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Schraiber JG, Edge MD, Pennell M. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579721. [PMID: 38496530 PMCID: PMC10942266 DOI: 10.1101/2024.02.10.579721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
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Mathioudakis L, Dimovasili C, Bourbouli M, Latsoudis H, Kokosali E, Gouna G, Vogiatzi E, Basta M, Kapetanaki S, Panagiotakis S, Kanterakis A, Boumpas D, Lionis C, Plaitakis A, Simos P, Vgontzas A, Kafetzopoulos D, Zaganas I. Study of Alzheimer's disease- and frontotemporal dementia-associated genes in the Cretan Aging Cohort. Neurobiol Aging 2023; 123:111-128. [PMID: 36117051 DOI: 10.1016/j.neurobiolaging.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 02/02/2023]
Abstract
Using exome sequencing, we analyzed 196 participants of the Cretan Aging Cohort (CAC; 95 with Alzheimer's disease [AD], 20 with mild cognitive impairment [MCI], and 81 cognitively normal controls). The APOE ε4 allele was more common in AD patients (23.2%) than in controls (7.4%; p < 0.01) and the PSEN2 p.Arg29His and p.Cys391Arg variants were found in 3 AD and 1 MCI patient, respectively. Also, we found the frontotemporal dementia (FTD)-associated TARDBP gene p.Ile383Val variant in 2 elderly patients diagnosed with AD and in 2 patients, non CAC members, with the amyotrophic lateral sclerosis/FTD phenotype. Furthermore, the p.Ser498Ala variant in the positively selected GLUD2 gene was less frequent in AD patients (2.11%) than in controls (16%; p < 0.01), suggesting a possible protective effect. While the same trend was found in another local replication cohort (n = 406) and in section of the ADNI cohort (n = 808), this finding did not reach statistical significance and therefore it should be considered preliminary. Our results attest to the value of genetic testing to study aged adults with AD phenotype.
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Affiliation(s)
- Lambros Mathioudakis
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Christina Dimovasili
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Mara Bourbouli
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Helen Latsoudis
- Minotech Genomics Facility, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Heraklion, Crete, Greece
| | - Evgenia Kokosali
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Garyfallia Gouna
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Emmanouella Vogiatzi
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Maria Basta
- University of Crete, Medical School, Psychiatry Department, Heraklion, Crete, Greece
| | - Stefania Kapetanaki
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Simeon Panagiotakis
- University of Crete, Medical School, Internal Medicine Department, Heraklion, Crete, Greece
| | - Alexandros Kanterakis
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology - Hellas (ICS-FORTH), Heraklion, Crete, Greece
| | - Dimitrios Boumpas
- University of Crete, Medical School, Internal Medicine Department, Heraklion, Crete, Greece
| | - Christos Lionis
- University of Crete, Medical School, Clinic of Social and Family Medicine, Heraklion, Crete, Greece
| | - Andreas Plaitakis
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece
| | - Panagiotis Simos
- University of Crete, Medical School, Psychiatry Department, Heraklion, Crete, Greece
| | - Alexandros Vgontzas
- University of Crete, Medical School, Psychiatry Department, Heraklion, Crete, Greece
| | - Dimitrios Kafetzopoulos
- Minotech Genomics Facility, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Heraklion, Crete, Greece
| | - Ioannis Zaganas
- University of Crete, Medical School, Neurology/Neurogenetics Laboratory, Heraklion, Crete, Greece.
