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Daskoulidou N, Shaw B, Torvell M, Watkins L, Cope EL, Carpanini SM, Allen ND, Morgan BP. Complement receptor 1 is expressed on brain cells and in the human brain. Glia 2023; 71:1522-1535. [PMID: 36825534 PMCID: PMC10953339 DOI: 10.1002/glia.24355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023]
Abstract
Genome wide association studies (GWAS) have highlighted the importance of the complement cascade in pathogenesis of Alzheimer's disease (AD). Complement receptor 1 (CR1; CD35) is among the top GWAS hits. The long variant of CR1 is associated with increased risk for AD; however, roles of CR1 in brain health and disease are poorly understood. A critical confounder is that brain expression of CR1 is controversial; failure to demonstrate brain expression has provoked the suggestion that peripherally expressed CR1 influences AD risk. We took a multi-pronged approach to establish whether CR1 is expressed in brain. Expression of CR1 at the protein and mRNA level was assessed in human microglial lines, induced pluripotent stem cell (iPSC)-derived microglia from two sources and brain tissue from AD and control donors. CR1 protein was detected in microglial lines and iPSC-derived microglia expressing different CR1 variants when immunostained with a validated panel of CR1-specific antibodies; cell extracts were positive for CR1 protein and mRNA. CR1 protein was detected in control and AD brains, co-localizing with astrocytes and microglia, and expression was significantly increased in AD compared to controls. CR1 mRNA expression was detected in all AD and control brain samples tested; expression was significantly increased in AD. The data unequivocally demonstrate that the CR1 transcript and protein are expressed in human microglia ex vivo and on microglia and astrocytes in situ in the human brain; the findings support the hypothesis that CR1 variants affect AD risk by directly impacting glial functions.
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Affiliation(s)
| | - Bethany Shaw
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Megan Torvell
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Lewis Watkins
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Emma L. Cope
- School of Biosciences, Cardiff UniversityCardiffUK
| | | | - Nicholas D. Allen
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
- School of Biosciences, Cardiff UniversityCardiffUK
| | - B. Paul Morgan
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
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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: 31] [Impact Index Per Article: 15.5] [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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Deep post-GWAS analysis identifies potential risk genes and risk variants for Alzheimer's disease, providing new insights into its disease mechanisms. Sci Rep 2021; 11:20511. [PMID: 34654853 PMCID: PMC8519945 DOI: 10.1038/s41598-021-99352-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Alzheimer’s disease (AD) is a genetically complex, multifactorial neurodegenerative disease. It affects more than 45 million people worldwide and currently remains untreatable. Although genome-wide association studies (GWAS) have identified many AD-associated common variants, only about 25 genes are currently known to affect the risk of developing AD, despite its highly polygenic nature. Moreover, the risk variants underlying GWAS AD-association signals remain unknown. Here, we describe a deep post-GWAS analysis of AD-associated variants, using an integrated computational framework for predicting both disease genes and their risk variants. We identified 342 putative AD risk genes in 203 risk regions spanning 502 AD-associated common variants. 246 AD risk genes have not been identified as AD risk genes by previous GWAS collected in GWAS catalogs, and 115 of 342 AD risk genes are outside the risk regions, likely under the regulation of transcriptional regulatory elements contained therein. Even more significantly, for 109 AD risk genes, we predicted 150 risk variants, of both coding and regulatory (in promoters or enhancers) types, and 85 (57%) of them are supported by functional annotation. In-depth functional analyses showed that AD risk genes were overrepresented in AD-related pathways or GO terms—e.g., the complement and coagulation cascade and phosphorylation and activation of immune response—and their expression was relatively enriched in microglia, endothelia, and pericytes of the human brain. We found nine AD risk genes—e.g., IL1RAP, PMAIP1, LAMTOR4—as predictors for the prognosis of AD survival and genes such as ARL6IP5 with altered network connectivity between AD patients and normal individuals involved in AD progression. Our findings open new strategies for developing therapeutics targeting AD risk genes or risk variants to influence AD pathogenesis.
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Ma Y, Liu Y, Zhang Z, Yang GY. Significance of Complement System in Ischemic Stroke: A Comprehensive Review. Aging Dis 2019; 10:429-462. [PMID: 31011487 PMCID: PMC6457046 DOI: 10.14336/ad.2019.0119] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/19/2019] [Indexed: 12/14/2022] Open
Abstract
The complement system is an essential part of innate immunity, typically conferring protection via eliminating pathogens and accumulating debris. However, the defensive function of the complement system can exacerbate immune, inflammatory, and degenerative responses in various pathological conditions. Cumulative evidence indicates that the complement system plays a critical role in the pathogenesis of ischemic brain injury, as the depletion of certain complement components or the inhibition of complement activation could reduce ischemic brain injury. Although multiple candidates modulating or inhibiting complement activation show massive potential for the treatment of ischemic stroke, the clinical availability of complement inhibitors remains limited. The complement system is also involved in neural plasticity and neurogenesis during cerebral ischemia. Thus, unexpected side effects could be induced if the systemic complement system is inhibited. In this review, we highlighted the recent concepts and discoveries of the roles of different kinds of complement components, such as C3a, C5a, and their receptors, in both normal brain physiology and the pathophysiology of brain ischemia. In addition, we comprehensively reviewed the current development of complement-targeted therapy for ischemic stroke and discussed the challenges of bringing these therapies into the clinic. The design of future experiments was also discussed to better characterize the role of complement in both tissue injury and recovery after cerebral ischemia. More studies are needed to elucidate the molecular and cellular mechanisms of how complement components exert their functions in different stages of ischemic stroke to optimize the intervention of targeting the complement system.
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Affiliation(s)
- Yuanyuan Ma
- 1Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,2Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yanqun Liu
- 3Department of Neurology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhijun Zhang
- 2Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Yuan Yang
- 1Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,2Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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5
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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: 194] [Impact Index Per Article: 38.8] [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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6
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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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Contribution of Neurons and Glial Cells to Complement-Mediated Synapse Removal during Development, Aging and in Alzheimer's Disease. Mediators Inflamm 2018; 2018:2530414. [PMID: 30533998 PMCID: PMC6252206 DOI: 10.1155/2018/2530414] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/13/2018] [Accepted: 09/24/2018] [Indexed: 01/03/2023] Open
Abstract
Synapse loss is an early manifestation of pathology in Alzheimer's disease (AD) and is currently the best correlate to cognitive decline. Microglial cells are involved in synapse pruning during development via the complement pathway. Moreover, recent evidence points towards a key role played by glial cells in synapse loss during AD. However, further contribution of glial cells and the role of neurons to synapse pathology in AD remain not well understood. This review is aimed at comprehensively reporting the source and/or cellular localization in the CNS—in microglia, astrocytes, or neurons—of the triggering components (C1q, C3) of the classical complement pathway involved in synapse pruning in development, adulthood, and AD.
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Stem Cells as Potential Targets of Polyphenols in Multiple Sclerosis and Alzheimer's Disease. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1483791. [PMID: 30112360 PMCID: PMC6077677 DOI: 10.1155/2018/1483791] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) and multiple sclerosis are major neurodegenerative diseases, which are characterized by the accumulation of abnormal pathogenic proteins due to oxidative stress, mitochondrial dysfunction, impaired autophagy, and pathogens, leading to neurodegeneration and behavioral deficits. Herein, we reviewed the utility of plant polyphenols in regulating proliferation and differentiation of stem cells for inducing brain self-repair in AD and multiple sclerosis. Firstly, we discussed the genetic, physiological, and environmental factors involved in the pathophysiology of both the disorders. Next, we reviewed various stem cell therapies available and how they have proved useful in animal models of AD and multiple sclerosis. Lastly, we discussed how polyphenols utilize the potential of stem cells, either complementing their therapeutic effects or stimulating endogenous and exogenous neurogenesis, against these diseases. We suggest that polyphenols could be a potential candidate for stem cell therapy against neurodegenerative disorders.
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Johansson JU, Brubaker WD, Javitz H, Bergen AW, Nishita D, Trigunaite A, Crane A, Ceballos J, Mastroeni D, Tenner AJ, Sabbagh M, Rogers J. Peripheral complement interactions with amyloid β peptide in Alzheimer's disease: Polymorphisms, structure, and function of complement receptor 1. Alzheimers Dement 2018; 14:1438-1449. [PMID: 29792870 DOI: 10.1016/j.jalz.2018.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/23/2018] [Accepted: 04/09/2018] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Genome-wide association studies consistently show that single nucleotide polymorphisms (SNPs) in the complement receptor 1 (CR1) gene modestly but significantly alter Alzheimer's disease (AD) risk. Follow-up research has assumed that CR1 is expressed in the human brain despite a paucity of evidence for its function there. Alternatively, erythrocytes contain >80% of the body's CR1, where, in primates, it is known to bind circulating pathogens. METHODS Multidisciplinary methods were employed. RESULTS Conventional Western blots and quantitative polymerase chain reaction failed to detect CR1 in the human brain. Brain immunohistochemistry revealed only vascular CR1. By contrast, erythrocyte CR1 immunoreactivity was readily observed and was significantly deficient in AD, as was CR1-mediated erythrocyte capture of circulating amyloid β peptide. CR1 SNPs associated with decreased erythrocyte CR1 increased AD risk, whereas a CR1 SNP associated with increased erythrocyte CR1 decreased AD risk. DISCUSSION SNP effects on erythrocyte CR1 likely underlie the association of CR1 polymorphisms with AD risk.
