1
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Ji S, Kang J, Han C, Xu X, Chen M, Chen J, Chhetri JK, Pan J, Chan P. Potential role of APOE ɛ4 allele as a modifier for the association of BDNF Val66Met polymorphisms and cognitive impairment in community-dwelling older adults. Front Aging Neurosci 2024; 16:1330193. [PMID: 38374884 PMCID: PMC10876185 DOI: 10.3389/fnagi.2024.1330193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Objective To determine whether the brain-derived neurotrophic factor (BDNF) Val66Met polymorphism is associated with cognitive impairment (CI) in community-dwelling Chinese older adults, and to investigate whether this relationship is modified by the Apolipoprotein E (APOE) ɛ4 allele. Methods The study is a secondary analysis of 703 participants aged ≥60 years randomly enrolled from the Beijing Longitudinal Study of Aging II prospective cohort. The education-adjusted Mini-Mental State Examination and the Clinical Dementia Rating Scale were used to measure the cognitive performance of the subjects. The main effects and interactions (additive and multiplicative) of the BDNF Met and the APOE ε4 alleles on CI were estimated by logistic regression models. Results In total, 84 out of 703 older adults aged ≥60 years old had CI. No significant difference was observed in the risk of CI between participants with the BDNF Met allele and that of subjects without the BDNF Met allele (p = 0.213; p = 0.164). Individuals carrying both the BDNF Met and APOE ε4 alleles had an almost 1.5-fold increased odds of CI compared with carriers of the BDNF Met allele but without the APOE ε4 allele. The additive association indicated a positive interaction of both BDNF Met and APOE ε4 alleles with wide CIs (p = 0.021; p = 0.018). Conclusion The results suggest that the APOE ε4 allele may be a potential modifier for the association of the BDNF Val66Met polymorphism with CI in community-dwelling older adults.
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Affiliation(s)
- Shaozhen Ji
- Department of Neurology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia Kang
- Department of Neurology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Chao Han
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xitong Xu
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Meijie Chen
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jie Chen
- Department of Geriatrics, Shenzhen Hospital, Peking University, Shenzhen, China
| | - Jagadish K Chhetri
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Jing Pan
- Department of Neurology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Piu Chan
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
- Department of Neurobiology, Neurology and Geriatrics, Xuanwu Hospital of Capital Medical University, Beijing, China
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2
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Branciamore S, Gogoshin G, Rodin AS, Myers AJ. The Human Brainome: changes in expression of VGF, SPECC1L, HLA-DRA and RANBP3L act with APOE E4 to alter risk for late onset Alzheimer's disease. RESEARCH SQUARE 2023:rs.3.rs-3678057. [PMID: 38168398 PMCID: PMC10760217 DOI: 10.21203/rs.3.rs-3678057/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
While there are currently over 40 replicated genes with mapped risk alleles for Late Onset Alzheimer's disease (LOAD), the Apolipoprotein E locus E4 haplotype is still the biggest driver of risk, with odds ratios for neuropathologically confirmed E44 carriers exceeding 30 (95% confidence interval 16.59-58.75). We sought to address whether the APOE E4 haplotype modifies expression globally through networks of expression to increase LOAD risk. We have used the Human Brainome data to build expression networks comparing APOE E4 carriers to non-carriers using scalable mixed-datatypes Bayesian network (BN) modeling. We have found that VGF had the greatest explanatory weight. High expression of VGF is a protective signal, even on the background of APOE E4 alleles. LOAD risk signals, considering an APOE background, include high levels of SPECC1L, HLA-DRA and RANBP3L. Our findings nominate several new transcripts, taking a combined approach to network building including known LOAD risk loci.
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3
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Hoffmann M, Poschenrieder JM, Incudini M, Baier S, Fitz A, Maier A, Hartung M, Hoffmann C, Trummer N, Adamowicz K, Picciani M, Scheibling E, Harl MV, Lesch I, Frey H, Kayser S, Wissenberg P, Schwartz L, Hafner L, Acharya A, Hackl L, Grabert G, Lee SG, Cho G, Cloward M, Jankowski J, Lee HK, Tsoy O, Wenke N, Pedersen AG, Bønnelykke K, Mandarino A, Melograna F, Schulz L, Climente-González H, Wilhelm M, Iapichino L, Wienbrandt L, Ellinghaus D, Van Steen K, Grossi M, Furth PA, Hennighausen L, Di Pierro A, Baumbach J, Kacprowski T, List M, Blumenthal DB. Network medicine-based epistasis detection in complex diseases: ready for quantum computing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.07.23298205. [PMID: 38076997 PMCID: PMC10705612 DOI: 10.1101/2023.11.07.23298205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs)1-3. Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL is the first application that demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.
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Affiliation(s)
- Markus Hoffmann
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Julian M. Poschenrieder
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Massimiliano Incudini
- Dipartimento di Informatica, Universit’a di Verona, Strada le Grazie 15 - 34137, Verona, Italy
| | - Sylvie Baier
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Amelie Fitz
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs. Lyngby, Denmark
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Christian Hoffmann
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Nico Trummer
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Klaudia Adamowicz
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Mario Picciani
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Evelyn Scheibling
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Maximilian V. Harl
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Ingmar Lesch
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Hunor Frey
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Simon Kayser
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Paul Wissenberg
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Leon Schwartz
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Leon Hafner
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
| | - Aakriti Acharya
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, Technische Universität Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Braunschweig, Germany
| | - Lena Hackl
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Gordon Grabert
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, Technische Universität Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Braunschweig, Germany
| | - Sung-Gwon Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Korea
| | - Gyuhyeok Cho
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Matthew Cloward
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Jakub Jankowski
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Nina Wenke
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs. Lyngby, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Mandarino
- International Centre for Theory of Quantum Technologies, University of Gdańsk, 80-309 Gdańsk, Poland
| | - Federico Melograna
- BIO3 - Systems Genetics; GIGA-R Medical Genomics, University of Liège, Liège, Belgium
- BIO3 - Systems Medicine; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Laura Schulz
- Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities (LRZ), Garching b. München, Germany
| | | | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Luigi Iapichino
- Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities (LRZ), Garching b. München, Germany
| | - Lars Wienbrandt
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Kristel Van Steen
- BIO3 - Systems Genetics; GIGA-R Medical Genomics, University of Liège, Liège, Belgium
- BIO3 - Systems Medicine; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Michele Grossi
- European Organization for Nuclear Research (CERN), Geneva 1211, Switzerland
| | - Priscilla A. Furth
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Alessandra Di Pierro
- Dipartimento di Informatica, Universit’a di Verona, Strada le Grazie 15 - 34137, Verona, Italy
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, Technische Universität Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Braunschweig, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - David B. Blumenthal
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
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4
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Hahn O, Foltz AG, Atkins M, Kedir B, Moran-Losada P, Guldner IH, Munson C, Kern F, Pálovics R, Lu N, Zhang H, Kaur A, Hull J, Huguenard JR, Grönke S, Lehallier B, Partridge L, Keller A, Wyss-Coray T. Atlas of the aging mouse brain reveals white matter as vulnerable foci. Cell 2023; 186:4117-4133.e22. [PMID: 37591239 PMCID: PMC10528304 DOI: 10.1016/j.cell.2023.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/17/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
Abstract
Aging is the key risk factor for cognitive decline, yet the molecular changes underlying brain aging remain poorly understood. Here, we conducted spatiotemporal RNA sequencing of the mouse brain, profiling 1,076 samples from 15 regions across 7 ages and 2 rejuvenation interventions. Our analysis identified a brain-wide gene signature of aging in glial cells, which exhibited spatially defined changes in magnitude. By integrating spatial and single-nucleus transcriptomics, we found that glial aging was particularly accelerated in white matter compared with cortical regions, whereas specialized neuronal populations showed region-specific expression changes. Rejuvenation interventions, including young plasma injection and dietary restriction, exhibited distinct effects on gene expression in specific brain regions. Furthermore, we discovered differential gene expression patterns associated with three human neurodegenerative diseases, highlighting the importance of regional aging as a potential modulator of disease. Our findings identify molecular foci of brain aging, providing a foundation to target age-related cognitive decline.
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Affiliation(s)
- Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Aulden G Foltz
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Micaiah Atkins
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Blen Kedir
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Moran-Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ian H Guldner
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Christy Munson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU Langone Health, New York City, NY, USA
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Róbert Pálovics
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nannan Lu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hui Zhang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Achint Kaur
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob Hull
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Cologne, Germany; Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA; Stanford University, The Phil and Penny Knight Initiative for Brain Resilience, Stanford, CA, USA.
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5
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Sagar R, Azoidis I, Zivko C, Xydia A, Oh ES, Rosenberg PB, Lyketsos CG, Mahairaki V, Avramopoulos D. Excitatory Neurons Derived from Human-Induced Pluripotent Stem Cells Show Transcriptomic Differences in Alzheimer's Patients from Controls. Cells 2023; 12:1990. [PMID: 37566069 PMCID: PMC10417412 DOI: 10.3390/cells12151990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
The recent advances in creating pluripotent stem cells from somatic cells and differentiating them into a variety of cell types is allowing us to study them without the caveats associated with disease-related changes. We generated induced Pluripotent Stem Cells (iPSCs) from eight Alzheimer's disease (AD) patients and six controls and used lentiviral delivery to differentiate them into excitatory glutamatergic neurons. We then performed RNA sequencing on these neurons and compared the Alzheimer's and control transcriptomes. We found that 621 genes show differences in expression levels at adjusted p < 0.05 between the case and control derived neurons. These genes show significant overlap and directional concordance with genes reported from a single-cell transcriptome study of AD patients; they include five genes implicated in AD from genome-wide association studies and they appear to be part of a larger functional network as indicated by an excess of interactions between them observed in the protein-protein interaction database STRING. Exploratory analysis with Uniform Manifold Approximation and Projection (UMAP) suggests distinct clusters of patients, based on gene expression, who may be clinically different. Our research outcomes will enable the precise identification of distinct biological subtypes among individuals with Alzheimer's disease, facilitating the implementation of tailored precision medicine strategies.
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Affiliation(s)
- Ram Sagar
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ioannis Azoidis
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Cristina Zivko
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ariadni Xydia
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Esther S. Oh
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Paul B. Rosenberg
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Constantine G. Lyketsos
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vasiliki Mahairaki
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Association of GAB2 with Quality of Life and Negative Emotions in Patients with Gastric Cancer after Postoperative Comprehensive Care. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:1732214. [PMID: 35958936 PMCID: PMC9357693 DOI: 10.1155/2022/1732214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/01/2022] [Indexed: 11/18/2022]
Abstract
GRB2-associated binding protein 2 (GAB2), a highly conserved scaffold protein, is abnormally expressed and activated in patients with gastric cancer (GC). However, the genetic diversity of GAB2 in GC and its association with the clinical manifestations of patients are still unclear. Here, we explored the polymorphism of GAB2 rs2373115 in GC and its association with quality of life (QOL) and negative emotions of patients with GC after postoperative comprehensive care. A case-control study showed that the frequency of the GG genotype of GAB2 rs2373115 in the GC patients was higher than that in the healthy people, while the frequency of the TT + TG genotype was lower than that in the healthy people. Obvious distinctions were observed in the histological grade and TNM staging between the GG genotype and TT + TG genotype. In addition, SAS and SDS scores in the patients with GG genotype were higher than those in patients with TT + TG genotype, while the emotional function, cognitive function, dyspnea, fatigue, sleep disorder, and overall QOL in patients with GG genotype were lower than those in patients with TT + TG genotype. These results showed that GAB2 rs2373115 polymorphism was related to QOL and negative emotions in patients with GC after postoperative comprehensive care.