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Quach TT, Stratton HJ, Khanna R, Mackey-Alfonso S, Deems N, Honnorat J, Meyer K, Duchemin AM. Neurodegenerative Diseases: From Dysproteostasis, Altered Calcium Signalosome to Selective Neuronal Vulnerability to AAV-Mediated Gene Therapy. Int J Mol Sci 2022; 23:ijms232214188. [PMID: 36430666 PMCID: PMC9694178 DOI: 10.3390/ijms232214188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
Despite intense research into the multifaceted etiology of neurodegenerative diseases (ND), they remain incurable. Here we provide a brief overview of several major ND and explore novel therapeutic approaches. Although the cause (s) of ND are not fully understood, the accumulation of misfolded/aggregated proteins in the brain is a common pathological feature. This aggregation may initiate disruption of Ca++ signaling, which is an early pathological event leading to altered dendritic structure, neuronal dysfunction, and cell death. Presently, ND gene therapies remain unidimensional, elusive, and limited to modifying one pathological feature while ignoring others. Considering the complexity of signaling cascades in ND, we discuss emerging therapeutic concepts and suggest that deciphering the molecular mechanisms involved in dendritic pathology may broaden the phenotypic spectrum of ND treatment. An innovative multiplexed gene transfer strategy that employs silencing and/or over-expressing multiple effectors could preserve vulnerable neurons before they are lost. Such therapeutic approaches may extend brain health span and ameliorate burdensome chronic disease states.
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Affiliation(s)
- Tam T. Quach
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
- INSERM U1217/CNRS UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, 69677 Lyon, France
| | | | - Rajesh Khanna
- Department of Molecular Pathobiology, New York University, New York, NY 10010, USA
| | - Sabrina Mackey-Alfonso
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Nicolas Deems
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jérome Honnorat
- INSERM U1217/CNRS UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, 69677 Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677 Lyon, France
- SynatAc Team, Institut NeuroMyoGène, 69677 Lyon, France
| | - Kathrin Meyer
- The Research Institute of Nationwide Children Hospital, Columbus, OH 43205, USA
- Department of Pediatric, The Ohio State University, Columbus, OH 43210, USA
| | - Anne-Marie Duchemin
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +1-614-293-5517; Fax: +1-614-293-7599
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4
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Hoogmartens J, Cacace R, Van Broeckhoven C. Insight into the genetic etiology of Alzheimer's disease: A comprehensive review of the role of rare variants. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12155. [PMID: 33665345 PMCID: PMC7896636 DOI: 10.1002/dad2.12155] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
Early-onset Alzheimer's disease (EOAD) is generally known as a dominant disease due to highly penetrant pathogenic mutations in the amyloid precursor protein, presenilin 1 and 2. However, they explain only a fraction of EOAD patients (5% to 10%). Furthermore, only 10% to 15% of EOAD families present with clear autosomal dominant inheritance. Studies showed that only 35% to 60% of EOAD patients have at least one affected first-degree relative. Parent-offspring concordance in EOAD was estimated to be <10%, indicating that full penetrant dominant alleles are not the sole players in EOAD. We aim to summarize current knowledge of rare variants underlying familial and seemingly sporadic Alzheimer's disease (AD) patients. Genetic findings indicate that in addition to the amyloid beta pathway, other pathways are of importance in AD pathophysiology. We discuss the difficulties in interpreting the influence of rare variants on disease onset and we underline the value of carefully selected ethnicity-matched cohorts in AD genetic research.
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Affiliation(s)
- Julie Hoogmartens
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Rita Cacace
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
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5
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Schapansky J, Grinberg YY, Osiecki DM, Freeman EA, Walker SG, Karran E, Gopalakrishnan SM, Talanian RV. MEK1/2 activity modulates TREM2 cell surface recruitment. J Biol Chem 2020; 296:100218. [PMID: 33839686 PMCID: PMC7948395 DOI: 10.1074/jbc.ra120.014352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/18/2022] Open
Abstract
Rare sequence variants in the microglial cell surface receptor TREM2 have been shown to increase the risk for Alzheimer’s disease (AD). Disease-linked TREM2 mutations seem to confer a partial loss of function, and increasing TREM2 cell surface expression and thereby its function(s) might have therapeutic benefit in AD. However, druggable targets that could modulate microglial TREM2 surface expression are not known. To identify such targets, we conducted a screen of small molecule compounds with known pharmacology using human myeloid cells, searching for those that enhance TREM2 protein at the cell surface. Inhibitors of the kinases MEK1/2 displayed the strongest and most consistent increases in cell surface TREM2 protein, identifying a previously unreported pathway for TREM2 regulation. Unexpectedly, inhibitors of the downstream effector ERK kinases did not have the same effect, suggesting that noncanonical MEK signaling regulates TREM2 trafficking. In addition, siRNA knockdown experiments confirmed that decreased MEK1 and MEK2 were required for this recruitment. In iPSC-derived microglia, MEK inhibition increased cell surface TREM2 only modestly, so various cytokines were used to alter iPSC microglia phenotype, making cells more sensitive to MEK inhibitor-induced TREM2 recruitment. Of those tested, only IFN-gamma priming prior to MEK inhibitor treatment resulted in greater TREM2 recruitment. These data identify the first known mechanisms for increasing surface TREM2 protein and TREM2-regulated function in human myeloid cells and are the first to show a role for MEK1/MEK2 signaling in TREM2 activity.