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Affiliation(s)
| | | | - Harold Javitz
- Education Division, SRI International, Menlo Park, CA, USA
| | - Andrew W Bergen
- Biosciences Division, SRI International, Menlo Park, CA, USA
| | - Denise Nishita
- Biosciences Division, SRI International, Menlo Park, CA, USA
| | | | - Andrés Crane
- Biosciences Division, SRI International, Menlo Park, CA, USA
| | | | - Diego Mastroeni
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Andrea J Tenner
- Departments of Molecular Biology and Biochemistry, Pathology, and Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Marwan Sabbagh
- Alzheimer's and Memory Disorders Division, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Joseph Rogers
- Biosciences Division, SRI International, Menlo Park, CA, USA.
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Liu Z, Dai X, Zhang J, Li X, Chen Y, Ma C, Chen K, Peng D, Zhang Z. The Interactive Effects of Age and PICALM rs541458 Polymorphism on Cognitive Performance, Brain Structure, and Function in Non-demented Elderly. Mol Neurobiol 2018; 55:1271-1283. [PMID: 28116548 PMCID: PMC5820373 DOI: 10.1007/s12035-016-0358-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/28/2016] [Indexed: 12/04/2022]
Abstract
The PICALM rs541458 T allele has been recognized as a risk factor for late-onset Alzheimer's disease, and age might modulate the effects that genetic factors have on cognitive functions and brain. Thus, the current study intended to examine whether the effects of rs541458 on cognitive functions, brain structure, and function were modulated by age in non-demented Chinese elderly. We enrolled 638 subjects aged 50 to 82 years and evaluated their cognitive functions through a series of neuropsychological tests. Seventy-eight of these participants also received T1-weighted structural and resting state functional magnetic resonance imaging. Dividing subjects into groups <65 and ≥65 years old, results of neuropsychological tests showed that interactive effects of rs541458 × age existed with regard to executive function and processing speed after controlling for gender, years of education and APOE ε4 status. In addition, the effects of rs541458 on resting state functional connectivity of left superior parietal gyrus within left frontal-parietal network and on gray matter volume of left middle temporal gyrus were modulated by age. Furthermore, reduction of functional connectivity of left superior parietal gyrus was closely related with better executive function in the T allele carriers <65 years old. Further, greater volume of left middle temporal gyrus was significantly related to better executive function in both CC genotype <65 years old and CC genotype ≥65 years old groups, separately. Pending further confirmation from additional studies, our results support the hypothesis that the modulation of age, with respect to the rs541458, has interactional effects on cognitive performance, brain function, and structural measurements.
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Affiliation(s)
- Zhen Liu
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, People's Republic of China
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiangwei Dai
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, People's Republic of China
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Junying Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, People's Republic of China
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xin Li
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, People's Republic of China
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Yaojing Chen
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, People's Republic of China
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Chao Ma
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, People's Republic of China
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Kewei Chen
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China
- Banner Alzheimer's Institute, Phoenix, AZ, 85006, USA
| | - Dantao Peng
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, People's Republic of China.
| | - Zhanjun Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, People's Republic of China.
- BABRI Centre, Beijing Normal University, Beijing, 100875, People's Republic of China.
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Andersen MS, Howard E, Lu S, Richard M, Gregory M, Ogembo G, Mazor O, Gorelik P, Shapiro NI, Sharda AV, Ghiran I. Detection of membrane-bound and soluble antigens by magnetic levitation. LAB ON A CHIP 2017; 17:3462-3473. [PMID: 28905952 PMCID: PMC5642277 DOI: 10.1039/c7lc00402h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Magnetic levitation is a technique for measuring the density and the magnetic properties of objects suspended in a paramagnetic field. We describe a novel magnetic levitation-based method that can specifically detect cell membrane-bound and soluble antigens by measurable changes in levitation height that result from the formation of antibody-coated bead and antigen complex. We demonstrate our method's ability to sensitively detect an array of membrane-bound and soluble antigens found in blood, including T-cell antigen CD3, eosinophil antigen Siglec-8, red blood cell antigens CD35 and RhD, red blood cell-bound Epstein-Barr viral particles, and soluble IL-6, and validate the results by flow cytometry and immunofluorescence microscopy performed in parallel. Additionally, employing an inexpensive, single lens, manual focus, wifi-enabled camera, we extend the portability of our method for its potential use as a point-of-care diagnostic assay.
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Affiliation(s)
- Mikkel Schou Andersen
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, MA, USA
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12
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Geographical distribution of complement receptor type 1 variants and their associated disease risk. PLoS One 2017; 12:e0175973. [PMID: 28520715 PMCID: PMC5435133 DOI: 10.1371/journal.pone.0175973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/03/2017] [Indexed: 11/19/2022] Open
Abstract
Background Pathogens exert selective pressure which may lead to substantial changes in host immune responses. The human complement receptor type 1 (CR1) is an innate immune recognition glycoprotein that regulates the activation of the complement pathway and removes opsonized immune complexes. CR1 genetic variants in exon 29 have been associated with expression levels, C1q or C3b binding and increased susceptibility to several infectious diseases. Five distinct CR1 nucleotide substitutions determine the Knops blood group phenotypes, namely Kna/b, McCa/b, Sl1/Sl2, Sl4/Sl5 and KCAM+/-. Methods CR1 variants were genotyped by direct sequencing in a cohort of 441 healthy individuals from Brazil, Vietnam, India, Republic of Congo and Ghana. Results The distribution of the CR1 alleles, genotypes and haplotypes differed significantly among geographical settings (p≤0.001). CR1 variants rs17047660A/G (McCa/b) and rs17047661A/G (Sl1/Sl2) were exclusively observed to be polymorphic in African populations compared to the groups from Asia and South-America, strongly suggesting that these two SNPs may be subjected to selection. This is further substantiated by a high linkage disequilibrium between the two variants in the Congolese and Ghanaian populations. A total of nine CR1 haplotypes were observed. The CR1*AGAATA haplotype was found more frequently among the Brazilian and Vietnamese study groups; the CR1*AGAATG haplotype was frequent in the Indian and Vietnamese populations, while the CR1*AGAGTG haplotype was frequent among Congolese and Ghanaian individuals. Conclusion The African populations included in this study might have a selective advantage conferred to immune genes involved in pathogen recognition and signaling, possibly contributing to disease susceptibility or resistance.
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13
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Peripheral complement interactions with amyloid β peptide: Erythrocyte clearance mechanisms. Alzheimers Dement 2017; 13:1397-1409. [PMID: 28475854 DOI: 10.1016/j.jalz.2017.03.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/28/2017] [Accepted: 03/27/2017] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Although amyloid β peptide (Aβ) is cleared from the brain to cerebrospinal fluid and the peripheral circulation, mechanisms for its removal from blood remain unresolved. Primates have uniquely evolved a highly effective peripheral clearance mechanism for pathogens, immune adherence, in which erythrocyte complement receptor 1 (CR1) plays a major role. METHODS Multidisciplinary methods were used to demonstrate immune adherence capture of Aβ by erythrocytes and its deficiency in Alzheimer's disease (AD). RESULTS Aβ was shown to be subject to immune adherence at every step in the pathway. Aβ dose-dependently activated serum complement. Complement-opsonized Aβ was captured by erythrocytes via CR1. Erythrocytes, Aβ, and hepatic Kupffer cells were colocalized in the human liver. Significant deficits in erythrocyte Aβ levels were found in AD and mild cognitive impairment patients. DISCUSSION CR1 polymorphisms elevate AD risk, and >80% of human CR1 is vested in erythrocytes to subserve immune adherence. The present results suggest that this pathway is pathophysiologically relevant in AD.