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7
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Nabirotchkin S, Bouaziz J, Glibert F, Mandel J, Foucquier J, Hajj R, Callizot N, Cholet N, Guedj M, Cohen D. Combinational Drug Repurposing from Genetic Networks Applied to Alzheimer’s Disease. J Alzheimers Dis 2022; 88:1585-1603. [DOI: 10.3233/jad-220120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Human diseases are multi-factorial biological phenomena resulting from perturbations of numerous functional networks. The complex nature of human diseases explains frequently observed marginal or transitory efficacy of mono-therapeutic interventions. For this reason, combination therapy is being increasingly evaluated as a biologically plausible strategy for reversing disease state, fostering the development of dedicated methodological and experimental approaches. In parallel, genome-wide association studies (GWAS) provide a prominent opportunity for disclosing human-specific therapeutic targets and rational drug repurposing. Objective: In this context, our objective was to elaborate an integrated computational platform to accelerate discovery and experimental validation of synergistic combinations of repurposed drugs for treatment of common human diseases. Methods: The proposed approach combines adapted statistical analysis of GWAS data, pathway-based functional annotation of genetic findings using gene set enrichment technique, computational reconstruction of signaling networks enriched in disease-associated genes, selection of candidate repurposed drugs and proof-of-concept combinational experimental screening. Results: It enables robust identification of signaling pathways enriched in disease susceptibility loci. Therapeutic targeting of the disease-associated signaling networks provides a reliable way for rational drug repurposing and rapid development of synergistic drug combinations for common human diseases. Conclusion: Here we demonstrate the feasibility and efficacy of the proposed approach with an experiment application to Alzheimer’s disease.
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8
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The role and therapeutic implication of protein tyrosine phosphatases in Alzheimer's disease. Biomed Pharmacother 2022; 151:113188. [PMID: 35676788 DOI: 10.1016/j.biopha.2022.113188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 11/24/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are important regulator of neuronal signal transduction and a growing number of PTPs have been implicated in Alzheimer's disease (AD). In the brains of patients with AD, there are a variety of abnormally phosphorylated proteins, which are closely related to the abnormal expression and activity of PTPs. β-Amyloid plaques (Aβ) and hyperphosphorylated tau protein are two pathological hallmarks of AD, and their accumulation ultimately leads to neurodegeneration. Studies have shown that protein phosphorylation signaling pathways mediates intracellular accumulation of Aβ and tau during AD development and are involved in synaptic plasticity and other stress responses. Here, we summarized the roles of PTPs related to the pathogenesis of AD and analyzed their therapeutic potential in AD.
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9
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Ruffini N, Klingenberg S, Heese R, Schweiger S, Gerber S. The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Front Aging Neurosci 2022; 14:866886. [PMID: 35832065 PMCID: PMC9271745 DOI: 10.3389/fnagi.2022.866886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.
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Affiliation(s)
- Nicolas Ruffini
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research, Leibniz Association, Mainz, Germany
| | - Susanne Klingenberg
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Raoul Heese
- Fraunhofer Institute for Industrial Mathematics (ITWM), Kaiserslautern, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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10
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Salvetat N, Checa-Robles FJ, Patel V, Cayzac C, Dubuc B, Chimienti F, Abraham JD, Dupré P, Vetter D, Méreuze S, Lang JP, Kupfer DJ, Courtet P, Weissmann D. A game changer for bipolar disorder diagnosis using RNA editing-based biomarkers. Transl Psychiatry 2022; 12:182. [PMID: 35504874 PMCID: PMC9064541 DOI: 10.1038/s41398-022-01938-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
In clinical practice, differentiating Bipolar Disorder (BD) from unipolar depression is a challenge due to the depressive symptoms, which are the core presentations of both disorders. This misdiagnosis during depressive episodes results in a delay in proper treatment and a poor management of their condition. In a first step, using A-to-I RNA editome analysis, we discovered 646 variants (366 genes) differentially edited between depressed patients and healthy volunteers in a discovery cohort of 57 participants. After using stringent criteria and biological pathway analysis, candidate biomarkers from 8 genes were singled out and tested in a validation cohort of 410 participants. Combining the selected biomarkers with a machine learning approach achieved to discriminate depressed patients (n = 267) versus controls (n = 143) with an AUC of 0.930 (CI 95% [0.879-0.982]), a sensitivity of 84.0% and a specificity of 87.1%. In a second step by selecting among the depressed patients those with unipolar depression (n = 160) or BD (n = 95), we identified a combination of 6 biomarkers which allowed a differential diagnosis of bipolar disorder with an AUC of 0.935 and high specificity (Sp = 84.6%) and sensitivity (Se = 90.9%). The association of RNA editing variants modifications with depression subtypes and the use of artificial intelligence allowed developing a new tool to identify, among depressed patients, those suffering from BD. This test will help to reduce the misdiagnosis delay of bipolar patients, leading to an earlier implementation of a proper treatment.
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Affiliation(s)
- Nicolas Salvetat
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | | | - Vipul Patel
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Christopher Cayzac
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Benjamin Dubuc
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Fabrice Chimienti
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | | | - Pierrick Dupré
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Diana Vetter
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Sandie Méreuze
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Jean-Philippe Lang
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
- Les Toises. Center for Psychiatry and Psychotherapy, Lausanne, Switzerland
| | - David J Kupfer
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Philippe Courtet
- Department of Psychiatric Emergency & Acute Care, Lapeyronie Hospital, CHU Montpellier, Montpellier, France
| | - Dinah Weissmann
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France.
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11
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Niyasti P, Saberi A, Hatamyain H, Ajamian F, Shirkouhi SG, Mirzanejad L, Andalib S. Association of Insulin Receptor Substrate-1 Gene Polymorphism (rs1801278) with Alzheimer’s Disease. J Alzheimers Dis Rep 2022. [DOI: 10.3233/adr-210060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background: Alzheimer’s disease (AD) is the most common form of dementia. AD is also the leading cause of morbidity and mortality due to dementia worldwide. It has been shown that AD is associated with type 2 diabetes mellitus (T2DM) and brain insulin resistance. Rs1801278 is a polymorphism in insulin receptor substrate-1 (IRS-1) gene which changes the amino acid Arg972. This polymorphism has been found to be associated with susceptibility to AD in some populations. Objective: In the present study, our aim was to investigate the association of Arg972 IRS-1 (rs1801278) gene polymorphism and late-onset Alzheimer’s disease (LOAD) in an Iranian population. Methods: In this case-control study, 150 patients with LOAD and 150 unrelated healthy controls were recruited. Polymerase chain reaction (PCR) was performed to amplify a DNA segment of 263 base-pair (bp) length containing the single nucleotide polymorphism (SNP). The PCR product was then incubated with MvaI restriction enzyme to undergo enzymatic cleavage. Electrophoresis was thereafter carried out using agarose gel and DNA safe stain. The gel was ultimately visualized under a UV trans-illuminator. Allelic and genotypic frequencies were then compared. Results: A allele (mutant) of the gene was significantly associated with the risk of AD after adjustment for sex and age (p = 0.04, adjusted OR:1.77, 95% CI:1.00–3.11). Only AA genotype (mutant homozygote) was significantly associated with the risk of AD after adjustment for sex and age (p = 0.01, adjusted OR:2.39, 95% CI:1.22–4.66). Conclusion: SNP rs1801278 is significantly associated with the risk of developing AD in the studied Iranian population.
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Affiliation(s)
- Parham Niyasti
- School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Alia Saberi
- Neuroscience Research Center, Department of Neurology, Poursina Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Hamidreza Hatamyain
- Neuroscience Research Center, Department of Neurology, Poursina Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Farzam Ajamian
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Samaneh Ghorbani Shirkouhi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
- Neuroscience Research Center, Poursina Hospital, Guilan University of MedicalSciences, Rasht, Iran
| | - Laleh Mirzanejad
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Sasan Andalib
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Research Unit of Clinical Physiology and Nuclear Medicine, Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark
- Neuroscience Research Center, Poursina Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
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12
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Abstract
Alzheimer's disease (AD) is a complex and multifactorial neurodegenerative disease. Due to its long clinical course and lack of an effective treatment, AD has become a major public health problem in the USA and worldwide. Due to variation in age-at-onset, AD is classified into early-onset (< 60 years) and late-onset (≥ 60 years) forms with early-onset accounting for only 5-10% of all cases. With the exception of a small number of early-onset cases that are afflicted because of high penetrant single gene mutations in APP, PSEN1, and PSEN2 genes, AD is genetically heterogeneous, especially the late-onset form having a polygenic or oligogenic risk inheritance. Since the identification of APOE as the most significant risk factor for late-onset AD in 1993, the path to the discovery of additional AD risk genes had been arduous until 2009 when the use of large genome-wide association studies opened up the discovery gateways that led the identification of ~ 95 additional risk loci from 2009 to early 2022. This article reviews the history of AD genetics followed by the potential molecular pathways and recent application of functional genomics methods to identify the causal AD gene(s) among the many genes that reside within a single locus. The ultimate goal of integrating genomics and functional genomics is to discover novel pathways underlying the AD pathobiology in order to identify drug targets for the therapeutic treatment of this heterogeneous disorder.
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Affiliation(s)
- M Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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13
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Genetically regulated expression in late-onset Alzheimer's disease implicates risk genes within known and novel loci. Transl Psychiatry 2021; 11:618. [PMID: 34873149 PMCID: PMC8648734 DOI: 10.1038/s41398-021-01677-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 12/22/2022] Open
Abstract
Late-onset Alzheimer disease (LOAD) is highly polygenic, with a heritability estimated between 40 and 80%, yet risk variants identified in genome-wide studies explain only ~8% of phenotypic variance. Due to its increased power and interpretability, genetically regulated expression (GReX) analysis is an emerging approach to investigate the genetic mechanisms of complex diseases. Here, we conducted GReX analysis within and across 51 tissues on 39 LOAD GWAS data sets comprising 58,713 cases and controls from the Alzheimer's Disease Genetics Consortium (ADGC) and the International Genomics of Alzheimer's Project (IGAP). Meta-analysis across studies identified 216 unique significant genes, including 72 with no previously reported LOAD GWAS associations. Cross-brain-tissue and cross-GTEx models revealed eight additional genes significantly associated with LOAD. Conditional analysis of previously reported loci using established LOAD-risk variants identified eight genes reaching genome-wide significance independent of known signals. Moreover, the proportion of SNP-based heritability is highly enriched in genes identified by GReX analysis. In summary, GReX-based meta-analysis in LOAD identifies 216 genes (including 72 novel genes), illuminating the role of gene regulatory models in LOAD.