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Affiliation(s)
- Jason Schapansky
- AbbVie Inc, Cambridge Research Center, Cambridge, Massachusetts, USA.
| | - Yelena Y Grinberg
- AbbVie Inc, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - David M Osiecki
- AbbVie Inc, Drug Discovery Science and Technology, North Chicago, Illinois, USA
| | - Emily A Freeman
- AbbVie Inc, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Stephen G Walker
- AbbVie Inc, Drug Discovery Science and Technology, North Chicago, Illinois, USA
| | - Eric Karran
- AbbVie Inc, Cambridge Research Center, Cambridge, Massachusetts, USA
| | | | - Robert V Talanian
- AbbVie Inc, Cambridge Research Center, Cambridge, Massachusetts, USA
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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: 65] [Impact Index Per Article: 16.3] [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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Swerdlow RH, Hui D, Chalise P, Sharma P, Wang X, Andrews SJ, Pa J, Mahnken JD, Morris J, Wilkins HM, Burns JM, Michaelis ML, Michaelis EK. Exploratory analysis of mtDNA haplogroups in two Alzheimer's longitudinal cohorts. Alzheimers Dement 2020; 16:1164-1172. [PMID: 32543785 PMCID: PMC9847473 DOI: 10.1002/alz.12119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/06/2020] [Accepted: 04/29/2020] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Inherited mitochondrial DNA (mtDNA) variants may influence Alzheimer's disease (AD) risk. METHODS We sequenced mtDNA from 146 AD and 265 cognitively normal (CN) subjects from the University of Kansas AD Center (KUADC) and assigned haplogroups. We further considered 244 AD and 242 CN AD Neuroimaging Initiative (ADNI) subjects with equivalent data. RESULTS Without applying multiple comparisons corrections, KUADC haplogroup J AD and CN frequencies were 16.4% versus 7.6% (P = .007), and haplogroup K AD and CN frequencies were 4.8% versus 10.2% (P = .063). ADNI haplogroup J AD and CN frequencies were 10.7% versus 7.0% (P = .20), and haplogroup K frequencies were 4.9% versus 8.7% (P = .11). For the combined 390 AD and 507 CN cases haplogroup J frequencies were 12.8% versus 7.3% (P = .006), odds ratio (OR) = 1.87, and haplogroup K frequencies were 4.9% versus 9.5% (P = .010), OR = 0.49. Associations remained significant after adjusting for apolipoprotein E, age, and sex. CONCLUSION This exploratory analysis suggests inherited mtDNA variants influence AD risk.