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14
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N'Songo A, Carrasquillo MM, Wang X, Burgess JD, Nguyen T, Asmann YW, Serie DJ, Younkin SG, Allen M, Pedraza O, Duara R, Greig Custo MT, Graff-Radford NR, Ertekin-Taner N. African American exome sequencing identifies potential risk variants at Alzheimer disease loci. NEUROLOGY-GENETICS 2017; 3:e141. [PMID: 28480329 PMCID: PMC5406839 DOI: 10.1212/nxg.0000000000000141] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/10/2017] [Indexed: 01/14/2023]
Abstract
Objective: In African Americans, we sought to systematically identify coding Alzheimer disease (AD) risk variants at the previously reported AD genome-wide association study (GWAS) loci genes. Methods: We identified coding variants within genes at the 20 published AD GWAS loci by whole-exome sequencing of 238 African American participants, validated these in 300 additional participants, and tested their association with AD risk in the combined cohort of 538 and with memory endophenotypes in 319 participants. Results: Two ABCA7 missense variants (rs3764647 and rs3752239) demonstrated significant association with AD risk. Variants in MS4A6A, PTK2B, and ZCWPW1 showed significant gene-based association. In addition, coding variants in ZCWPW1 (rs6465770) and NME8 (rs10250905 and rs62001869) showed association with memory endophenotypes. Conclusions: Our findings support a role for ABCA7 missense variants in conferring AD risk in African Americans, highlight allelic heterogeneity at this locus, suggest the presence of AD-risk variants in MS4A6A, PTK2B, and ZCWPW1, nominate additional variants that may modulate cognition, and importantly provide a thorough screen of coding variants at AD GWAS loci that can guide future studies in this population.
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Affiliation(s)
- Aurelie N'Songo
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Minerva M Carrasquillo
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Xue Wang
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Jeremy D Burgess
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Thuy Nguyen
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Yan W Asmann
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Daniel J Serie
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Steven G Younkin
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Mariet Allen
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Otto Pedraza
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Ranjan Duara
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Maria T Greig Custo
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Neill R Graff-Radford
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience (A.N., M.M.C., J.D.B., T.N., S.G.Y., M.A., N.E.-T.), Department of Health Science Research (X.W., Y.W.A., D.J.S.), Department of Psychiatry and Psychology (O.P.), and Department of Neurology (N.R.G.-R., N.E.-T.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D., M.T.G.C.), Mount Sinai Medical Center, Miami Beach, FL
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15
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Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L. Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nat Commun 2017; 8:14864. [PMID: 28348404 PMCID: PMC5379071 DOI: 10.1038/ncomms14864] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/06/2017] [Indexed: 01/08/2023] Open
Abstract
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. Proteogenomic analysis also validates a number of predicted genomic targets in multiple receptor tyrosine kinases. However, several protein/phosphoprotein events such as overexpression of AKT proteins and ARAF, BRAF, HSP90AB1 phosphosites are not readily explainable by genomic analysis, suggesting that druggable translational and/or post-translational regulatory events may be uniquely diagnosed by MS. Drug treatment experiments targeting HER2 and components of the PI3K pathway supported proteogenomic response predictions in seven xenograft models. Our study demonstrates that MS-based proteomics can identify therapeutic targets and highlights the potential of PDX drug response evaluation to annotate MS-based pathway activities. Patient-derived xenografts recapitulate major genomic signatures and transcriptome profiles of their original tumours. Here, the authors, performing proteomic and phosphoproteomic analyses of 24 breast cancer PDX models, demonstrate that druggable candidates can be identified based on a comprehensive proteogenomic profiling.
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Affiliation(s)
- Kuan-Lin Huang
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Shunqiang Li
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Philipp Mertins
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Song Cao
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Harsha P Gunawardena
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Kelly V Ruggles
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Karl R Clauser
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Maki Tanioka
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jerry Usary
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Shyam M Kavuri
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ling Xie
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Christopher Yoon
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Jana W Qiao
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - John Wrobel
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Matthew A Wyczalkowski
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Petra Erdmann-Gilmore
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Jacqueline E Snider
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Jeremy Hoog
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Purba Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Beifung Niu
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Zhanfang Guo
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Sam Qiancheng Sun
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Souzan Sanati
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Emily Kawaler
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | - Xuya Wang
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | - Adam Scott
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Kai Ye
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Michael D McLellan
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Mathematics, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Anna Malovannaya
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jason M Held
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Michael A Gillette
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | | | - Mehdi Mesri
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Henry Rodriguez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sherri R Davies
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Cynthia Ma
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - R Reid Townsend
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Xian Chen
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA
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16
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Roshchupkin GV, Adams HH, van der Lee SJ, Vernooij MW, van Duijn CM, Uitterlinden AG, van der Lugt A, Hofman A, Niessen WJ, Ikram MA. Fine-mapping the effects of Alzheimer's disease risk loci on brain morphology. Neurobiol Aging 2016; 48:204-211. [PMID: 27718423 DOI: 10.1016/j.neurobiolaging.2016.08.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 07/30/2016] [Accepted: 08/26/2016] [Indexed: 12/14/2022]
Abstract
The neural substrate of genetic risk variants for Alzheimer's disease (AD) remains unknown. We studied their effect on healthy brain morphology to provide insight into disease etiology in the preclinical phase. We included 4071 nondemented, elderly participants of the population-based Rotterdam Study who underwent brain magnetic resonance imaging and genotyping. We performed voxel-based morphometry (VBM) on all gray-matter voxels for 19 previously identified, common AD risk variants. Whole-brain expression data from the Allen Human Brain Atlas was used to examine spatial overlap between VBM association results and expression of genes in AD risk loci regions. Brain regions most significantly associated with AD risk variants were the left postcentral gyrus with ABCA7 (rs4147929, p = 4.45 × 10-6), right superior frontal gyrus by ZCWPW1 (rs1476679, p = 5.12 × 10-6), and right postcentral gyrus by APOE (p = 6.91 × 10-6). Although no individual voxel passed multiple-testing correction, we found significant spatial overlap between the effects of AD risk loci on VBM and the expression of genes (MEF2C, CLU, and SLC24A4) in the Allen Brain Atlas. Results are available online on www.imagene.nl/ADSNPs/. In this single largest imaging genetics data set worldwide, we found that AD risk loci affect cortical gray matter in several brain regions known to be involved in AD, as well as regions that have not been implicated before.
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Affiliation(s)
- Gennady V Roshchupkin
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands; Department of Medical Informatics, Erasmus MC, Rotterdam, the Netherlands
| | - Hieab H Adams
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Meike W Vernooij
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Aad van der Lugt
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Wiro J Niessen
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands; Department of Medical Informatics, Erasmus MC, Rotterdam, the Netherlands; Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Mohammad A Ikram
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands; Department of Neurology, Erasmus MC, Rotterdam, the Netherlands.
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17
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De Rossi P, Buggia-Prévot V, Clayton BLL, Vasquez JB, van Sanford C, Andrew RJ, Lesnick R, Botté A, Deyts C, Salem S, Rao E, Rice RC, Parent A, Kar S, Popko B, Pytel P, Estus S, Thinakaran G. Predominant expression of Alzheimer's disease-associated BIN1 in mature oligodendrocytes and localization to white matter tracts. Mol Neurodegener 2016; 11:59. [PMID: 27488240 PMCID: PMC4973113 DOI: 10.1186/s13024-016-0124-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 07/27/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified BIN1 within the second most significant susceptibility locus in late-onset Alzheimer's disease (AD). BIN1 undergoes complex alternative splicing to generate multiple isoforms with diverse functions in multiple cellular processes including endocytosis and membrane remodeling. An increase in BIN1 expression in AD and an interaction between BIN1 and Tau have been reported. However, disparate descriptions of BIN1 expression and localization in the brain previously reported in the literature and the lack of clarity on brain BIN1 isoforms present formidable challenges to our understanding of how genetic variants in BIN1 increase the risk for AD. METHODS In this study, we analyzed BIN1 mRNA and protein levels in human brain samples from individuals with or without AD. In addition, we characterized the BIN1 expression and isoform diversity in human and rodent tissue by immunohistochemistry and immunoblotting using a panel of BIN1 antibodies. RESULTS Here, we report on BIN1 isoform diversity in the human brain and document alterations in the levels of select BIN1 isoforms in individuals with AD. In addition, we report striking BIN1 localization to white matter tracts in rodent and the human brain, and document that the large majority of BIN1 is expressed in mature oligodendrocytes whereas neuronal BIN1 represents a minor fraction. This predominant non-neuronal BIN1 localization contrasts with the strict neuronal expression and presynaptic localization of the BIN1 paralog, Amphiphysin 1. We also observe upregulation of BIN1 at the onset of postnatal myelination in the brain and during differentiation of cultured oligodendrocytes. Finally, we document that the loss of BIN1 significantly correlates with the extent of demyelination in multiple sclerosis lesions. CONCLUSION Our study provides new insights into the brain distribution and cellular expression of an important risk factor associated with late-onset AD. We propose that efforts to define how genetic variants in BIN1 elevate the risk for AD would behoove to consider BIN1 function in the context of its main expression in mature oligodendrocytes and the potential for a role of BIN1 in the membrane remodeling that accompanies the process of myelination.