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14
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Rowe TW, Katzourou IK, Stevenson-Hoare JO, Bracher-Smith MR, Ivanov DK, Escott-Price V. Machine learning for the life-time risk prediction of Alzheimer's disease: a systematic review. Brain Commun 2021; 3:fcab246. [PMID: 34805994 PMCID: PMC8598986 DOI: 10.1093/braincomms/fcab246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022] Open
Abstract
Alzheimer’s disease is a neurodegenerative disorder and the most common form of dementia. Early diagnosis may assist interventions to delay onset and reduce the progression rate of the disease. We systematically reviewed the use of machine learning algorithms for predicting Alzheimer’s disease using single nucleotide polymorphisms and instances where these were combined with other types of data. We evaluated the ability of machine learning models to distinguish between controls and cases, while also assessing their implementation and potential biases. Articles published between December 2009 and June 2020 were collected using Scopus, PubMed and Google Scholar. These were systematically screened for inclusion leading to a final set of 12 publications. Eighty-five per cent of the included studies used the Alzheimer's Disease Neuroimaging Initiative dataset. In studies which reported area under the curve, discrimination varied (0.49–0.97). However, more than half of the included manuscripts used other forms of measurement, such as accuracy, sensitivity and specificity. Model calibration statistics were also found to be reported inconsistently across all studies. The most frequent limitation in the assessed studies was sample size, with the total number of participants often numbering less than a thousand, whilst the number of predictors usually ran into the many thousands. In addition, key steps in model implementation and validation were often not performed or unreported, making it difficult to assess the capability of machine learning models.
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Affiliation(s)
- Thomas W Rowe
- UK Dementia Research Institute, Cardiff University, Cardiff, UK
| | | | | | - Matthew R Bracher-Smith
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Dobril K Ivanov
- UK Dementia Research Institute, Cardiff University, Cardiff, UK
| | - Valentina Escott-Price
- UK Dementia Research Institute, Cardiff University, Cardiff, UK.,Division of Psychological Medicine and Clinical Neurosciences, School of Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
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15
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The potential roles of genetic factors in predicting ageing-related cognitive change and Alzheimer's disease. Ageing Res Rev 2021; 70:101402. [PMID: 34242808 DOI: 10.1016/j.arr.2021.101402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/22/2021] [Accepted: 07/02/2021] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a complex neurological disorder of uncertain aetiology, although substantial research has been conducted to explore important factors related to risk of onset and progression. Both lifestyle (e.g., complex mental stimulation, vascular health) and genetic factors (e.g., APOE, BDNF, PICALM, CLU, APP, PSEN1, PSEN2, and other genes) have been associated with AD risk. Despite more than thirty years of genetic research, much of the heritability of AD is not explained by measured loci. This suggests that the missing heritability of AD might be potentially related to rare variants, gene-environment and gene-gene interactions, and potentially epigenetic modulators. Moreover, while ageing is the most substantial factor risk for AD, there are limited longitudinal studies examining the association of genetic factors with decline in cognitive function due to ageing and the preclinical stages of this condition. This review summarises findings from currently available research on the genetic factors of ageing-related cognitive change and AD and suggests some future research directions.
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16
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Blumenthal DB, Baumbach J, Hoffmann M, Kacprowski T, List M. A framework for modeling epistatic interaction. Bioinformatics 2021; 37:1708-1716. [PMID: 33252645 DOI: 10.1093/bioinformatics/btaa990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/21/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Recently, various tools for detecting single nucleotide polymorphisms (SNPs) involved in epistasis have been developed. However, no studies evaluate the employed statistical epistasis models such as the χ2-test or quadratic regression independently of the tools that use them. Such an independent evaluation is crucial for developing improved epistasis detection tools, for it allows to decide if a tool's performance should be attributed to the epistasis model or to the optimization strategy run on top of it. RESULTS We present a protocol for evaluating epistasis models independently of the tools they are used in and generalize existing models designed for dichotomous phenotypes to the categorical and quantitative case. In addition, we propose a new model which scores candidate SNP sets by computing maximum likelihood distributions for the observed phenotypes in the cells of their penetrance tables. Extensive experiments show that the proposed maximum likelihood model outperforms three widely used epistasis models in most cases. The experiments also provide valuable insights into the properties of existing models, for instance, that quadratic regression perform particularly well on instances with quantitative phenotypes. AVAILABILITY AND IMPLEMENTATION The evaluation protocol and all compared models are implemented in C++ and are supported under Linux and macOS. They are available at https://github.com/baumbachlab/genepiseeker/, along with test datasets and scripts to reproduce the experiments. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David B Blumenthal
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus Hoffmann
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Tim Kacprowski
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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17
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Hsieh TJ, Lee WJ, Liao YC, Hsu CC, Fang YH, Chen TY, Lin YS, Chang IS, Wang SJ, Hsiung CA, Fuh JL. Association between Alzheimer's disease genes and trajectories of cognitive function decline in Han Chinese in Taiwan. Aging (Albany NY) 2021; 13:17237-17252. [PMID: 34214049 PMCID: PMC8312434 DOI: 10.18632/aging.203204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 06/08/2021] [Indexed: 01/01/2023]
Abstract
Genetic background has been considered one of the important contributors to the rate of cognitive decline among patients with Alzheimer’s disease (AD). We conducted a 4-year longitudinal follow-up study, recruited 255 AD and 44 mild cognitive impairment (MCI) patients, and used a data-driven trajectory analysis to examine the influence of selected AD risk genes on the age for and the rate of cognitive decline in Han Chinese population. Genotyping of selected single-nucleotide polymorphisms in the APOE, ABCA7, SORL1, BIN1, GAB2, and CD33 genes was conducted, and a Bayesian hierarchical model was fitted to analyze the trajectories of cognitive decline among different genotypes. After adjusting for sex and education years, the APOE ε4 allele was associated with an earlier mean change of −2.39 years in the age at midpoint of cognitive decline, the G allele in ABCA7 rs3764650 was associated with an earlier mean change of −1.75 years, and the T allele in SORL1 rs3737529 was associated with a later mean change of 2.6 years. Additionally, the rate of cognitive decline was associated with the APOE ε4 allele and SORL1 rs3737529. In summary, APOE and SORL1 might be the most important genetic factors related to cognitive decline in Han Chinese population.
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Affiliation(s)
- Tsung-Jen Hsieh
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan.,School of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Wei-Ju Lee
- Neurological Institute, Taichung Veterans General Hospital, Taichung, Taiwan.,Faculty of Medicine, National Yang-Ming University Schools of Medicine, Taipei, Taiwan.,Dementia Center, Taichung Veterans General Hospital, Taichung, Taiwan.,Center for Geriatrics and Gerontology, Taichung Veterans General Hospital, Taichung, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chu Liao
- Faculty of Medicine, National Yang-Ming University Schools of Medicine, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chih-Cheng Hsu
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Yao-Hwei Fang
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Tzu-Yu Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Yung-Shuan Lin
- Faculty of Medicine, National Yang-Ming University Schools of Medicine, Taipei, Taiwan.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Shuu-Jiun Wang
- Faculty of Medicine, National Yang-Ming University Schools of Medicine, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Jong-Ling Fuh
- Faculty of Medicine, National Yang-Ming University Schools of Medicine, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
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18
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Scaffolding protein Gab2 is involved in postnatal development and lipopolysaccharide-induced activation of microglia in the mouse brain. Biochem Biophys Res Commun 2021; 567:112-117. [PMID: 34146905 DOI: 10.1016/j.bbrc.2021.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022]
Abstract
Grb2-associated-binding protein-2 (Gab2) is a member of the Gab/DOS family and functions as an adapter protein downstream of several growth factor signaling pathways. Gab2 is considered an Alzheimer's disease susceptibility gene. However, the role of Gab2 in the brain is still largely unknown. Herein, we report that Gab2 is involved in the postnatal development of microglia in mice. The Gab2 expression in the brain was detected at postnatal day 1 (P1) and increased until P14 but decreased thereafter. The tyrosine phosphorylation of Gab2 (pGab2) was also detected at P1 and increased until P14. Next, we focused on microglial development in Gab2 knockout and heterozygous mice. Although differences were not detected in the cytoplasmic area of Iba1-labeled microglia between Gab2(±) and Gab2(-/-) mice, the analysis of CD68 and cathepsin D (indicators of microglial lysosomal activation) immunolabeling within Iba1+ cells revealed significant underdevelopment of microglial lysosomes in Gab2(-/-) mice at P60. In addition to the developmental abnormality of microglia in Gab2(-/-) mice, lipopolysaccharide-induced lysosomal activation was selectively suppressed in Gab2(-/-) mice compared to that in Gab2(±) mice. Our findings suggest that Gab2 is involved not only in postnatal development but also in lysosomal activation of microglia, therefore Gab2 dysfunction in microglia might potentially contribute to the development of neurodegenerative diseases.
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19
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Kondreddy V, Magisetty J, Keshava S, Rao LVM, Pendurthi UR. Gab2 (Grb2-Associated Binder2) Plays a Crucial Role in Inflammatory Signaling and Endothelial Dysfunction. Arterioscler Thromb Vasc Biol 2021; 41:1987-2005. [PMID: 33827252 PMCID: PMC8147699 DOI: 10.1161/atvbaha.121.316153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/19/2021] [Indexed: 01/21/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Vijay Kondreddy
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler
| | - Jhansi Magisetty
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler
| | - Shiva Keshava
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler
| | - L. Vijaya Mohan Rao
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler
| | - Usha R. Pendurthi
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler
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20
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Ruffini N, Klingenberg S, Schweiger S, Gerber S. Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale. Cells 2020; 9:E2642. [PMID: 33302607 PMCID: PMC7764447 DOI: 10.3390/cells9122642] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/24/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS) are heterogeneous, progressive diseases with frequently overlapping symptoms characterized by a loss of neurons. Studies have suggested relations between neurodegenerative diseases for many years (e.g., regarding the aggregation of toxic proteins or triggering endogenous cell death pathways). We gathered publicly available genomic, transcriptomic, and proteomic data from 177 studies and more than one million patients to detect shared genetic patterns between the neurodegenerative diseases on three analyzed omics-layers. The results show a remarkably high number of shared differentially expressed genes between the transcriptomic and proteomic levels for all conditions, while showing a significant relation between genomic and proteomic data between AD and PD and AD and ALS. We identified a set of 139 genes being differentially expressed in several transcriptomic experiments of all four diseases. These 139 genes showed overrepresented gene ontology (GO) Terms involved in the development of neurodegeneration, such as response to heat and hypoxia, positive regulation of cytokines and angiogenesis, and RNA catabolic process. Furthermore, the four analyzed neurodegenerative diseases (NDDs) were clustered by their mean direction of regulation throughout all transcriptomic studies for this set of 139 genes, with the closest relation regarding this common gene set seen between AD and HD. GO-Term and pathway analysis of the proteomic overlap led to biological processes (BPs), related to protein folding and humoral immune response. Taken together, we could confirm the existence of many relations between Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis on transcriptomic and proteomic levels by analyzing the pathways and GO-Terms arising in these intersections. The significance of the connection and the striking relation of the results to processes leading to neurodegeneration between the transcriptomic and proteomic data for all four analyzed neurodegenerative diseases showed that exploring many studies simultaneously, including multiple omics-layers of different neurodegenerative diseases simultaneously, holds new relevant insights that do not emerge from analyzing these data separately. Furthermore, the results shed light on processes like the humoral immune response that have previously been described only for certain diseases. Our data therefore suggest human patients with neurodegenerative diseases should be addressed as complex biological systems by integrating multiple underlying data sources.