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Affiliation(s)
- Russell H. Swerdlow
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Dongwei Hui
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Prabhakar Chalise
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Palash Sharma
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Xinkun Wang
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Shea J. Andrews
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy Pa
- Alzheimer’s Disease Research Center, Mark and Mary Stevens Neuroimaging and Informatics InstituteUniversity of Southern California, Los Angeles, California, USA
| | - Jonathan D. Mahnken
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jill Morris
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Heather M. Wilkins
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jeffrey M. Burns
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Mary L. Michaelis
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Elias K. Michaelis
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
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Klück V, van Deuren RC, Cavalli G, Shaukat A, Arts P, Cleophas MC, Crișan TO, Tausche AK, Riches P, Dalbeth N, Stamp LK, Hindmarsh JH, Jansen TLTA, Janssen M, Steehouwer M, Lelieveld S, van de Vorst M, Gilissen C, Dagna L, Van de Veerdonk FL, Eisenmesser EZ, Kim S, Merriman TR, Hoischen A, Netea MG, Dinarello CA, Joosten LA. Rare genetic variants in interleukin-37 link this anti-inflammatory cytokine to the pathogenesis and treatment of gout. Ann Rheum Dis 2020; 79:536-544. [PMID: 32114511 DOI: 10.1136/annrheumdis-2019-216233] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Gout is characterised by severe interleukin (IL)-1-mediated joint inflammation induced by monosodium urate crystals. Since IL-37 is a pivotal anti-inflammatory cytokine suppressing the activity of IL-1, we conducted genetic and functional studies aimed at elucidating the role of IL-37 in the pathogenesis and treatment of gout. METHODS Variant identification was performed by DNA sequencing of all coding bases of IL37 using molecular inversion probe-based resequencing (discovery cohort: gout n=675, controls n=520) and TaqMan genotyping (validation cohort: gout n=2202, controls n=2295). Predictive modelling of the effects of rare variants on protein structure was followed by in vitro experiments evaluating the impact on protein function. Treatment with recombinant IL-37 was evaluated in vitro and in vivo in a mouse model of gout. RESULTS We identified four rare variants in IL37 in six of the discovery gout patients; p.(A144P), p.(G174Dfs*16), p.(C181*) and p.(N182S), whereas none emerged in healthy controls (Fisher's exact p-value=0.043). All variants clustered in the functional domain of IL-37 in exon 5 (p-value=5.71×10-5). Predictive modelling and functional studies confirmed loss of anti-inflammatory functions and we substantiated the therapeutic potential of recombinant IL-37 in the treatment of gouty inflammation. Furthermore, the carrier status of p.(N182S)(rs752113534) was associated with increased risk (OR=1.81, p-value=0.031) of developing gout in hyperuricaemic individuals of Polynesian ancestry. CONCLUSION Here, we provide genetic as well as mechanistic evidence for the role of IL-37 in the pathogenesis of gout, and highlight the therapeutic potential of recombinant IL-37 for the treatment of gouty arthritis.
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Affiliation(s)
- Viola Klück
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rosanne C van Deuren
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Giulio Cavalli
- Internal Medicine and Clinical Immunology, Vita-Salute San Raffaele University, Milan, Italy.,Department of Medicine, University of Colorado Denver, Denver, Colorado, USA
| | - Amara Shaukat
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Peer Arts
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Maartje C Cleophas
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tania O Crișan
- Department of Medical Genetics, Universitatea de Medicina si Farmacie Iuliu Hatieganu, Cluj-Napoca, Romania
| | - Anne-Kathrin Tausche
- Department of Internal Medicine, Section of Rheumatology, University Clinic Carl Gustav Carus, Dresden, Saxonia, Germany
| | - Philip Riches
- Rheumatology and Bone Disease, University of Edinburgh, Edinburgh, UK
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Lisa K Stamp
- Department of Medicine, Otago University, Christchurch, Canterbury, New Zealand
| | - Jennie Harré Hindmarsh
- Te Rangawairua o Paratene Ngata Research Centre, Ngāti Porou Hauora Charitable Trust, Te Puia Springs, Tairāwhiti, New Zealand
| | - Tim L Th A Jansen
- Department of Rheumatology, VieCuri Medical Center, Venlo, The Netherlands
| | - Matthijs Janssen
- Department of Rheumatology, VieCuri Medical Center, Venlo, The Netherlands
| | - Marloes Steehouwer
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stefan Lelieveld
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lorenzo Dagna
- Internal Medicine and Clinical Immunology, Vita-Salute San Raffaele University, Milan, Italy
| | - Frank L Van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elan Z Eisenmesser
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Denver, Colorado, USA
| | - SooHyun Kim
- Laboratory of Cytokine Immunology, Konkuk University, Seoul, Korea (the Republic of)
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Alexander Hoischen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Charles A Dinarello