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Affiliation(s)
- Pierre De Rossi
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Virginie Buggia-Prévot
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | | | - Jared B. Vasquez
- Sanders-Brown Center on Aging and Department of Physiology, University of Kentucky, Lexington, KY 40536 USA
| | - Carson van Sanford
- Sanders-Brown Center on Aging and Department of Physiology, University of Kentucky, Lexington, KY 40536 USA
| | - Robert J. Andrew
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Ruben Lesnick
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Alexandra Botté
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Carole Deyts
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Someya Salem
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Eshaan Rao
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Richard C. Rice
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Angèle Parent
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Satyabrata Kar
- Centre for prions and protein folding diseases, University of Alberta, Edmonton, AB T6G 2B7 Canada
| | - Brian Popko
- Department of Neurology, The University of Chicago, Chicago, IL 60637 USA
| | - Peter Pytel
- Department of Pathology, The University of Chicago, Chicago, IL 60637 USA
| | - Steven Estus
- Sanders-Brown Center on Aging and Department of Physiology, University of Kentucky, Lexington, KY 40536 USA
| | - Gopal Thinakaran
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
- Department of Neurology, The University of Chicago, Chicago, IL 60637 USA
- Department of Pathology, The University of Chicago, Chicago, IL 60637 USA
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18
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Adams SL, Tilton K, Kozubek JA, Seshadri S, Delalle I. Subcellular Changes in Bridging Integrator 1 Protein Expression in the Cerebral Cortex During the Progression of Alzheimer Disease Pathology. J Neuropathol Exp Neurol 2016; 75:779-790. [PMID: 27346750 DOI: 10.1093/jnen/nlw056] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome-wide association studies have established BIN1 (Bridging Integrator 1) as the most significant late-onset Alzheimer disease (AD) susceptibility locus after APOE We analyzed BIN1 protein expression using automated immunohistochemistry on the hippocampal CA1 region in 19 patients with either no, mild, or moderate-to-marked AD pathology, who had been assessed by Clinical Dementia Rating and CERAD scores. We also examined the amygdala, prefrontal, temporal, and occipital regions in a subset of these patients. In non-demented controls without AD pathology, BIN1 protein was expressed in white matter, glia, particularly oligodendrocytes, and in the neuropil in which the BIN1 signal decorated axons. With increasing severity of AD, BIN1 in the CA1 region showed: 1) sustained expression in glial cells, 2) decreased areas of neuropil expression, and 3) increased cytoplasmic neuronal expression that did not correlate with neurofibrillary tangle load. In patients with AD, both the prefrontal cortex and CA1 showed a decrease in BIN1-immunoreactive (BIN1-ir) neuropil areas and increases in numbers of BIN1-ir neurons. The numbers of CA1 BIN1-ir pyramidal neurons correlated with hippocampal CERAD neuritic plaque scores; BIN1 neuropil signal was absent in neuritic plaques. Our data provide novel insight into the relationship between BIN1 protein expression and the progression of AD-associated pathology and its diagnostic hallmarks.
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Affiliation(s)
- Stephanie L Adams
- From the Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts (SLA, KT, ID); Broad Institute, Cambridge, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts (JAK) Department of Neurology, Boston University School of Medicine, Boston, Massachusetts (SS)
| | - Kathy Tilton
- From the Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts (SLA, KT, ID); Broad Institute, Cambridge, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts (JAK) Department of Neurology, Boston University School of Medicine, Boston, Massachusetts (SS)
| | - James A Kozubek
- From the Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts (SLA, KT, ID); Broad Institute, Cambridge, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts (JAK) Department of Neurology, Boston University School of Medicine, Boston, Massachusetts (SS)
| | - Sudha Seshadri
- From the Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts (SLA, KT, ID); Broad Institute, Cambridge, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts (JAK) Department of Neurology, Boston University School of Medicine, Boston, Massachusetts (SS)
| | - Ivana Delalle
- From the Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts (SLA, KT, ID); Broad Institute, Cambridge, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts (JAK) Department of Neurology, Boston University School of Medicine, Boston, Massachusetts (SS).
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Abstract
Alzheimer's disease (AD) is a progressive, neurodegenerative disease and the most common form of dementia in elderly people. It is an emerging public health problem that poses a huge societal burden. Linkage analysis was the first milestone in unraveling the mutations in APP, PSEN1, and PSEN2 that cause early-onset AD, followed by the discovery of apolipoprotein E-ε4 allele as the only one genetic risk factor for late-onset AD. Genome-wide association studies have revolutionized genetic research and have identified over 20 genetic loci associated with late-onset AD. Recently, next-generation sequencing technologies have enabled the identification of rare disease variants, including unmasking small mutations with intermediate risk of AD in PLD3, TREM2, UNC5C, AKAP9, and ADAM10. This review provides an overview of the genetic basis of AD and the relationship between these risk genes and the neuropathologic features of AD. An understanding of genetic mechanisms underlying AD pathogenesis and the potentially implicated pathways will lead to the development of novel treatment for this devastating disease.
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Affiliation(s)
- Mohan Giri
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, People’s Republic of China
| | - Man Zhang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, People’s Republic of China
| | - Yang Lü
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, People’s Republic of China
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20
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Karch CM, Ezerskiy LA, Bertelsen S, Goate AM. Alzheimer's Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci. PLoS One 2016; 11:e0148717. [PMID: 26919393 PMCID: PMC4769299 DOI: 10.1371/journal.pone.0148717] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/17/2015] [Indexed: 11/18/2022] Open
Abstract
Late onset Alzheimer’s disease (LOAD) is a genetically complex and clinically heterogeneous disease. Recent large-scale genome wide association studies (GWAS) have identified more than twenty loci that modify risk for AD. Despite the identification of these loci, little progress has been made in identifying the functional variants that explain the association with AD risk. Thus, we sought to determine whether the novel LOAD GWAS single nucleotide polymorphisms (SNPs) alter expression of LOAD GWAS genes and whether expression of these genes is altered in AD brains. The majority of LOAD GWAS SNPs occur in gene dense regions under large linkage disequilibrium (LD) blocks, making it unclear which gene(s) are modified by the SNP. Thus, we tested for brain expression quantitative trait loci (eQTLs) between LOAD GWAS SNPs and SNPs in high LD with the LOAD GWAS SNPs in all of the genes within the GWAS loci. We found a significant eQTL between rs1476679 and PILRB and GATS, which occurs within the ZCWPW1 locus. PILRB and GATS expression levels, within the ZCWPW1 locus, were also associated with AD status. Rs7120548 was associated with MTCH2 expression, which occurs within the CELF1 locus. Additionally, expression of several genes within the CELF1 locus, including MTCH2, were highly correlated with one another and were associated with AD status. We further demonstrate that PILRB, as well as other genes within the GWAS loci, are most highly expressed in microglia. These findings together with the function of PILRB as a DAP12 receptor supports the critical role of microglia and neuroinflammation in AD risk.
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Affiliation(s)
- Celeste M. Karch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (CMK); (AMG)
| | - Lubov A. Ezerskiy
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sarah Bertelsen
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States of America
| | | | - Alison M. Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States of America
- * E-mail: (CMK); (AMG)
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21
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Saad M, Brkanac Z, Wijsman EM. Family-based genome scan for age at onset of late-onset Alzheimer's disease in whole exome sequencing data. GENES, BRAIN, AND BEHAVIOR 2015; 14:607-17. [PMID: 26394601 PMCID: PMC4715764 DOI: 10.1111/gbb.12250] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/08/2015] [Accepted: 08/24/2015] [Indexed: 01/31/2023]
Abstract
Alzheimer's disease (AD) is a common and complex neurodegenerative disease. Age at onset (AAO) of AD is an important component phenotype with a genetic basis, and identification of genes in which variation affects AAO would contribute to identification of factors that affect timing of onset. Increase in AAO through prevention or therapeutic measures would have enormous benefits by delaying AD and its associated morbidities. In this paper, we performed a family-based genome-wide association study for AAO of late-onset AD in whole exome sequence data generated in multigenerational families with multiple AD cases. We conducted single marker and gene-based burden tests for common and rare variants, respectively. We combined association analyses with variance component linkage analysis, and with reference to prior studies, in order to enhance evidence of the identified genes. For variants and genes implicated by the association study, we performed a gene-set enrichment analysis to identify potential novel pathways associated with AAO of AD. We found statistically significant association with AAO for three genes (WRN, NTN4 and LAMC3) with common associated variants, and for four genes (SLC8A3, SLC19A3, MADD and LRRK2) with multiple rare-associated variants that have a plausible biological function related to AD. The genes we have identified are in pathways that are strong candidates for involvement in the development of AD pathology and may lead to a better understanding of AD pathogenesis.