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Affiliation(s)
- Nicolas Ruffini
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
- Leibniz Institute for Resilience Research, Leibniz Association, Wallstraße 7, 55122 Mainz, Germany
| | - Susanne Klingenberg
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susann Schweiger
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
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21
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Huang Y, Zhang T, Chen L, Yu M, Liu Q, Zhou C, Tang Q, Zhou L, Zhan H, Li J, Xu K, Lin J. Elevated expressions of SHP2 and GAB2 correlated with VEGF in eutopic and ectopic endometrium of women with ovarian endometriosis. Gynecol Endocrinol 2020; 36:813-818. [PMID: 32619126 DOI: 10.1080/09513590.2020.1787378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Aims: Protein tyrosine phosphatase Src-homology-2-domain-containing phosphatase 2 (SHP2) and adaptor protein Grb2-associated binding protein 2 (GAB2) can bind to each other in various signal transduction. However, the expression of SHP2 and GAB2 have not been investigated in endometriosis. The aim of the study was to evaluate the expressions of SHP2 and GAB2, and explore the correlation with Ki67 and VEGF in ovarian endometriosis.Materials and methods: The protein expressions and localizations were assessed immunohistochemically in ectopic, eutopic endometrium and normal endometrium from patients with (n = 30) and without (n = 30) ovarian endometriosis.Results: SHP2 was mainly present in the endometrial glandular epithelium, with increased expression in eutopic endometrium and even higher expression in ectopic endometrium compared to control endometrium (p < .05). GAB2 was immunolocalized in endometrial epithelium and stroma, increasing its expression from control endometrium to eutopic and ectopic endometrium (p < .05). Positive correlation was found between SHP2 and GAB2 in endometrium (p < .01). SHP2 and GAB2 both positively correlated with VEGF (p < .05), but not Ki67 in endometrium.Conclusions: We provide the first evidence that the protein expressions of SHP2 and GAB2 were elevated in ectopic and eutopic endometrium, suggesting GAB2-SHP2 axis regulating VEGF might contribute to the pathomechanism of endometriosis.
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Affiliation(s)
- Yizhou Huang
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Tao Zhang
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Liqing Chen
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Minghua Yu
- Department of Pathology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qin Liu
- Department of Pathology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Caiyun Zhou
- Department of Pathology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qile Tang
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, People's Republic of China
| | - Linpo Zhou
- School of Medicine, Zhejiang University City College, Hangzhou, People's Republic of China
| | - Hong Zhan
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Juanqing Li
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Kaihong Xu
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Jun Lin
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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Neuner SM, Tcw J, Goate AM. Genetic architecture of Alzheimer's disease. Neurobiol Dis 2020; 143:104976. [PMID: 32565066 PMCID: PMC7409822 DOI: 10.1016/j.nbd.2020.104976] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023] Open
Abstract
Advances in genetic and genomic technologies over the last thirty years have greatly enhanced our knowledge concerning the genetic architecture of Alzheimer's disease (AD). Several genes including APP, PSEN1, PSEN2, and APOE have been shown to exhibit large effects on disease susceptibility, with the remaining risk loci having much smaller effects on AD risk. Notably, common genetic variants impacting AD are not randomly distributed across the genome. Instead, these variants are enriched within regulatory elements active in human myeloid cells, and to a lesser extent liver cells, implicating these cell and tissue types as critical to disease etiology. Integrative approaches are emerging as highly effective for identifying the specific target genes through which AD risk variants act and will likely yield important insights related to potential therapeutic targets in the coming years. In the future, additional consideration of sex- and ethnicity-specific contributions to risk as well as the contribution of complex gene-gene and gene-environment interactions will likely be necessary to further improve our understanding of AD genetic architecture.
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Affiliation(s)
- Sarah M Neuner
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Julia Tcw
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alison M Goate
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
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23
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The Interaction Between Contactin and Amyloid Precursor Protein and Its Role in Alzheimer’s Disease. Neuroscience 2020; 424:184-202. [DOI: 10.1016/j.neuroscience.2019.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 01/06/2023]
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24
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Ertuzun T, Semerci A, Cakir ME, Ekmekcioglu A, Gok MO, Soltys DT, de Souza-Pinto NC, Sezerman U, Muftuoglu M. Investigation of base excision repair gene variants in late-onset Alzheimer's disease. PLoS One 2019; 14:e0221362. [PMID: 31415677 PMCID: PMC6695184 DOI: 10.1371/journal.pone.0221362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/05/2019] [Indexed: 12/03/2022] Open
Abstract
Base excision repair (BER) defects and concomitant oxidative DNA damage accumulation play a role in the etiology and progression of late-onset Alzheimer’s disease (LOAD). However, it is not known whether genetic variant(s) of specific BER genes contribute to reduced BER activity in LOAD patients and whether they are associated with risk, development and/or progression of LOAD. Therefore, we performed targeted next generation sequencing for three BER genes, uracil glycosylase (UNG), endonuclease VIII-like DNA glycosylase 1 (NEIL1) and polymerase β (POLβ) including promoter, exonic and intronic regions in peripheral blood samples and postmortem brain tissues (temporal cortex, TC and cerebellum, CE) from LOAD patients, high-pathology control and cognitively normal age-matched controls. In addition, the known LOAD risk factor, APOE was included in this study to test whether any BER gene variants associate with APOE variants, particularly APOE ε4. We show that UNG carry five significant variants (rs1610925, rs2268406, rs80001089, rs1018782 and rs1018783) in blood samples of Turkish LOAD patients compared to age-matched controls and one of them (UNG rs80001089) is also significant in TC from Brazilian LOAD patients (p<0.05). The significant variants present only in CE and TC from LOAD are UNG rs2569987 and POLβ rs1012381950, respectively. There is also significant epistatic relationship (p = 0.0410) between UNG rs80001089 and NEIL1 rs7182283 in TC from LOAD subjects. Our results suggest that significant BER gene variants may be associated with the risk of LOAD in non-APOE ε4 carriers. On the other hand, there are no significant UNG, NEIL1 and POLβ variants that could affect their protein level and function, suggesting that there may be other factors such as post-transcriptional or–translational modifications responsible for the reduced activities and protein levels of these genes in LOAD pathogenesis. Further studies with increased sample size are needed to confirm the relationship between BER variants and LOAD risk.
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Affiliation(s)
- Tugce Ertuzun
- Department of Molecular Biology and Genetics
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Asli Semerci
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Mehmet Emin Cakir
- Department of Neurology, Medeniyet University, Goztepe Training and Research Hospital, Istanbul, Turkey
| | - Aysegul Ekmekcioglu
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Mehmet Oguz Gok
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Daniela T. Soltys
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Nadja C. de Souza-Pinto
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ugur Sezerman
- Department of Biostatistics and Medical Informatics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Meltem Muftuoglu
- Department of Molecular Biology and Genetics
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- * E-mail:
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25
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Zhang C, Hu R, Zhang G, Zhe Y, Hu B, He J, Wang Z, Qi X. A Weighted Genetic Risk Score Based on Four APOE-Independent Alzheimer’s Disease Risk Loci May Supplement APOE E4 for Better Disease Prediction. J Mol Neurosci 2019; 69:433-443. [DOI: 10.1007/s12031-019-01372-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 06/26/2019] [Indexed: 12/13/2022]
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26
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Kim Y, Liu G, Leugers CJ, Mueller JD, Francis MB, Hefti MM, Schneider JA, Lee G. Tau interacts with SHP2 in neuronal systems and in Alzheimer's disease brains. J Cell Sci 2019; 132:jcs.229054. [PMID: 31201283 DOI: 10.1242/jcs.229054] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/05/2019] [Indexed: 01/14/2023] Open
Abstract
Microtubule-associated protein tau, an integral component of neurofibrillary tangles, interacts with a variety of signaling molecules. Previously, our laboratory reported that nerve growth factor (NGF)-induced MAPK activation in a PC12-derived cell line was potentiated by tau, with phosphorylation at T231 being required. Therefore, we sought to identify a signaling molecule involved in the NGF-induced Ras-MAPK pathway that interacted with phospho-T231-tau. Here, we report that the protein tyrosine phosphatase SHP2 (also known as PTPN11) interacted with tau, with phospho-T231 significantly enhancing the interaction. By using proximity ligation assays, we found that endogenous tau-SHP2 complexes were present in neuronal cells, where the number of tau-SHP2 complexes significantly increased when the cells were treated with NGF, with phosphorylation at T231 being required for the increase. The interaction did not require microtubule association, and an association between tau and activated SHP2 was also found. Tau-SHP2 complexes were also found in both primary mouse hippocampal cultures and adult mouse brain. Finally, SHP2 levels were upregulated in samples from patients with mild and severe Alzheimer's disease (AD), and the level of tau-SHP2 complexes were increased in AD patient samples. These findings strongly suggest a role for the tau-SHP2 interaction in NGF-stimulated neuronal development and in AD.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yohan Kim
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Guanghao Liu
- Interdisciplinary Program in Neuroscience, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Chad J Leugers
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Joseph D Mueller
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Meghan B Francis
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Marco M Hefti
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Julie A Schneider
- Department of Pathology, Rush Medical College, Chicago, IL 60612, USA
| | - Gloria Lee
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA .,Interdisciplinary Program in Neuroscience, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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27
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He K, Nie L, Zhou Q, Rahman SU, Liu J, Yang X, Li S. Proteomic Profiles of the Early Mitochondrial Changes in APP/PS1 and ApoE4 Transgenic Mice Models of Alzheimer’s Disease. J Proteome Res 2019; 18:2632-2642. [DOI: 10.1021/acs.jproteome.9b00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kaiwu He
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan
District, Shenzhen 518055, PR China
| | - Lulin Nie
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan
District, Shenzhen 518055, PR China
| | - Qiang Zhou
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Shafiq Ur Rahman
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
- Department of Pharmacy, Shaheed Benazir Bhutto University, Sheringal, Dir, 18000, Pakistan
| | - Jianjun Liu
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan
District, Shenzhen 518055, PR China
| | - Xifei Yang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan
District, Shenzhen 518055, PR China
| | - Shupeng Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
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28
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Hishimoto A, Pletnikova O, Lang DL, Troncoso JC, Egan JM, Liu QR. Neurexin 3 transmembrane and soluble isoform expression and splicing haplotype are associated with neuron inflammasome and Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2019; 11:28. [PMID: 30902061 PMCID: PMC6429815 DOI: 10.1186/s13195-019-0475-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/17/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Synaptic damage precedes neuron death in Alzheimer's disease (AD). Neurexins, NRXN1, NRXN2, and NRXN3, are presynaptic adhesion molecules that specify neuron synapses and regulate neurotransmitter release. Neurexins and postsynaptic neuroligins interact with amyloid beta oligomer (AβO) deposits in damaged synapses. NRXN3 gene variants have been associated with autism, addiction, and schizophrenia, however, not fully investigated in Alzheimer's disease. In the present study, we investigated an AD association of a 3'-splicing allele of rs8019381 that produces altered expression of transmembrane or soluble NRXN3 isoforms. METHODS We carried out RT-PCR (reverse transcription polymerase chain reaction), PCR-RFLP (PCR and restriction fragment length polymorphism), Sanger sequencing, and in situ hybridization (ISH) assays for NRXN3 neuron expression and genotyping. Genetic associations were analyzed by χ2 tests, and ISH signals were analyzed by FISH v1.0 module of Indica Labs HALO software. RESULTS We previously identified a functional haplotype in the 3' region of neurexin 3 (NRXN3) gene that alters the expression ratios between NRXN3 transmembrane and soluble isoforms. In this study, we found that expression and ratio of transmembrane and soluble NRXN3 isoforms were reduced in AD postmortem brains and inversely correlated with inflammasome component NLRP3 in AD brain regions. The splicing haplotype related to the transmembrane and soluble NRXN3 expression was associated with AD samples with P = 6.3 × 10-5 (odds ratio = 2.48) and interacted with APOE genotypes. CONCLUSIONS We found that the SNP rs8019381 of NRXN3 that is located adjacent to splicing site #5 (SS#5) interacts with the APOE ε4 haplotype and alters NRXN3 transmembrane or soluble isoform expression in AD postmortem cortex. Dysregulation of presynaptic NRXN3 expression and splicing might increase neuron inflammation in AD brain.