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Medicine, University of Colorado Denver, Denver, Colorado, USA
| | - Leo Ab Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands .,Department of Medical Genetics, Universitatea de Medicina si Farmacie Iuliu Hatieganu, Cluj-Napoca, Romania
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9
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Olive C, Ibanez L, Farias FHG, Wang F, Budde JP, Norton JB, Gentsch J, Morris JC, Li Z, Dube U, Del-Aguila J, Bergmann K, Bradley J, Benitez BA, Harari O, Fagan A, Ances B, Cruchaga C, Fernandez MV. Examination of the Effect of Rare Variants in TREM2, ABI3, and PLCG2 in LOAD Through Multiple Phenotypes. J Alzheimers Dis 2020; 77:1469-1482. [PMID: 32894242 PMCID: PMC7927150 DOI: 10.3233/jad-200019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Rare variants in PLCG2 (p.P522R), ABI3 (p.S209F), and TREM2 (p.R47H, p.R62H) have been associated with late onset Alzheimer's disease (LOAD) risk in Caucasians. After the initial report, several studies have found positive results in cohorts of different ethnic background and with different phenotype. OBJECTIVE In this study, we aim to evaluate the association of rare coding variants in PLCG2, ABI3, and TREM2 with LOAD risk and their effect at different time points of the disease. METHODS We used a European American cohort to assess the association of the variants prior onset (using CSF Aβ42, tau, and pTau levels, and amyloid imaging as endophenotypes) and after onset (measured as rate of memory decline). RESULTS We confirm the association with LOAD risk of TREM2 p.R47H, p.R62H and ABI3 p.S209F variants, and the protective effect of PLCG2 p.P522R. In addition, ABI3 and TREM2 gene-sets showed significant association with LOAD risk. TREM2 p.R47H and PLCG2 p.P522R variants were also statistically associated with increase of amyloid imaging and AD progression, respectively. We did not observe any association of ABI3 p.S209F with any of the other AD endophenotypes. CONCLUSION The results of this study highlight the importance of including biomarkers and alternative phenotypes to better understand the role of novel candidate genes with the disease.
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Affiliation(s)
- Claudia Olive
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Laura Ibanez
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Fabiana H. Geraldo Farias
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Fengxian Wang
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John P. Budde
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Joanne B. Norton
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jen Gentsch
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Zeran Li
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Umber Dube
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Jorge Del-Aguila
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristy Bergmann
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph Bradley
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruno A. Benitez
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Oscar Harari
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Fagan
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Beau Ances
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Neurogenomics and Informatics Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
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10
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Zhao L, He Z, Zhang D, Wang GT, Renton AE, Vardarajan BN, Nothnagel M, Goate AM, Mayeux R, Leal SM. A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data. Am J Hum Genet 2019; 105:822-835. [PMID: 31585107 DOI: 10.1016/j.ajhg.2019.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 09/05/2019] [Indexed: 10/25/2022] Open
Abstract
To analyze family-based whole-genome sequence (WGS) data for complex traits, we developed a rare variant (RV) non-parametric linkage (NPL) analysis method, which has advantages over association methods. The RV-NPL differs from the NPL in that RVs are analyzed, and allele sharing among affected relative-pairs is estimated only for minor alleles. Analyzing families can increase power because causal variants with familial aggregation usually have larger effect sizes than those underlying sporadic diseases. Differing from association analysis, for NPL only affected individuals are analyzed, which can increase power, since unaffected family members can be susceptibility variant carriers. RV-NPL is robust to population substructure and admixture, inclusion of nonpathogenic variants, as well as allelic and locus heterogeneity and can readily be applied outside of coding regions. In contrast to analyzing common variants using NPL, where loci localize to large genomic regions (e.g., >50 Mb), mapped regions are well defined for RV-NPL. Using simulation studies, we demonstrate that RV-NPL is substantially more powerful than applying traditional NPL methods to analyze RVs. The RV-NPL was applied to analyze 107 late-onset Alzheimer disease (LOAD) pedigrees of Caribbean Hispanic and European ancestry with WGS data, and statistically significant linkage (LOD ≥ 3.8) was found with RVs in PSMF1 and PTPN21 which have been shown to be involved in LOAD etiology. Additionally, nominally significant linkage was observed with RVs in ABCA7, ACE, EPHA1, and SORL1, genes that were previously reported to be associated with LOAD. RV-NPL is an ideal method to elucidate the genetic etiology of complex familial diseases.
