016/j.cca.2010.06.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 06/15/2010] [Accepted: 06/15/2010] [Indexed: 11/20/2022]
Abstract
BACKGROUND Clusterin (also called apolipoprotein J) has a potential central role in the pathogenesis of Alzheimer's disease (AD). Recently, two genome-wide association studies have identified three variants in CLU gene encoding clusterin associated with AD risk in Caucasians, while there are no studies on the association of CLU with AD risk in Asians. METHODS The study investigated 324 sporadic late-onset AD (LOAD) and 388 healthy controls matched for sex and age in a Han Chinese population. Three common genetic variants (rs2279590, rs11136000 and rs9331888) in CLU gene were genotyped using MALDI-TOF mass spectrometry. RESULTS The minor allele (G) of the rs9331888 polymorphism within CLU was significantly associated with an increased risk of LOAD (OR=1.39, 95% CI=1.13-1.72, P=0.002). Logistic regression analysis revealed that the rs9331888 polymorphism presented strong associations with LOAD in the dominant, recessive and additive models. No significant differences in genotype and allele frequencies of the rs2279590 and rs11136000 polymorphisms were found between LOAD patients and controls. Haplotype analysis identified a risk haplotype (CCG) (OR=1.66) and a protective haplotype (CCC)(OR=0.70). CONCLUSIONS Our findings implicate CLU as a susceptibility gene for LOAD in Han Chinese.
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Corneveaux JJ, Myers AJ, Allen AN, Pruzin JJ, Ramirez M, Engel A, Nalls MA, Chen K, Lee W, Chewning K, Villa SE, Meechoovet HB, Gerber JD, Frost D, Benson HL, O'Reilly S, Chibnik LB, Shulman JM, Singleton AB, Craig DW, Van Keuren-Jensen KR, Dunckley T, Bennett DA, De Jager PL, Heward C, Hardy J, Reiman EM, Huentelman MJ. Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals. Hum Mol Genet 2010; 19:3295-301. [PMID: 20534741 DOI: 10.1093/hmg/ddq221] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we assess 34 of the most replicated genetic associations for Alzheimer's disease (AD) using data generated on Affymetrix SNP 6.0 arrays and imputed at over 5.7 million markers from a unique cohort of over 1600 neuropathologically defined AD cases and controls (1019 cases and 591 controls). Testing the top genes from the AlzGene meta-analysis, we confirm the well-known association with APOE single nucleotide polymorphisms (SNPs), the CLU, PICALM and CR1 SNPs recently implicated in unusually large data sets, and previously implicated CST3 and ACE SNPs. In the cases of CLU, PICALM and CR1, as well as in APOE, the odds ratios we find are slightly larger than those previously reported in clinical samples, consistent with what we believe to be more accurate classification of disease in the clinically characterized and neuropathologically confirmed AD cases and controls.
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Affiliation(s)
- Jason J Corneveaux
- Neurogenomics Division, The Translational Genomics Research Institute (Gen, 445 N Fifth Street, Phoenix, AZ 85004, USA
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