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Affiliation(s)
- Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe, 650-0017, Japan
| | - Olga Pletnikova
- Departments of Pathology, Neuropathology Division, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Doyle Lu Lang
- Lab of Clinical Investigation, NIA-NIH, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Juan C Troncoso
- Departments of Pathology, Neuropathology Division, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Josephine M Egan
- Lab of Clinical Investigation, NIA-NIH, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Qing-Rong Liu
- Lab of Clinical Investigation, NIA-NIH, 251 Bayview Blvd, Baltimore, MD, 21224, USA.
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29
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Jochner MCE, An J, Lättig-Tünnemann G, Kirchner M, Dagane A, Dittmar G, Dirnagl U, Eickholt BJ, Harms C. Unique properties of PTEN-L contribute to neuroprotection in response to ischemic-like stress. Sci Rep 2019; 9:3183. [PMID: 30816308 PMCID: PMC6395706 DOI: 10.1038/s41598-019-39438-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/14/2018] [Indexed: 12/18/2022] Open
Abstract
Phosphatase and tensin homolog (PTEN) signalling might influence neuronal survival after brain ischemia. However, the influence of the less studied longer variant termed PTEN-L (or PTENα) has not been studied to date. Therefore, we examined the translational variant PTEN-L in the context of neuronal survival. We identified PTEN-L by proteomics in murine neuronal cultures and brain lysates and established a novel model to analyse PTEN or PTEN-L variants independently in vitro while avoiding overexpression. We found that PTEN-L, unlike PTEN, localises predominantly in the cytosol and translocates to the nucleus 10-20 minutes after glutamate stress. Genomic ablation of PTEN and PTEN-L increased neuronal susceptibility to oxygen-glucose deprivation. This effect was rescued by expression of either PTEN-L indicating that both PTEN isoforms might contribute to a neuroprotective response. However, in direct comparison, PTEN-L replaced neurons were protected against ischemic-like stress compared to neurons expressing PTEN. Neurons expressing strictly nuclear PTEN-L NLS showed increased vulnerability, indicating that nuclear PTEN-L alone is not sufficient in protecting against stress. We identified mutually exclusive binding partners of PTEN-L or PTEN in cytosolic or nuclear fractions, which were regulated after ischemic-like stress. GRB2-associated-binding protein 2, which is known to interact with phosphoinositol-3-kinase, was enriched specifically with PTEN-L in the cytosol in proximity to the plasma membrane and their interaction was lost after glutamate exposure. The present study revealed that PTEN and PTEN-L have distinct functions in response to stress and might be involved in different mechanisms of neuroprotection.
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Affiliation(s)
- Magdalena C E Jochner
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Neurocure Cluster of Excellence, Department of Experimental Neurology, Berlin, Germany
- Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), QUEST-Centre for Transforming Biomedical Research, 10178 Berlin, Germany
| | - Junfeng An
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Neurocure Cluster of Excellence, Department of Experimental Neurology, Berlin, Germany
- Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Medical Research Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gisela Lättig-Tünnemann
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Neurocure Cluster of Excellence, Department of Experimental Neurology, Berlin, Germany
- Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Centre for Molecular Medicine (MDC), Proteomics Platform, Robert-Rössle-Straße 10, 13125, Berlin, Germany
- Berlin Institute of Health (BIH), Proteomics Platform, 10178 Berlin, Germany
| | - Alina Dagane
- Max Delbrück Centre for Molecular Medicine (MDC), Proteomics Platform, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Gunnar Dittmar
- Max Delbrück Centre for Molecular Medicine (MDC), Proteomics Platform, Robert-Rössle-Straße 10, 13125, Berlin, Germany
- Proteome and Genome Research Laboratory, Luxembourg institute of Health, 1a Rue Thomas Edison, 1224, Strassen, Luxembourg
| | - Ulrich Dirnagl
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Neurocure Cluster of Excellence, Department of Experimental Neurology, Berlin, Germany
- Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), QUEST-Centre for Transforming Biomedical Research, 10178 Berlin, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Charité-Universitätsmedizin Berlin, Institute of Biochemistry, Berlin, Germany
| | - Britta J Eickholt
- Charité-Universitätsmedizin Berlin, Institute of Biochemistry, Berlin, Germany
| | - Christoph Harms
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Neurocure Cluster of Excellence, Department of Experimental Neurology, Berlin, Germany.
- Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Institute of Health (BIH), QUEST-Centre for Transforming Biomedical Research, 10178 Berlin, Germany.
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Association between selected cholesterol-related gene polymorphisms and Alzheimer's disease in a Turkish cohort. Mol Biol Rep 2019; 46:1701-1707. [PMID: 30684189 DOI: 10.1007/s11033-019-04619-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
Abstract
Numerous genetic evidence has pointed out that variations in cholesterol-related genes may be associated with an Alzheimer's disease (AD) risk. We aimed to investigate the association between polymorphisms in several cholesterol-related genes [APOA5 (rs662799), APOC1 (rs11568822), APOD (rs1568565), CH25H (rs13500), LDLR (rs5930), SORL1 (rs2282649)] and AD in a cohort of Turkish patients. The study group consisted of 257 AD patients (mean age: 75.9 years ± 10.4) and 414 controls (mean age: 62.2 years ± 13.1). Genotyping was performed by quantitative real-time polymerase chain reaction using hydrolysis probes. Our results showed that the 'TT' genotype of CH25H rs13500 polymorphism was significantly more frequent in the AD group (p < 0.001) and individuals carrying the CH25H 'T' allele had an increased risk for AD (OR 3.07, 95% CI 2.13-4.44, p = 2.20e-09) independently from age, gender and APOE ε4 allele. Moreover, this risk was excessively increased (OR 14.04, 95% CI 6.99-28.23, p = 9.78e-14) in the presence of APOE ε4 allele. The 'ins/ins' genotype of APOC1 rs11568822 was significantly more frequent in the AD group compared to controls (p = 1.95e-08). However, this increased AD risk in 'ins/ins' carriers was found to be dependent on their APOE ε4 carrier status. No significant associations were found in allele and genotype distributions of APOA5, APOD, LDLR and SORL1 gene polymorphisms. Our results suggest that the association between APOC1 'ins/ins' genotype and AD risk can be explained by linkage disequilibrium with the APOE locus. CH25H rs13500 polymorphism is associated with an AD risk in the Turkish population and CH25H might have a role in the pathogenesis of AD together with, and independently from APOE.
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31
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García JC, Bustos RH. The Genetic Diagnosis of Neurodegenerative Diseases and Therapeutic Perspectives. Brain Sci 2018; 8:brainsci8120222. [PMID: 30551598 PMCID: PMC6316116 DOI: 10.3390/brainsci8120222] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/26/2018] [Accepted: 12/07/2018] [Indexed: 12/12/2022] Open
Abstract
Genetics has led to a new focus regarding approaches to the most prevalent diseases today. Ascertaining the molecular secrets of neurodegenerative diseases will lead to developing drugs that will change natural history, thereby affecting the quality of life and mortality of patients. The sequencing of candidate genes in patients suffering neurodegenerative pathologies is faster, more accurate, and has a lower cost, thereby enabling algorithms to be proposed regarding the risk of neurodegeneration onset in healthy persons including the year of onset and neurodegeneration severity. Next generation sequencing has resulted in an explosion of articles regarding the diagnosis of neurodegenerative diseases involving exome sequencing or sequencing a whole gene for correlating phenotypical expression with genetic mutations in proteins having key functions. Many of them occur in neuronal glia, which can trigger a proinflammatory effect leading to defective proteins causing sporadic or familial mutations. This article reviews the genetic diagnosis techniques and the importance of bioinformatics in interpreting results from neurodegenerative diseases. Risk scores must be established in the near future regarding diseases with a high incidence in healthy people for defining prevention strategies or an early start for giving drugs in the absence of symptoms.
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Affiliation(s)
- Julio-César García
- Evidence-Based Therapeutics Group, Department of Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia.
- Department of Clinical Pharmacology, Clínica Universidad de La Sabana, Chía 140013, Colombia.
| | - Rosa-Helena Bustos
- Evidence-Based Therapeutics Group, Department of Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia.
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32
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Shi Z, Yu H, Wu Y, Ford M, Perschon C, Wang C, Zheng SL, Xu J. Genetic risk score modifies the effect of APOE on risk and age onset of Alzheimer's disease. Clin Genet 2018; 95:302-309. [PMID: 30460685 DOI: 10.1111/cge.13479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 01/08/2023]
Abstract
Single nucleotide polymorphism (SNP)-based genetic risk score (GRS) and APOE genotype are both important in risk prediction of Alzheimer's disease (AD); however, the interaction between GRS and APOE has not been extensively investigated. Our objective was to determine whether GRS modifies the APOE effect on AD risk and age at onset (AAO). The study included 774 AD cases and 767 controls of European descent. Population standardized GRS was calculated based on 17 previously implicated AD risk-associated SNPs. Association was analyzed using logistic regression, Cox proportional hazards model and Kaplan-Meier curve. We found that GRS was significantly associated with AD risk and the association was stronger among APOE ε4 carriers. Compared to ε4 non-carriers, the Odds Ratio (OR) for AD was 8.09 (95% Confidence Interval [CI]: 4.98-13.63) for ε4 carriers with high-GRS (≥1.5). In contrast, the OR was 2.55 (95% CI: 1.46-4.49) for ε4 carriers with low-GRS (<0.6). In conclusion, these results suggest SNP-based GRS may supplement APOE for better assessment of inherited risk and age of onset of AD.