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Affiliation(s)
- Mohamad Saad
- Department of Biostatistics, University of Washington, Seattle, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, USA
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, USA
| | - Ellen M. Wijsman
- Department of Biostatistics, University of Washington, Seattle, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, USA
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22
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Gentier RJ, van Leeuwen FW. Misframed ubiquitin and impaired protein quality control: an early event in Alzheimer's disease. Front Mol Neurosci 2015; 8:47. [PMID: 26388726 PMCID: PMC4557111 DOI: 10.3389/fnmol.2015.00047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/18/2015] [Indexed: 12/21/2022] Open
Abstract
Amyloid β (Aβ) plaque formation is a prominent cellular hallmark of Alzheimer's disease (AD). To date, immunization trials in AD patients have not been effective in terms of curing or ameliorating dementia. In addition, γ-secretase inhibitor strategies await clinical improvements in AD. These approaches were based upon the idea that autosomal dominant mutations in amyloid precursor protein (APP) and Presenilin 1 (PS1) genes are predictive for treatment of all AD patients. However most AD patients are of the sporadic form which partly explains the failures to treat this multifactorial disease. The major risk factor for developing sporadic AD (SAD) is aging whereas the Apolipoprotein E polymorphism (ε4 variant) is the most prominent genetic risk factor. Other medium-risk factors such as triggering receptor expressed on myeloid cells 2 (TREM2) and nine low risk factors from Genome Wide Association Studies (GWAS) were associated with AD. Recently, pooled GWAS studies identified protein ubiquitination as one of the key modulators of AD. In addition, a brain site specific strategy was used to compare the proteomes of AD patients by an Ingenuity Pathway Analysis. This strategy revealed numerous proteins that strongly interact with ubiquitin (UBB) signaling, and pointing to a dysfunctional ubiquitin proteasome system (UPS) as a causal factor in AD. We reported that DNA-RNA sequence differences in several genes including ubiquitin do occur in AD, the resulting misframed protein of which accumulates in the neurofibrillary tangles (NFTs). This suggests again a functional link between neurodegeneration of the AD type and loss of protein quality control by the UPS. Progress in this field is discussed and modulating the activity of the UPS opens an attractive avenue of research towards slowing down the development of AD and ameliorating its effects by discovering prime targets for AD therapeutics.
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Affiliation(s)
- Romina J. Gentier
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastricht, Netherlands
| | - Fred W. van Leeuwen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastricht, Netherlands
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23
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Allen M, Kachadoorian M, Carrasquillo MM, Karhade A, Manly L, Burgess JD, Wang C, Serie D, Wang X, Siuda J, Zou F, Chai HS, Younkin C, Crook J, Medway C, Nguyen T, Ma L, Malphrus K, Lincoln S, Petersen RC, Graff-Radford NR, Asmann YW, Dickson DW, Younkin SG, Ertekin-Taner N. Late-onset Alzheimer disease risk variants mark brain regulatory loci. NEUROLOGY-GENETICS 2015; 1:e15. [PMID: 27066552 PMCID: PMC4807909 DOI: 10.1212/nxg.0000000000000012] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/08/2015] [Indexed: 11/15/2022]
Abstract
Objective: To investigate the top late-onset Alzheimer disease (LOAD) risk loci detected or confirmed by the International Genomics of Alzheimer's Project for association with brain gene expression levels to identify variants that influence Alzheimer disease (AD) risk through gene expression regulation. Methods: Expression levels from the cerebellum (CER) and temporal cortex (TCX) were obtained using Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation assay (WG-DASL) for ∼400 autopsied patients (∼200 with AD and ∼200 with non-AD pathologies). We tested 12 significant LOAD genome-wide association study (GWAS) index single nucleotide polymorphisms (SNPs) for cis association with levels of 34 genes within ±100 kb. We also evaluated brain levels of 14 LOAD GWAS candidate genes for association with 1,899 cis-SNPs. Significant associations were validated in a subset of TCX samples using next-generation RNA sequencing (RNAseq). Results: We identified strong associations of brain CR1, HLA-DRB1, and PILRB levels with LOAD GWAS index SNPs. We also detected other strong cis-SNPs for LOAD candidate genes MEF2C, ZCWPW1, and SLC24A4. MEF2C and SLC24A4, but not ZCWPW1 cis-SNPs, also associate with LOAD risk, independent of the index SNPs. The TCX expression associations could be validated with RNAseq for CR1, HLA-DRB1, ZCWPW1, and SLC24A4. Conclusions: Our results suggest that some LOAD GWAS variants mark brain regulatory loci, nominate genes under regulation by LOAD risk variants, and annotate these variants for their brain regulatory effects.
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Affiliation(s)
- Mariet Allen
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Michaela Kachadoorian
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Minerva M Carrasquillo
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Aditya Karhade
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Lester Manly
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Jeremy D Burgess
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Chen Wang
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Daniel Serie
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Xue Wang
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Joanna Siuda
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Fanggeng Zou
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - High Seng Chai
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Curtis Younkin
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Julia Crook
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Christopher Medway
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Thuy Nguyen
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Li Ma
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Kimberly Malphrus
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Sarah Lincoln
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Ronald C Petersen
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Neill R Graff-Radford
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Yan W Asmann
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Dennis W Dickson
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Steven G Younkin
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience (M.A., M.K., M.M.C., A.K., L. Manly, J.D.B., J.S., F.Z., C.Y., C.M., T.N., L. Ma, K.M., S.L., D.W.D., S.G.Y., N.E.-T.), Department of Neurology (N.R.G.-R., N.E.-T.), and Health Sciences Research (D.S., X.W., J.C., Y.W.A.), Mayo Clinic, Jacksonville, FL; Department of Neurology (R.C.P.) and Health Sciences Research (C.W., H.S.C.), Mayo Clinic, Rochester, MN; and Department of Neurology (J.S.), Medical University of Silesia, Katowice, Poland
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24
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Song F, Han G, Bai Z, Peng X, Wang J, Lei H. Alzheimer's Disease: Genomics and Beyond. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 121:1-24. [PMID: 26315760 DOI: 10.1016/bs.irn.2015.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is a major form of senile dementia. Despite the critical roles of Aβ and tau in AD pathology, drugs targeting Aβ or tau have so far reached limited success. The advent of genomic technologies has made it possible to gain a more complete picture regarding the molecular network underlying the disease progression which may lead to discoveries of novel treatment targets. In this review, we will discuss recent progresses in AD research focusing on genome, transcriptome, epigenome, and related subjects. Advancements have been made in the finding of novel genetic risk factors, new hypothesis for disease mechanism, candidate biomarkers for early diagnosis, and potential drug targets. As an integration effort, we have curated relevant data in a database named AlzBase.
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Affiliation(s)
- Fuhai Song
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Guangchun Han
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
| | - Zhouxian Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Xing Peng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Jiajia Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China; Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, PR China.
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25
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Aeinehband S, Lindblom RPF, Al Nimer F, Vijayaraghavan S, Sandholm K, Khademi M, Olsson T, Nilsson B, Ekdahl KN, Darreh-Shori T, Piehl F. Complement component C3 and butyrylcholinesterase activity are associated with neurodegeneration and clinical disability in multiple sclerosis. PLoS One 2015; 10:e0122048. [PMID: 25835709 PMCID: PMC4383591 DOI: 10.1371/journal.pone.0122048] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/06/2015] [Indexed: 12/22/2022] Open
Abstract
Dysregulation of the complement system is evident in many CNS diseases but mechanisms regulating complement activation in the CNS remain unclear. In a recent large rat genome-wide expression profiling and linkage analysis we found co-regulation of complement C3 immediately downstream of butyrylcholinesterase (BuChE), an enzyme hydrolyzing acetylcholine (ACh), a classical neurotransmitter with immunoregulatory effects. We here determined levels of neurofilament-light (NFL), a marker for ongoing nerve injury, C3 and activity of the two main ACh hydrolyzing enzymes, acetylcholinesterase (AChE) and BuChE, in cerebrospinal fluid (CSF) from patients with MS (n = 48) and non-inflammatory controls (n = 18). C3 levels were elevated in MS patients compared to controls and correlated both to disability and NFL. C3 levels were not induced by relapses, but were increased in patients with ≥9 cerebral lesions on magnetic resonance imaging and in patients with progressive disease. BuChE activity did not differ at the group level, but was correlated to both C3 and NFL levels in individual samples. In conclusion, we show that CSF C3 correlates both to a marker for ongoing nerve injury and degree of disease disability. Moreover, our results also suggest a potential link between intrathecal cholinergic activity and complement activation. These results motivate further efforts directed at elucidating the regulation and effector functions of the complement system in MS, and its relation to cholinergic tone.