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Affiliation(s)
- Zhuqing Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Yishuo Wu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Madison Ford
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chihsiung Wang
- Center for Biomedical Research Informatics, NorthShore University Health System, Evanston, Illinois
| | - Siqun L Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
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33
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Lemche E. Early Life Stress and Epigenetics in Late-onset Alzheimer's Dementia: A Systematic Review. Curr Genomics 2018; 19:522-602. [PMID: 30386171 PMCID: PMC6194433 DOI: 10.2174/1389202919666171229145156] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 07/27/2017] [Accepted: 12/12/2017] [Indexed: 11/22/2022] Open
Abstract
Involvement of life stress in Late-Onset Alzheimer's Disease (LOAD) has been evinced in longitudinal cohort epidemiological studies, and endocrinologic evidence suggests involvements of catecholamine and corticosteroid systems in LOAD. Early Life Stress (ELS) rodent models have successfully demonstrated sequelae of maternal separation resulting in LOAD-analogous pathology, thereby supporting a role of insulin receptor signalling pertaining to GSK-3beta facilitated tau hyper-phosphorylation and amyloidogenic processing. Discussed are relevant ELS studies, and findings from three mitogen-activated protein kinase pathways (JNK/SAPK pathway, ERK pathway, p38/MAPK pathway) relevant for mediating environmental stresses. Further considered were the roles of autophagy impairment, neuroinflammation, and brain insulin resistance. For the meta-analytic evaluation, 224 candidate gene loci were extracted from reviews of animal studies of LOAD pathophysiological mechanisms, of which 60 had no positive results in human LOAD association studies. These loci were combined with 89 gene loci confirmed as LOAD risk genes in previous GWAS and WES. Of the 313 risk gene loci evaluated, there were 35 human reports on epigenomic modifications in terms of methylation or histone acetylation. 64 microRNA gene regulation mechanisms were published for the compiled loci. Genomic association studies support close relations of both noradrenergic and glucocorticoid systems with LOAD. For HPA involvement, a CRHR1 haplotype with MAPT was described, but further association of only HSD11B1 with LOAD found; however, association of FKBP1 and NC3R1 polymorphisms was documented in support of stress influence to LOAD. In the brain insulin system, IGF2R, INSR, INSRR, and plasticity regulator ARC, were associated with LOAD. Pertaining to compromised myelin stability in LOAD, relevant associations were found for BIN1, RELN, SORL1, SORCS1, CNP, MAG, and MOG. Regarding epigenetic modifications, both methylation variability and de-acetylation were reported for LOAD. The majority of up-to-date epigenomic findings include reported modifications in the well-known LOAD core pathology loci MAPT, BACE1, APP (with FOS, EGR1), PSEN1, PSEN2, and highlight a central role of BDNF. Pertaining to ELS, relevant loci are FKBP5, EGR1, GSK3B; critical roles of inflammation are indicated by CRP, TNFA, NFKB1 modifications; for cholesterol biosynthesis, DHCR24; for myelin stability BIN1, SORL1, CNP; pertaining to (epi)genetic mechanisms, hTERT, MBD2, DNMT1, MTHFR2. Findings on gene regulation were accumulated for BACE1, MAPK signalling, TLR4, BDNF, insulin signalling, with most reports for miR-132 and miR-27. Unclear in epigenomic studies remains the role of noradrenergic signalling, previously demonstrated by neuropathological findings of childhood nucleus caeruleus degeneration for LOAD tauopathy.
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Affiliation(s)
- Erwin Lemche
- Section of Cognitive Neuropsychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
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34
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Liu G, Wang T, Tian R, Hu Y, Han Z, Wang P, Zhou W, Ren P, Zong J, Jin S, Jiang Q. Alzheimer's Disease Risk Variant rs2373115 Regulates GAB2 and NARS2 Expression in Human Brain Tissues. J Mol Neurosci 2018; 66:37-43. [PMID: 30088171 DOI: 10.1007/s12031-018-1144-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
Abstract
Genetic association studies have identified significant association between the GAB2 rs2373115 variant and Alzheimer's disease (AD). However, it is unknown whether rs2373115 affects the regulation of nearby genes. Here, we evaluate the potential effect of rs2373115 on gene expression using multiple eQTL (expression quantitative trait loci) datasets from human brain tissues from the Mayo Clinic brain expression genome-wide association study (eGWAS), the UK Brain Expression Consortium (UKBEC), the Genotype-Tissue Expression (GTEx) project, and the Brain xQTL Serve. Our findings indicate that the rs2373115 C allele is associated with increased NARS2 expression, and both reduced and increased GAB2 expression in human tissues. Using a large-scale AD case-control expression dataset, we found increased GAB2 expression and reduced NARS2 expression in AD cases compared with controls. We believe that our findings provide important information regarding the rs2373115 variant and expression of nearby genes with respect to AD risk.
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Affiliation(s)
- Guiyou Liu
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China.
| | - Tao Wang
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Rui Tian
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Yang Hu
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Zhifa Han
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Peng Ren
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Jian Zong
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Shuilin Jin
- Department of Mathematics, Harbin Institute of Technology, 1030, Science Building, Yikuang Street, Nangang District, Harbin, 150080, China.
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Room 307, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China.
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Kumar S, Yadav N, Pandey S, Thelma BK. Advances in the discovery of genetic risk factors for complex forms of neurodegenerative disorders: contemporary approaches, success, challenges and prospects. J Genet 2018. [DOI: 10.1007/s12041-018-0953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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36
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Kumar S, Yadav N, Pandey S, Thelma BK. Advances in the discovery of genetic risk factors for complex forms of neurodegenerative disorders: contemporary approaches, success, challenges and prospects. J Genet 2018; 97:625-648. [PMID: 30027900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Neurodegenerative diseases constitute a large proportion of disorders in elderly, majority being sporadic in occurrence with ∼5-10% familial. A strong genetic component underlies the Mendelian forms but nongenetic factors together with genetic vulnerability contributes to the complex sporadic forms. Several gene discoveries in the familial forms have provided novel insights into the pathogenesis of neurodegeneration with implications for treatment. Conversely, findings from genetic dissection of the sporadic forms, despite large genomewide association studies and more recently whole exome and whole genome sequencing, have been limited. This review provides a concise account of the genetics that we know, the pathways that they implicate, the challenges that are faced and the prospects that are envisaged for the sporadic, complex forms of neurodegenerative diseases, taking four most common conditions, namely Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington disease as examples. Poor replication across studies, inability to establish genotype-phenotype correlations and the overall failure to predict risk and/or prevent disease in this group poses a continuing challenge. Among others, clinical heterogeneity emerges as the most important impediment warranting newer approaches. Advanced computational and system biology tools to analyse the big data are being generated and the alternate strategy such as subgrouping of case-control cohorts based on deep phenotyping using the principles of Ayurveda to overcome current limitation of phenotype heterogeneity seem to hold promise. However, at this point, with advances in discovery genomics and functional analysis of putative determinants with translation potential for the complex forms being minimal, stem cell therapies are being attempted as potential interventions. In this context, the possibility to generate patient derived induced pluripotent stem cells, mutant/gene/genome correction through CRISPR/Cas9 technology and repopulating the specific brain regions with corrected neurons, which may fulfil the dream of personalized medicine have been mentioned briefly. Understanding disease pathways/biology using this technology, with implications for development of novel therapeutics are optimistic expectations in the near future.
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Affiliation(s)
- Sumeet Kumar
- Department of Genetics, University of Delhi South Campus, New Delhi 110 021, India.
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Amber S, Zahid S. Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility. Gene 2018; 672:115-125. [PMID: 29883757 DOI: 10.1016/j.gene.2018.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci. A large proportion of genome wide significant variants lie outside the coding region. However, the plausible function of these variants is still unexplored. OBJECTIVE The present study aimed to unravel the regulatory role of proxy single nucleotide polymorphisms (SNPs), to determine their risk of developing AD. METHODS The RegulomeDB was employed to predict the regulatory role of proxy SNPs. Protein association network and functional enrichment analysis was performed using String10.5 and gene ontology, respectively. RESULTS A total of 451 SNPs were examined through SNAP web portal (r2 ≤ 0.80) which returned 2186 proxy SNPs in linkage disequilibrium (LD) with genome wide significant SNPs for AD. Out of 2186 SNPs analyzed in RegulomeDB, 151 had the scores < 3 that indicates the high degree of their potential regulatory function. Further analysis revealed that out of these 151 SNPs, 37 were genome wide significant for AD, 17 were significantly associated with diseases other than AD, 89 were proxy SNPs (not genome wide significant) for various diseases including AD while 8 SNPs were novel proxy SNPs for AD. CONCLUSION These findings support the notion that the non-coding variants can be strongly associated with disease risk. Further validation through genome wide association studies will be helpful for the elucidation of their regulatory potential.
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Affiliation(s)
- Sanila Amber
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Zahid
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
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38
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Zhang A, Zhao Q, Xu D, Jiang S. Brain APOE expression quantitative trait loci-based association study identified one susceptibility locus for Alzheimer's disease by interacting with APOE ε4. Sci Rep 2018; 8:8068. [PMID: 29795290 PMCID: PMC5966425 DOI: 10.1038/s41598-018-26398-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/08/2018] [Indexed: 02/05/2023] Open
Abstract
Some studies have demonstrated interactions of AD-risk single nucleotide polymorphisms (SNPs) in non-APOE regions with APOE genotype. Nevertheless, no study reported interactions of expression quantitative trait locus (eQTL) for APOE with APOE genotype. In present study, we included 9286 unrelated AD patients and 8479 normal controls from 12 cohorts of NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) and Alzheimer’s Disease Neuroimaging Initiative (ADNI). 34 unrelated brain eQTLs for APOE were compiled from BRAINEAC and GTEx. We used multi-covariate logistic regression analysis to identify eQTLs interacted with APOE ε4. Adjusted for age and gender, substantia nigra eQTL rs438811 for APOE showed significantly strong interaction with APOE ε4 status (OR, 1.448; CI, 1.124–1.430; P-value = 7.94 × 10−6). APOE ε4-based sub-group analyses revealed that carrying one minor allele T of rs438811 can increase the opportunity of developing to AD by 26.75% in APOE ε4 carriers but not in non-carriers. We revealed substantia nigra eQTL rs438811 for APOE can interact with APOE ε4 and confers risk in APOE ε4 carriers only.
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Affiliation(s)
- Aiqian Zhang
- Department of Gynecology, Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qingnan Zhao
- Department of Pediatrics, The University of Texas MD Anderson Cancer center, Houston, Texas, USA
| | - Dabao Xu
- Department of Gynecology, Third Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Shan Jiang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
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39
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Chen XX, Guo RR, Cao XP, Tan L, Tan L. The impact of GAB2 genetic variations on cerebrospinal fluid markers in Alzheimer's disease. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:171. [PMID: 29951493 DOI: 10.21037/atm.2018.04.11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Growth factor receptor-bound protein-associated binding protein 2 gene (GAB2) has been regarded as one of the susceptibility gene associated with Alzheimer's disease (AD). However, the role of GAB2 polymorphisms on cerebrospinal fluid (CSF) proteins in AD continuum remains unclear. Methods We evaluated the connection between four single nucleotide polymorphisms (SNPs) of GAB2 and AD-related CSF biomarkers including amyloid β (Aβ), total tau (T-tau) and phosphorylated tau (P-tau) level in 627 Alzheimer's Disease Neuroimaging Initiative (ADNI) subjects. Results rs1385600 and rs1007837 were significantly associated with all the three biomarkers in CSF (rs1385600: Aβ Pc =0.0112, T-tau Pc =0.0356, P-tau Pc =0.0116; rs1007837: Aβ Pc =0.0058, T-tau Pc =0.0278, P-tau Pc =0.0231). rs2373115 only showed significant association with Aβ and P-tau (Aβ, Pc=0.0398, P-tau, Pc=0.0329). rs10793294 showed no significant association with all the three biomarkers. Conclusions Our study suggested that GAB2 variants were significantly associated with the level of the three CSF biomarkers, which further supported that GAB2 genetic variation modulates AD risk via the alteration of both Aβ and tau pathology.
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Affiliation(s)
- Xiao-Xiao Chen
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Run-Rong Guo
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Xi-Peng Cao
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Lin Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
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40
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Babenko VN, Afonnikov DA, Ignatieva EV, Klimov AV, Gusev FE, Rogaev EI. Haplotype analysis of APOE intragenic SNPs. BMC Neurosci 2018; 19:16. [PMID: 29745836 PMCID: PMC5998902 DOI: 10.1186/s12868-018-0413-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background APOE ε4 allele is most common genetic risk factor for Alzheimer’s disease (AD) and cognitive decline. However, it remains poorly understood why only some carriers of APOE ε4 develop AD and how ethnic variabilities in APOE locus contribute to AD risk. Here, to address the role of APOE haplotypes, we reassessed the diversity of APOE locus in major ethnic groups and in Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset on patients with AD, and subjects with mild cognitive impairment (MCI), and control non-demented individuals. Results We performed APOE gene haplotype analysis for a short block of five SNPs across the gene using the ADNI whole genome sequencing dataset. The compilation of ADNI data with 1000 Genomes identified the APOE ε4 linked haplotypes, which appeared to be distant for the Asian, African and European populations. The common European ε4-bearing haplotype is associated with AD but not with MCI, and the Africans lack this haplotype. Haplotypic inference revealed alleles that may confer protection against AD. By assessing the DNA methylation profile of the APOE haplotypes, we found that the AD-associated haplotype features elevated APOE CpG content, implying that this locus can also be regulated by genetic-epigenetic interactions. Conclusions We showed that SNP frequency profiles within APOE locus are highly skewed to population-specific haplotypes, suggesting that the ancestral background within different sites at APOE gene may shape the disease phenotype. We propose that our results can be utilized for more specific risk assessment based on population descent of the individuals and on higher specificity of five site haplotypes associated with AD. Electronic supplementary material The online version of this article (10.1186/s12868-018-0413-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vladimir N Babenko
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090.
| | - Dmitry A Afonnikov
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090
| | - Elena V Ignatieva
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090
| | - Anton V Klimov
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090
| | - Fedor E Gusev
- Vavilov Institute of General Genetics RAS, Gubkina str. 3, Moscow, Russia, 119991
| | - Evgeny I Rogaev
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Vavilov Institute of General Genetics RAS, Gubkina str. 3, Moscow, Russia, 119991.,Department of Psychiatry, University of Massachusetts Medical School, BNRI, Worcester, MA, 15604, USA.,Faculty of Biology, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119234
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Abstract
Alzheimer's disease (AD), the main form of dementia in the elderly, is the most common progressive neurodegenerative disease characterized by rapidly progressive cognitive dysfunction and behavior impairment. AD exhibits a considerable heritability and great advances have been made in approaches to searching the genetic etiology of AD. In AD genetic studies, methods have developed from classic linkage-based and candidate-gene-based association studies to genome-wide association studies (GWAS) and next generation sequencing (NGS). The identification of new susceptibility genes has provided deeper insights to understand the mechanisms underlying AD. In addition to searching novel genes associated with AD in large samples, the NGS technologies can also be used to shed light on the 'black matter' discovery even in smaller samples. The shift in AD genetics between traditional studies and individual sequencing will allow biomaterials of each patient as the central unit of genetic studies. This review will cover genetic findings in AD and consequences of AD genetic findings. Firstly, we will discuss the discovery of mutations in APP, PSEN1, PSEN2, APOE, and ADAM10. Then we will summarize and evaluate the information obtained from GWAS of AD. Finally, we will outline the efforts to identify rare variants associated with AD using NGS.
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Winick-Ng W, Rylett RJ. Into the Fourth Dimension: Dysregulation of Genome Architecture in Aging and Alzheimer's Disease. Front Mol Neurosci 2018. [PMID: 29541020 PMCID: PMC5835833 DOI: 10.3389/fnmol.2018.00060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by synapse dysfunction and cognitive impairment. Understanding the development and progression of AD is challenging, as the disease is highly complex and multifactorial. Both environmental and genetic factors play a role in AD pathogenesis, highlighted by observations of complex DNA modifications at the single gene level, and by new evidence that also implicates changes in genome architecture in AD patients. The four-dimensional structure of chromatin in space and time is essential for context-dependent regulation of gene expression in post-mitotic neurons. Dysregulation of epigenetic processes have been observed in the aging brain and in patients with AD, though there is not yet agreement on the impact of these changes on transcription. New evidence shows that proteins involved in genome organization have altered expression and localization in the AD brain, suggesting that the genomic landscape may play a critical role in the development of AD. This review discusses the role of the chromatin organizers and epigenetic modifiers in post-mitotic cells, the aging brain, and in the development and progression of AD. How these new insights can be used to help determine disease risk and inform treatment strategies will also be discussed.
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Affiliation(s)
- Warren Winick-Ng
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.,Molecular Medicine Research Laboratories, Robarts Research Institute, University of Western Ontario, London, ON, Canada
| | - R Jane Rylett
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.,Molecular Medicine Research Laboratories, Robarts Research Institute, University of Western Ontario, London, ON, Canada
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Zhao Q, Shen Y, Zhao Y, Si L, Jiang S, Qiu Y. Val66Met Polymorphism in BDNF Has No Sexual and APOE ε4 Status-Based Dimorphic Effects on Susceptibility to Alzheimer's Disease: Evidence From an Updated Meta-Analysis of Case-Control Studies and High-Throughput Genotyping Cohorts. Am J Alzheimers Dis Other Demen 2018; 33:55-63. [PMID: 28984138 PMCID: PMC10852485 DOI: 10.1177/1533317517733037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Some studies showed that Val66Met polymorphism of brain-derived neurotrophic factor (BDNF) conveys susceptibility to Alzheimer's disease (AD) in females only. However, the confounding effects of some risk factors for AD were omitted in these studies. The aim of this meta-analysis comprising 19 604 patients with AD and 26 333 controls was to reexamine the association between Val66Met and AD by conditioning the effects of age, sex, and/or apolipoprotein E ( APOE) ε4 status. In agreement with the previous meta-analysis, Val66Met was associated with AD in females without confounding adjustment (odds ratio [OR], 1.08; 95% confidence interval [CI], 1.03-1.14; P = .003). Nevertheless, after adjusting for age and APOE ε4 status, Val66Met was not associated with AD in females (OR, 1.02; 95% CI, 0.94-1.11; P = .57). This comprehensive meta-analysis with the largest sample size demonstrated no association could be observed between Val66Met and AD in general or by dividing samples based on sex or APOE ε4.
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Affiliation(s)
- Qingnan Zhao
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Department of Pediatrics, The University of Texas MD Anderson Cancer center, Houston, TX, USA
| | - Yaqi Shen
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yanli Zhao
- Basic Medical Sciences Department, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Lining Si
- Department of Critical Care Medicine, Affiliated Hospital of Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Shan Jiang
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Department of Psychiatry, The University of Illinois at Chicago, Chicago, IL, USA
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Yu Qiu
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
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Mäkelä M, Kaivola K, Valori M, Paetau A, Polvikoski T, Singleton AB, Traynor BJ, Stone DJ, Peuralinna T, Tienari PJ, Tanskanen M, Myllykangas L. Alzheimer risk loci and associated neuropathology in a population-based study (Vantaa 85+). NEUROLOGY-GENETICS 2018; 4:e211. [PMID: 29379882 PMCID: PMC5773846 DOI: 10.1212/nxg.0000000000000211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 11/26/2017] [Indexed: 01/23/2023]
Abstract
Objective To test the association of distinct neuropathologic features of Alzheimer disease (AD) with risk loci identified in genome-wide association studies. Methods Vantaa 85+ is a population-based study that includes 601 participants aged ≥85 years, of which 256 were neuropathologically examined. We analyzed 29 AD risk loci in addition to APOE ε4, which was studied separately and used as a covariate. Genotyping was performed using a single nucleotide polymorphism (SNP) array (341 variants) and imputation (6,038 variants). Participants with Consortium to Establish a Registry for Alzheimer Disease (CERAD) (neuritic Aβ plaques) scores 0 (n = 65) vs score M + F (n = 171) and Braak (neurofibrillary tangle pathology) stages 0–II (n = 74) vs stages IV–VI (n = 119), and with capillary Aβ (CapAβ, n = 77) vs without (n = 179) were compared. Cerebral amyloid angiopathy (CAA) percentage was analyzed as a continuous variable. Results Altogether, 24 of the 29 loci were associated (at p < 0.05) with one or more AD-related neuropathologic features in either SNP array or imputation data. Fifteen loci associated with CERAD score, smallest p = 0.0002122, odds ratio (OR) 2.67 (1.58–4.49) at MEF2C locus. Fifteen loci associated with Braak stage, smallest p = 0.004372, OR 0.31 (0.14–0.69) at GAB2 locus. Twenty loci associated with CAA, smallest p = 7.17E-07, β 14.4 (8.88–20) at CR1 locus. Fifteen loci associated with CapAβ smallest p = 0.002594, OR 0.54 (0.37–0.81) at HLA-DRB1 locus. Certain loci associated with specific neuropathologic features. CASS4, CLU, and ZCWPW1 associated only with CAA, while TREM2 and HLA-DRB5 associated only with CapAβ. Conclusions AD risk loci differ in their association with neuropathologic features, and we show for the first time distinct risk loci for CAA and CapAβ.
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Affiliation(s)
- Mira Mäkelä
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Karri Kaivola
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Miko Valori
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Anders Paetau
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Tuomo Polvikoski
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Andrew B Singleton
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Bryan J Traynor
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - David J Stone
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Terhi Peuralinna
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Pentti J Tienari
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Maarit Tanskanen
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
| | - Liisa Myllykangas
- Department of Pathology (M.M., A.E.P., M.T., L.M.), University of Helsinki, and Helsinki University Hospital, Finland; Molecular Neurology (K.K., M.V., T. Peuralinna, P.J.T.), Research Programs Unit, University of Helsinki, and Department of Neurology, Helsinki University Hospital, Finland; Institute of Neuroscience (T. Polvikoski), Newcastle University, United Kingdom; Laboratory of Neurogenetics (A.B.S., B.J.T.), National Institutes on Aging, NIH, Bethesda, MD; and Merck Research Laboratories (D.J.S.), Merck & Co., Inc., West Point, PA, USA
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Genetic Risk Factors for Complex Forms of Alzheimer’s Disease. NEURODEGENER DIS 2018. [DOI: 10.1007/978-3-319-72938-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Metheetrairut C, Ahuja Y, Slack FJ. acn-1, a C. elegans homologue of ACE, genetically interacts with the let-7 microRNA and other heterochronic genes. Cell Cycle 2017; 16:1800-1809. [PMID: 28933985 DOI: 10.1080/15384101.2017.1344798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The heterochronic pathway in C. elegans controls the relative timing of cell fate decisions during post-embryonic development. It includes a network of microRNAs (miRNAs), such as let-7, and protein-coding genes, such as the stemness factors, LIN-28 and LIN-41. Here we identified the acn-1 gene, a homologue of mammalian angiotensin-converting enzyme (ACE), as a new suppressor of the stem cell developmental defects of let-7 mutants. Since acn-1 null mutants die during early larval development, we used RNAi to characterize the role of acn-1 in C. elegans seam cell development, and determined its interaction with heterochronic factors, including let-7 and its downstream interactors - lin-41, hbl-1, and apl-1. We demonstrate that although RNAi knockdown of acn-1 is insufficient to cause heterochronic defects on its own, loss of acn-1 suppresses the retarded phenotypes of let-7 mutants and enhances the precocious phenotypes of hbl-1, though not lin-41, mutants. Conversely, the pattern of acn-1 expression, which oscillates during larval development, is disrupted by lin-41 mutants but not by hbl-1 mutants. Finally, we show that acn-1(RNAi) enhances the let-7-suppressing phenotypes caused by loss of apl-1, a homologue of the Alzheimer's disease-causing amyloid precursor protein (APP), while significantly disrupting the expression of apl-1 during the L4 larval stage. In conclusion, acn-1 interacts with heterochronic genes and appears to function downstream of let-7 and its target genes, including lin-41 and apl-1.