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Affiliation(s)
- Shahin Aeinehband
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Rickard P. F. Lindblom
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Faiez Al Nimer
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Swetha Vijayaraghavan
- Division of Alzheimer Neurobiology Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | | | - Mohsen Khademi
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Bo Nilsson
- Division of Clinical Immunology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kristina Nilsson Ekdahl
- Division of Clinical Immunology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- School of Natural Sciences, Linnæus University, Kalmar, Sweden
| | - Taher Darreh-Shori
- Division of Alzheimer Neurobiology Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Piehl
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
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26
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Gentier RJG, Verheijen BM, Zamboni M, Stroeken MMA, Hermes DJHP, Küsters B, Steinbusch HWM, Hopkins DA, Van Leeuwen FW. Localization of mutant ubiquitin in the brain of a transgenic mouse line with proteasomal inhibition and its validation at specific sites in Alzheimer's disease. Front Neuroanat 2015; 9:26. [PMID: 25852488 PMCID: PMC4362318 DOI: 10.3389/fnana.2015.00026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 02/21/2015] [Indexed: 11/13/2022] Open
Abstract
Loss of protein quality control by the ubiquitin-proteasome system (UPS) during aging is one of the processes putatively contributing to cellular stress and Alzheimer's disease (AD) pathogenesis. Recently, pooled Genome Wide Association Studies (GWAS), pathway analysis and proteomics identified protein ubiquitination as one of the key modulators of AD. Mutations in ubiquitin B mRNA that result in UBB+1 dose-dependently cause an impaired UPS, subsequent accumulation of UBB+1 and most probably depositions of other aberrant proteins present in plaques and neurofibrillary tangles. We used specific immunohistochemical probes for a comprehensive topographic mapping of the UBB+1 distribution in the brains of transgenic mouse line 3413 overexpressing UBB+1. We also mapped the expression of UBB+1 in brain areas of AD patients selected based upon the distribution of UBB+1 in line 3413. Therefore, we focused on the olfactory bulb, basal ganglia, nucleus basalis of Meynert, inferior colliculus and raphe nuclei. UBB+1 distribution was compared with established probes for pre-tangles and tangles and Aβ plaques. UBB+1 distribution found in line 3413 is partly mirrored in the AD brain. Specifically, nuclei with substantial accumulations of tangle-bearing neurons, such as the nucleus basalis of Meynert and raphe nuclei also present high densities of UBB+1 positive tangles. Line 3413 is useful for studying the contribution of proteasomal dysfunction in AD. The findings are consistent with evidence that areas outside the forebrain are also affected in AD. Line 3413 may also be predictive for other conformational diseases, including related tauopathies and polyglutamine diseases, in which UBB+1 accumulates in their cellular hallmarks.
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Affiliation(s)
- Romina J G Gentier
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands
| | - Bert M Verheijen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands
| | - Margherita Zamboni
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands
| | - Maartje M A Stroeken
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands
| | - Denise J H P Hermes
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands
| | - Benno Küsters
- Department of Pathology, Radboud University Nijmegen Medical Center Nijmegen, Netherlands ; Department of Pathology, Maastricht University Medical Center Maastricht, Netherlands
| | - Harry W M Steinbusch
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands
| | - David A Hopkins
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands ; Department of Medical Neuroscience, Dalhousie University Halifax, NS, Canada
| | - Fred W Van Leeuwen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University Maastricht, Netherlands
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27
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Young JE, Boulanger-Weill J, Williams DA, Woodruff G, Buen F, Revilla AC, Herrera C, Israel MA, Yuan SH, Edland SD, Goldstein LSB. Elucidating molecular phenotypes caused by the SORL1 Alzheimer's disease genetic risk factor using human induced pluripotent stem cells. Cell Stem Cell 2015; 16:373-85. [PMID: 25772071 DOI: 10.1016/j.stem.2015.02.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/11/2015] [Accepted: 02/10/2015] [Indexed: 12/20/2022]
Abstract
Predisposition to sporadic Alzheimer's disease (SAD) involves interactions between a person's unique combination of genetic variants and the environment. The molecular effect of these variants may be subtle and difficult to analyze with standard in vitro or in vivo models. Here we used hIPSCs to examine genetic variation in the SORL1 gene and possible contributions to SAD-related phenotypes in human neurons. We found that human neurons carrying SORL1 variants associated with an increased SAD risk show a reduced response to treatment with BDNF, at the level of both SORL1 expression and APP processing. shRNA knockdown of SORL1 demonstrates that the differences in BDNF-induced APP processing between genotypes are dependent on SORL1 expression. We propose that the variation in SORL1 expression induction by BDNF is modulated by common genetic variants and can explain how genetic variation in this one locus can contribute to an individual's risk of developing SAD.
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Affiliation(s)
- Jessica E Young
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan Boulanger-Weill
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel A Williams
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace Woodruff
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Floyd Buen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arra C Revilla
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cheryl Herrera
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mason A Israel
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shauna H Yuan
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steven D Edland
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Division of Biostatistics, Department of Family and Preventive Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lawrence S B Goldstein
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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28
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Beach TG, Adler CH, Sue LI, Serrano G, Shill HA, Walker DG, Lue L, Roher AE, Dugger BN, Maarouf C, Birdsill AC, Intorcia A, Saxon-Labelle M, Pullen J, Scroggins A, Filon J, Scott S, Hoffman B, Garcia A, Caviness JN, Hentz JG, Driver-Dunckley E, Jacobson SA, Davis KJ, Belden CM, Long KE, Malek-Ahmadi M, Powell JJ, Gale LD, Nicholson LR, Caselli RJ, Woodruff BK, Rapscak SZ, Ahern GL, Shi J, Burke AD, Reiman EM, Sabbagh MN. Arizona Study of Aging and Neurodegenerative Disorders and Brain and Body Donation Program. Neuropathology 2015; 35:354-89. [PMID: 25619230 DOI: 10.1111/neup.12189] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/11/2014] [Indexed: 12/13/2022]
Abstract
The Brain and Body Donation Program (BBDP) at Banner Sun Health Research Institute (http://www.brainandbodydonationprogram.org) started in 1987 with brain-only donations and currently has banked more than 1600 brains. More than 430 whole-body donations have been received since this service was commenced in 2005. The collective academic output of the BBDP is now described as the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND). Most BBDP subjects are enrolled as cognitively normal volunteers residing in the retirement communities of metropolitan Phoenix, Arizona. Specific recruitment efforts are also directed at subjects with Alzheimer's disease, Parkinson's disease and cancer. The median age at death is 82. Subjects receive standardized general medical, neurological, neuropsychological and movement disorders assessments during life and more than 90% receive full pathological examinations by medically licensed pathologists after death. The Program has been funded through a combination of internal, federal and state of Arizona grants as well as user fees and pharmaceutical industry collaborations. Subsets of the Program are utilized by the US National Institute on Aging Arizona Alzheimer's Disease Core Center and the US National Institute of Neurological Disorders and Stroke National Brain and Tissue Resource for Parkinson's Disease and Related Disorders. Substantial funding has also been received from the Michael J. Fox Foundation for Parkinson's Research. The Program has made rapid autopsy a priority, with a 3.0-hour median post-mortem interval for the entire collection. The median RNA Integrity Number (RIN) for frozen brain and body tissue is 8.9 and 7.4, respectively. More than 2500 tissue requests have been served and currently about 200 are served annually. These requests have been made by more than 400 investigators located in 32 US states and 15 countries. Tissue from the BBDP has contributed to more than 350 publications and more than 200 grant-funded projects.
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Affiliation(s)
- Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Geidy Serrano
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Holly A Shill
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - LihFen Lue
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alex E Roher
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Chera Maarouf
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alex C Birdsill
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | - Joel Pullen
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Jessica Filon
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Sarah Scott
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Angelica Garcia
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | | | | | - Kathryn J Davis
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Kathy E Long
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | - Lisa D Gale
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | | | | | | | - Jiong Shi
- Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Anna D Burke
- Banner Alzheimer Institute, Phoenix, Arizona, USA
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29
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Pahnke J, Langer O, Krohn M. Alzheimer's and ABC transporters--new opportunities for diagnostics and treatment. Neurobiol Dis 2014; 72 Pt A:54-60. [PMID: 24746857 PMCID: PMC4199932 DOI: 10.1016/j.nbd.2014.04.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 12/26/2022] Open
Abstract
Much has been said about the increasing number of demented patients and the main risk factor 'age'. Frustratingly, we do not know the precise pattern and all modulating factors that provoke the pathologic changes in the brains of affected elderly. We have to diagnose early to be able to stop the progression of diseases that irreversibly destroy brain substance. Familiar AD cases have mislead some researchers for almost 20 years, which has unfortunately narrowed the scientific understanding and has, thus, lead to insufficient funding of independent approaches. Therefore, basic researchers hardly have been able to develop causative treatments and clinicians still do not have access to prognostic and early diagnostic tools. During the recent years it became clear that insufficient Aβ export, physiologically facilitated by the ABC transporter superfamily at the brain's barriers, plays a fundamental role in disease initiation and progression. Furthermore, export mechanisms that are deficient in affected elderly are new targets for activation and, thus, treatment, but ideally also for prevention. In sporadic AD disturbed clearance of β-amyloid from the brain is so far the most important factor for its accumulation in the parenchyma and vessel walls. Here, we review findings about the contribution of ABC transporters and of the perivascular drainage/glymphatic system on β-amyloid clearance. We highlight their potential value for innovative early diagnostics using PET and describe recently described, effective ABC transporter-targeting agents as potential causative treatment for neurodegenerative proteopathies/dementias.
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Affiliation(s)
- Jens Pahnke
- Neurodegeneration Research Lab (NRL), Department of Neurology, University of Magdeburg, Leipziger Str. 44, Bldg. 64, 39120 Magdeburg, Germany; German Center for Neurodegenerative Diseases (DZNE) Magdeburg, Leipziger Str. 44, Bldg. 64, 39120 Magdeburg, Germany.
| | - Oliver Langer
- Health and Environment Department, AIT - Austrian Institute of Technology GmbH, 2444 Seibersdorf, Austria; Department of Clinical Pharmacology, Medical University of Vienna, Währinger-Gürtel 18-20, 1090 Vienna, Austria
| | - Markus Krohn
- Neurodegeneration Research Lab (NRL), Department of Neurology, University of Magdeburg, Leipziger Str. 44, Bldg. 64, 39120 Magdeburg, Germany
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30
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Abstract
Alzheimer's disease/senile dementia of the Alzheimer type (AD/SDAT) is the most common neuropathologic substrate of dementia. It is characterized by synapse loss (predominantly within neocortex) as well as deposition of certain distinctive lesions (the result of protein misfolding) throughout the brain. The latter include senile plaques, composed mainly of an amyloid (Aβ) core and a neuritic component; neurofibrillary tangles, composed predominantly of hyperphosphorylated tau; and cerebral amyloid angiopathy, a microangiopathy affecting both cerebral cortical capillaries and arterioles and resulting from Aβ deposition within their walls or (in the case of capillaries) immediately adjacent brain parenchyma. In this article, I discuss the hypothesized role these lesions play in causing cerebral dysfunction, as well as CSF and neuroimaging biomarkers (for dementia) that are especially relevant as immunotherapeutic approaches are being developed to remove Aβ from the brain parenchyma. In addition, I address the role of neuropathology in characterizing the sequelae of new AD/SDAT therapies and helping to validate CSF and neuroimaging biomarkers of disease. Comorbidity of AD/SDAT and various types of cerebrovascular disease is a major theme in dementia research, especially as cognitive impairment develops in the oldest old, who are especially vulnerable to ischemic and hemorrhagic brain lesions.
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Affiliation(s)
- Harry V Vinters
- Department of Pathology and Laboratory Medicine (Neuropathology), UCLA Medical Center, Los Angeles, California 90095-1732;
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31
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Shen L, Thompson PM, Potkin SG, Bertram L, Farrer LA, Foroud TM, Green RC, Hu X, Huentelman MJ, Kim S, Kauwe JSK, Li Q, Liu E, Macciardi F, Moore JH, Munsie L, Nho K, Ramanan VK, Risacher SL, Stone DJ, Swaminathan S, Toga AW, Weiner MW, Saykin AJ. Genetic analysis of quantitative phenotypes in AD and MCI: imaging, cognition and biomarkers. Brain Imaging Behav 2014; 8:183-207. [PMID: 24092460 PMCID: PMC3976843 DOI: 10.1007/s11682-013-9262-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Genetics Core of the Alzheimer's Disease Neuroimaging Initiative (ADNI), formally established in 2009, aims to provide resources and facilitate research related to genetic predictors of multidimensional Alzheimer's disease (AD)-related phenotypes. Here, we provide a systematic review of genetic studies published between 2009 and 2012 where either ADNI APOE genotype or genome-wide association study (GWAS) data were used. We review and synthesize ADNI genetic associations with disease status or quantitative disease endophenotypes including structural and functional neuroimaging, fluid biomarker assays, and cognitive performance. We also discuss the diverse analytical strategies used in these studies, including univariate and multivariate analysis, meta-analysis, pathway analysis, and interaction and network analysis. Finally, we perform pathway and network enrichment analyses of these ADNI genetic associations to highlight key mechanisms that may drive disease onset and trajectory. Major ADNI findings included all the top 10 AD genes and several of these (e.g., APOE, BIN1, CLU, CR1, and PICALM) were corroborated by ADNI imaging, fluid and cognitive phenotypes. ADNI imaging genetics studies discovered novel findings (e.g., FRMD6) that were later replicated on different data sets. Several other genes (e.g., APOC1, FTO, GRIN2B, MAGI2, and TOMM40) were associated with multiple ADNI phenotypes, warranting further investigation on other data sets. The broad availability and wide scope of ADNI genetic and phenotypic data has advanced our understanding of the genetic basis of AD and has nominated novel targets for future studies employing next-generation sequencing and convergent multi-omics approaches, and for clinical drug and biomarker development.
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Affiliation(s)
- Li Shen
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - Paul M. Thompson
- Imaging Genetics Center, Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
| | - Steven G. Potkin
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92617 USA
| | - Lars Bertram
- Neuropsychiatric Genetics Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lindsay A. Farrer
- Biomedical Genetics L320, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118 USA
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Robert C. Green
- Division of Genetics and Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA
| | - Xiaolan Hu
- Clinical Genetics, Exploratory Clinical & Translational Research, Bristol-Myers Squibbs, Pennington, NJ 08534 USA
| | - Matthew J. Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Sungeun Kim
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - John S. K. Kauwe
- Departments of Biology, Neuroscience, Brigham Young University, 675 WIDB, Provo, UT 84602 USA
| | - Qingqin Li
- Department of Neuroscience Biomarkers, Janssen Research and Development, LLC, Raritan, NJ 08869 USA
| | - Enchi Liu
- Biomarker Discovery, Janssen Alzheimer Immunotherapy Research and Development, LLC, South San Francisco, CA 94080 USA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92617 USA
- Department of Sciences and Biomedical Technologies, University of Milan, Segrate, MI Italy
| | - Jason H. Moore
- Department of Genetics, Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, NH 03756 USA
| | - Leanne Munsie
- Tailored Therapeutics, Eli Lilly and Company, Indianapolis, IN 46285 USA
| | - Kwangsik Nho
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - Vijay K. Ramanan
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Shannon L. Risacher
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - David J. Stone
- Merck Research Laboratories, 770 Sumneytown Pike, WP53B-120, West Point, PA 19486 USA
| | - Shanker Swaminathan
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - Arthur W. Toga
- Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
| | - Michael W. Weiner
- Departments of Radiology, Medicine and Psychiatry, UC San Francisco, San Francisco, CA 94143 USA
| | - Andrew J. Saykin
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - for the Alzheimer’s Disease Neuroimaging Initiative
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
- Imaging Genetics Center, Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92617 USA
- Neuropsychiatric Genetics Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany
- Biomedical Genetics L320, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Division of Genetics and Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA
- Clinical Genetics, Exploratory Clinical & Translational Research, Bristol-Myers Squibbs, Pennington, NJ 08534 USA
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- Departments of Biology, Neuroscience, Brigham Young University, 675 WIDB, Provo, UT 84602 USA
- Department of Neuroscience Biomarkers, Janssen Research and Development, LLC, Raritan, NJ 08869 USA
- Biomarker Discovery, Janssen Alzheimer Immunotherapy Research and Development, LLC, South San Francisco, CA 94080 USA
- Department of Sciences and Biomedical Technologies, University of Milan, Segrate, MI Italy
- Department of Genetics, Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, NH 03756 USA
- Tailored Therapeutics, Eli Lilly and Company, Indianapolis, IN 46285 USA
- Merck Research Laboratories, 770 Sumneytown Pike, WP53B-120, West Point, PA 19486 USA
- Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
- Departments of Radiology, Medicine and Psychiatry, UC San Francisco, San Francisco, CA 94143 USA
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Abstract
Alzheimer’s disease (AD) is a complex and heterogeneous neurodegenerative disorder, classified as either early onset (under 65 years of age), or late onset (over 65 years of age). Three main genes are involved in early onset AD: amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2). The apolipoprotein E (APOE) E4 allele has been found to be a main risk factor for late-onset Alzheimer’s disease. Additionally, genome-wide association studies (GWASs) have identified several genes that might be potential risk factors for AD, including clusterin (CLU), complement receptor 1 (CR1), phosphatidylinositol binding clathrin assembly protein (PICALM), and sortilin-related receptor (SORL1). Recent studies have discovered additional novel genes that might be involved in late-onset AD, such as triggering receptor expressed on myeloid cells 2 (TREM2) and cluster of differentiation 33 (CD33). Identification of new AD-related genes is important for better understanding of the pathomechanisms leading to neurodegeneration. Since the differential diagnoses of neurodegenerative disorders are difficult, especially in the early stages, genetic testing is essential for diagnostic processes. Next-generation sequencing studies have been successfully used for detecting mutations, monitoring the epigenetic changes, and analyzing transcriptomes. These studies may be a promising approach toward understanding the complete genetic mechanisms of diverse genetic disorders such as AD.