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Affiliation(s)
- Chanatip Metheetrairut
- a Department of Molecular, Cellular, and Developmental Biology , Yale University , New Haven , CT , USA
| | - Yuri Ahuja
- a Department of Molecular, Cellular, and Developmental Biology , Yale University , New Haven , CT , USA
| | - Frank J Slack
- a Department of Molecular, Cellular, and Developmental Biology , Yale University , New Haven , CT , USA
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Neu SC, Pa J, Kukull W, Beekly D, Kuzma A, Gangadharan P, Wang LS, Romero K, Arneric SP, Redolfi A, Orlandi D, Frisoni GB, Au R, Devine S, Auerbach S, Espinosa A, Boada M, Ruiz A, Johnson SC, Koscik R, Wang JJ, Hsu WC, Chen YL, Toga AW. Apolipoprotein E Genotype and Sex Risk Factors for Alzheimer Disease: A Meta-analysis. JAMA Neurol 2017; 74:1178-1189. [PMID: 28846757 PMCID: PMC5759346 DOI: 10.1001/jamaneurol.2017.2188] [Citation(s) in RCA: 396] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Importance It is unclear whether female carriers of the apolipoprotein E (APOE) ε4 allele are at greater risk of developing Alzheimer disease (AD) than men, and the sex-dependent association of mild cognitive impairment (MCI) and APOE has not been established. Objective To determine how sex and APOE genotype affect the risks for developing MCI and AD. Data Sources Twenty-seven independent research studies in the Global Alzheimer's Association Interactive Network with data on nearly 58 000 participants. Study Selection Non-Hispanic white individuals with clinical diagnostic and APOE genotype data. Data Extraction and Synthesis Homogeneous data sets were pooled in case-control analyses, and logistic regression models were used to compute risks. Main Outcomes and Measures Age-adjusted odds ratios (ORs) and 95% confidence intervals for developing MCI and AD were calculated for men and women across APOE genotypes. Results Participants were men and women between ages 55 and 85 years. Across data sets most participants were white, and for many participants, racial/ethnic information was either not collected or not known. Men (OR, 3.09; 95% CI, 2.79-3.42) and women (OR, 3.31; CI, 3.03-3.61) with the APOE ε3/ε4 genotype from ages 55 to 85 years did not show a difference in AD risk; however, women had an increased risk compared with men between the ages of 65 and 75 years (women, OR, 4.37; 95% CI, 3.82-5.00; men, OR, 3.14; 95% CI, 2.68-3.67; P = .002). Men with APOE ε3/ε4 had an increased risk of AD compared with men with APOE ε3/ε3. The APOE ε2/ε3 genotype conferred a protective effect on women (OR, 0.51; 95% CI, 0.43-0.61) decreasing their risk of AD more (P value = .01) than men (OR, 0.71; 95% CI, 0.60-0.85). There was no difference between men with APOE ε3/ε4 (OR, 1.55; 95% CI, 1.36-1.76) and women (OR, 1.60; 95% CI, 1.43-1.81) in their risk of developing MCI between the ages of 55 and 85 years, but women had an increased risk between 55 and 70 years (women, OR, 1.43; 95% CI, 1.19-1.73; men, OR, 1.07; 95% CI, 0.87-1.30; P = .05). There were no significant differences between men and women in their risks for converting from MCI to AD between the ages of 55 and 85 years. Individuals with APOE ε4/ε4 showed increased risks vs individuals with ε3/ε4, but no significant differences between men and women with ε4/ε4 were seen. Conclusions and Relevance Contrary to long-standing views, men and women with the APOE ε3/ε4 genotype have nearly the same odds of developing AD from age 55 to 85 years, but women have an increased risk at younger ages.
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Affiliation(s)
- Scott C Neu
- Laboratory of Neuro Imaging, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles
| | - Judy Pa
- Laboratory of Neuro Imaging, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles
| | - Walter Kukull
- National Alzheimer's Coordinating Center, University of Washington, Seattle
| | - Duane Beekly
- National Alzheimer's Coordinating Center, University of Washington, Seattle
| | - Amanda Kuzma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia
| | | | - Li-San Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia
| | - Klaus Romero
- Coalition Against Major Disease, Critical Path Institute, Tucson, Arizona
| | - Stephen P Arneric
- Coalition Against Major Disease, Critical Path Institute, Tucson, Arizona
| | - Alberto Redolfi
- IRCCS Fatebenefratelli, The National Centre for Alzheimer's Disease, Brescia, Italy
| | - Daniele Orlandi
- IRCCS Fatebenefratelli, The National Centre for Alzheimer's Disease, Brescia, Italy
| | - Giovanni B Frisoni
- IRCCS Fatebenefratelli, The National Centre for Alzheimer's Disease, Brescia, Italy
- University Hospitals and University of Geneva, Geneva, Switzerland
| | - Rhoda Au
- Department of Anatomy and Neurobiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Department Neurology and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Framingham Heart Study, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Sherral Devine
- Department of Neurology, Framingham Heart Study, Boston University School of Medicine, Boston, Massachusetts
| | - Sanford Auerbach
- Department of Neurology, Framingham Heart Study, Boston University School of Medicine, Boston, Massachusetts
| | - Ana Espinosa
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Mercè Boada
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Agustín Ruiz
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | | | - Rebecca Koscik
- University of Wisconsin School of Medicine and Public Health, Madison
| | - Jiun-Jie Wang
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan City, Taiwan
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Wen-Chuin Hsu
- Department of Neurology, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
- Dementia Center, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Yao-Liang Chen
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
- Department of Medical Imaging and Intervention, Keelung Branch, Chang Gung Memorial Hospital, Keelung City, Taiwan
| | - Arthur W Toga
- Laboratory of Neuro Imaging, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles
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Gallego V, Luz Calle M, Oller R. Kernel-Based Measure of Variable Importance for Genetic Association Studies. Int J Biostat 2017. [PMID: 28628480 DOI: 10.1515/ijb-2016-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The identification of genetic variants that are associated with disease risk is an important goal of genetic association studies. Standard approaches perform univariate analysis where each genetic variant, usually Single Nucleotide Polymorphisms (SNPs), is tested for association with disease status. Though many genetic variants have been identified and validated so far using this univariate approach, for most complex diseases a large part of their genetic component is still unknown, the so called missing heritability. We propose a Kernel-based measure of variable importance (KVI) that provides the contribution of a SNP, or a group of SNPs, to the joint genetic effect of a set of genetic variants. KVI can be used for ranking genetic markers individually, sets of markers that form blocks of linkage disequilibrium or sets of genetic variants that lie in a gene or a genetic pathway. We prove that, unlike the univariate analysis, KVI captures the relationship with other genetic variants in the analysis, even when measured at the individual level for each genetic variable separately. This is specially relevant and powerful for detecting genetic interactions. We illustrate the results with data from an Alzheimer's disease study and show through simulations that the rankings based on KVI improve those rankings based on two measures of importance provided by the Random Forest. We also prove with a simulation study that KVI is very powerful for detecting genetic interactions.
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Shankarappa BM, Kota LN, Purushottam M, Nagpal K, Mukherjee O, Viswanath B, Varghese M, Bharath S, Jain S. Effect of CLU and PICALM polymorphisms on AD risk: A study from south India. Asian J Psychiatr 2017; 27:7-11. [PMID: 28558900 DOI: 10.1016/j.ajp.2016.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 11/21/2016] [Accepted: 12/27/2016] [Indexed: 01/29/2023]
Abstract
OBJECTIVES To study the association of apolipoprotein E (APOE), Clusterin (CLU) and phosphatidylinositol binding clathrin assembly protein (PICALM) polymorphisms in Alzheimer's disease (AD) subjects compared to cognitively normal control subjects in an Indian population. METHODS The study subjects included persons with AD (N=243) and age group matched healthy controls (N=164). All the AD subjects were evaluated using a standard protocol. DNA was isolated from whole blood. APOE (rs7412, rs429358), CLU (rs11136000) and PICALM (rs3851179) were genotyped. General linear model was used to test the association between the individual risk genotypes and AD. RESULTS The presence of APOE ε4 was associated with AD after adjusting for age and gender (p<0.0001). There was no association observed with AD at both rs11136000 CLU (p=0.25) and rs3851179 PICALM (p=0.54). CONCLUSION Our results confirmed a significant association of APOE ε4 carrier status with AD. No association was observed for CLU and PICALM with AD. This might be due to a different genetic background. There are no previous reports of these polymorphisms in an Indian cohort. Future Indian AD studies should investigate additional SNPs in a larger sample size in these genes.
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Affiliation(s)
| | - Lakshmi Narayanan Kota
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore 560029, India.
| | - Kavita Nagpal
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Odity Mukherjee
- Instem, National Centre for Biological Sciences (NCBS), Bangalore, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Mathew Varghese
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Srikala Bharath
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
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Li GD, Bi R, Zhang DF, Xu M, Luo R, Wang D, Fang Y, Li T, Zhang C, Yao YG. Female-specific effect of the BDNF gene on Alzheimer's disease. Neurobiol Aging 2017; 53:192.e11-192.e19. [PMID: 28202203 DOI: 10.1016/j.neurobiolaging.2016.12.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/21/2016] [Accepted: 12/24/2016] [Indexed: 02/05/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease influenced by genetic and environmental factors. Brain-derived neurotrophic factor (BDNF) plays an important role in the progression of AD, but the genetic association between BDNF and AD remains controversial. In this study, we aimed to explore the potential association between genetic variants in BDNF and AD in Han Chinese and to investigate whether the association is affected by gender. A 3-stage study was conducted to evaluate the genetic association between BDNF and AD. Data mining of the reported expression data, brain-imaging data, and biomarker data in AD patients was also performed to further validate the results. We found a female-specific genetic association of rs6265 with AD and a gender-related messenger RNA expression of BDNF in brain tissues of AD patients. In addition, we observed a clear female-specific risk trend for the effect of rs6265 on AD endophenotypes. Our results clarified the available controversies regarding the role of rs6265 in AD and indicated that BDNF may be a female-specific risk gene for AD.
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Affiliation(s)
- Guo-Dong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Rongcan Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | | | - Yiru Fang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Li
- The Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chen Zhang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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