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Affiliation(s)
- Eva Bagyinszky
- Department of BioNano Technology Gachon University, Gyeonggi-do, South Korea
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Seong Soo A An
- Department of BioNano Technology Gachon University, Gyeonggi-do, South Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University Budang Hospital, Gyeonggi-do, South Korea
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Rosenthal SL, Kamboh MI. Late-Onset Alzheimer's Disease Genes and the Potentially Implicated Pathways. CURRENT GENETIC MEDICINE REPORTS 2014; 2:85-101. [PMID: 24829845 PMCID: PMC4013444 DOI: 10.1007/s40142-014-0034-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Late-onset Alzheimer's disease (LOAD) is a devastating neurodegenerative disease with no effective treatment or cure. In addition to APOE, recent large genome-wide association studies have identified variation in over 20 loci that contribute to disease risk: CR1, BIN1, INPP5D, MEF2C, TREM2, CD2AP, HLA-DRB1/HLA-DRB5, EPHA1, NME8, ZCWPW1, CLU, PTK2B, PICALM, SORL1, CELF1, MS4A4/MS4A6E, SLC24A4/RIN3,FERMT2, CD33, ABCA7, CASS4. In addition, rare variants associated with LOAD have also been identified in APP, TREM2 and PLD3 genes. Previous research has identified inflammatory response, lipid metabolism and homeostasis, and endocytosis as the likely modes through which these gene products participate in Alzheimer's disease. Despite the clustering of these genes across a few common pathways, many of their roles in disease pathogenesis have yet to be determined. In this review, we examine both general and postulated disease functions of these genes and consider a comprehensive view of their potential roles in LOAD risk.
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Affiliation(s)
- Samantha L. Rosenthal
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - M. Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261 USA
- Alzheimer’s Disease Research Center, University of Pittsburgh, Pittsburgh, PA USA
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Transcriptome analysis of distinct mouse strains reveals kinesin light chain-1 splicing as an amyloid-β accumulation modifier. Proc Natl Acad Sci U S A 2014; 111:2638-43. [PMID: 24497505 DOI: 10.1073/pnas.1307345111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β (Aβ). The genes that govern this process, however, have remained elusive. To this end, we combined distinct mouse strains with transcriptomics to directly identify disease-relevant genes. We show that AD model mice (APP-Tg) with DBA/2 genetic backgrounds have significantly lower levels of Aβ accumulation compared with SJL and C57BL/6 mice. We then applied brain transcriptomics to reveal the genes in DBA/2 that suppress Aβ accumulation. To avoid detecting secondarily affected genes by Aβ, we used non-Tg mice in the absence of Aβ pathology and selected candidate genes differently expressed in DBA/2 mice. Additional transcriptome analysis of APP-Tg mice with mixed genetic backgrounds revealed kinesin light chain-1 (Klc1) as an Aβ modifier, indicating a role for intracellular trafficking in Aβ accumulation. Aβ levels correlated with the expression levels of Klc1 splice variant E and the genotype of Klc1 in these APP-Tg mice. In humans, the expression levels of KLC1 variant E in brain and lymphocyte were significantly higher in AD patients compared with unaffected individuals. Finally, functional analysis using neuroblastoma cells showed that overexpression or knockdown of KLC1 variant E increases or decreases the production of Aβ, respectively. The identification of KLC1 variant E suggests that the dysfunction of intracellular trafficking is a causative factor of Aβ pathology. This unique combination of distinct mouse strains and model mice with transcriptomics is expected to be useful for the study of genetic mechanisms of other complex diseases.
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Combarros O. Genetic Risk Factors for Alzheimer’s Disease. NEURODEGENER DIS 2014. [DOI: 10.1007/978-1-4471-6380-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Jiang T, Yu JT, Tan MS, Wang HF, Wang YL, Zhu XC, Zhang W, Tan L. Genetic variation in PICALM and Alzheimer's disease risk in Han Chinese. Neurobiol Aging 2013; 35:934.e1-3. [PMID: 24095218 DOI: 10.1016/j.neurobiolaging.2013.09.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 11/25/2022]
Abstract
The current study was conducted to investigate the association of phosphatidylinositol-binding clathrin assembly protein gene (PICALM) with late-onset Alzheimer's disease (LOAD) risk in Han Chinese. We first sequenced PICALM for variants in a small sample (n = 100), and the selected variants were then genotyped in a larger cohort (n = 2292). Sequencing analysis identified 16 variants within PICALM including 5 new variants with extreme low frequency in the northern Han Chinese population. However, in the subsequent genotyping, none showed a significant association with LOAD risk after Bonferroni correction. These findings implicate that PICALM might not play a major role in the genetic predisposition to LOAD in Han Chinese.
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Affiliation(s)
- Teng Jiang
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, China
| | - Jin-Tai Yu
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, China; Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, China; Department of Neurology, Qingdao Municipal Hospital, College of Medicine and Pharmaceutics, Ocean University of China, China.
| | - Meng-Shan Tan
- Department of Neurology, Qingdao Municipal Hospital, College of Medicine and Pharmaceutics, Ocean University of China, China
| | - Hui-Fu Wang
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, China
| | - Ying-Li Wang
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, China
| | - Xi-Chen Zhu
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, China
| | - Wei Zhang
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, China; Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, China; Department of Neurology, Qingdao Municipal Hospital, College of Medicine and Pharmaceutics, Ocean University of China, China.
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Tan MS, Yu JT, Tan L. Bridging integrator 1 (BIN1): form, function, and Alzheimer's disease. Trends Mol Med 2013; 19:594-603. [PMID: 23871436 DOI: 10.1016/j.molmed.2013.06.004] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/24/2013] [Accepted: 06/21/2013] [Indexed: 12/13/2022]
Abstract
The bridging integrator 1 (BIN1) gene, also known as amphiphysin 2, has recently been identified as the most important risk locus for late onset Alzheimer's disease (LOAD), after apolipoprotein E (APOE). Here, we summarize the known functions of BIN1 and discuss the polymorphisms associated with LOAD, as well as their possible physiological effects. Emerging data suggest that BIN1 affects AD risk primarily by modulating tau pathology, but other affected cellular functions are discussed, including endocytosis/trafficking, inflammation, calcium homeostasis, and apoptosis. Epigenetic modifications are important for AD pathogenesis, and we review data that suggests the possible DNA methylation of the BIN1 promoter. Finally, given the potential contributions of BIN1 to AD pathogenesis, targeting BIN1 might present novel opportunities for AD therapy.
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Affiliation(s)
- Meng-Shan Tan
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266003, China; Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
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Kohannim O, Hua X, Rajagopalan P, Hibar DP, Jahanshad N, Grill JD, Apostolova LG, Toga AW, Jack CR, Weiner MW, Thompson PM. Multilocus genetic profiling to empower drug trials and predict brain atrophy. NEUROIMAGE-CLINICAL 2013; 2:827-35. [PMID: 24179834 PMCID: PMC3777716 DOI: 10.1016/j.nicl.2013.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/14/2013] [Accepted: 05/11/2013] [Indexed: 12/16/2022]
Abstract
Designers of clinical trials for Alzheimer's disease (AD) and mild cognitive impairment (MCI) are actively considering structural and functional neuroimaging, cerebrospinal fluid and genetic biomarkers to reduce the sample sizes needed to detect therapeutic effects. Genetic pre-selection, however, has been limited to Apolipoprotein E (ApoE). Recently discovered polymorphisms in the CLU, CR1 and PICALM genes are also moderate risk factors for AD; each affects lifetime AD risk by ~ 10–20%. Here, we tested the hypothesis that pre-selecting subjects based on these variants along with ApoE genotype would further boost clinical trial power, relative to considering ApoE alone, using an MRI-derived 2-year atrophy rate as our outcome measure. We ranked subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) based on their cumulative risk from these four genes. We obtained sample size estimates in cohorts enriched in subjects with greater aggregate genetic risk. Enriching for additional genetic biomarkers reduced the required sample sizes by up to 50%, for MCI trials. Thus, AD drug trial enrichment with multiple genotypes may have potential implications for the timeliness, cost, and power of trials. ApoE genotype status helps enrich MCI trials, using a structural MRI outcome measure. CLU, PICALM and CR1 risk genes boost potential MCI trial power beyond ApoE alone. CLU, PICALM and CR1 show significant, aggregate effects on TBM maps of brain atrophy.
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Affiliation(s)
- Omid Kohannim
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Xue Hua
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Priya Rajagopalan
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Derrek P. Hibar
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Joshua D. Grill
- Mary Easton Center for Alzheimer's Disease Research, UCLA School of Medicine, Los Angeles, CA, USA
| | - Liana G. Apostolova
- Mary Easton Center for Alzheimer's Disease Research, UCLA School of Medicine, Los Angeles, CA, USA
| | - Arthur W. Toga
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | | | - Michael W. Weiner
- Depts. of Radiology, Medicine and Psychiatry, UCSF, San Francisco, CA, USA
- Dept. of Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Paul M. Thompson
- Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
- Corresponding author at: Imaging Genetics Center, Laboratory of Neuro Imaging, Dept. of Neurology, UCLA School of Medicine, Neuroscience Research Building 225E 635 Charles Young Drive, Los Angeles, CA 90095-1769, USA. Tel.: + 1 310 206 2101; fax: + 1 310 206 5518.
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