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11
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Day GS, Cruchaga C, Wingo T, Schindler SE, Coble D, Morris JC. Association of Acquired and Heritable Factors With Intergenerational Differences in Age at Symptomatic Onset of Alzheimer Disease Between Offspring and Parents With Dementia. JAMA Netw Open 2019; 2:e1913491. [PMID: 31617930 PMCID: PMC6806434 DOI: 10.1001/jamanetworkopen.2019.13491] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Acquired and heritable traits are associated with dementia risk; however, how these traits are associated with age at symptomatic onset (AAO) of Alzheimer disease (AD) is unknown. Identifying the associations of acquired and heritable factors with variability in intergenerational AAO of AD could facilitate diagnosis, assessment, and counseling of the offspring of parents with AD. OBJECTIVE To quantify the associations of acquired and heritable factors with intergenerational differences in AAO of AD. DESIGN, SETTING, AND PARTICIPANTS This nested cohort study used data from the Knight Alzheimer Disease Research Center that included community-dwelling participants with symptomatic AD, parental history of dementia, and available DNA data who were enrolled in prospective studies of memory and aging from September 1, 2005, to August 31, 2016. Clinical, biomarker, and genetic data were extracted on January 17, 2017, and data analyses were conducted from July 1, 2017, to August 20, 2019. MAIN OUTCOMES AND MEASURES The associations of acquired (ie, years of education; body mass index; history of cardiovascular disease, hypertension, hypercholesterolemia, diabetes, active depression within 2 years, traumatic brain injury, tobacco use, and unhealthy alcohol use; and retrospective determination of AAO) and heritable factors (ie, ethnicity/race, paternal or maternal inheritance, parental history of early-onset dementia, APOE ε4 allele status, and AD polygenic risk scores) to intergenerational difference in AAO of AD were quantified using stepwise forward multivariable regression. Missense or frameshift variants within genes associated with AD pathogenesis were screened using whole-exome sequencing. RESULTS There were 164 participants with symptomatic AD, known parental history of dementia, and available DNA data (mean [SD] age, 70.9 [8.3] years; 90 [54.9%] women) included in this study. Offspring were diagnosed with symptomatic AD a mean (SD) 6.1 (10.7) years earlier than their parents (P < .001). The adjusted R2 for measured acquired and heritable factors for intergenerational difference in AAO of AD was 0.29 (F8,155 = 9.13; P < .001). Paternal (β = -9.52 [95% CI, -13.79 to -5.25]) and maternal (β = -6.68 [95% CI, -11.61 to -1.75]) history of dementia, more years of education (β = -0.58 [95% CI -1.08 to -0.09]), and retrospective determination of AAO (β = -3.46 [95% CI, -6.40 to -0.52]) were associated with earlier-than-expected intergenerational difference in AAO of AD. Parental history of early-onset dementia (β = 21.30 [95% CI, 15.01 to 27.59]), presence of 1 APOE ε4 allele (β = 5.00 [95% CI, 2.11 to 7.88]), and history of hypertension (β = 3.81 [95% CI, 0.88 to 6.74]) were associated with later-than-expected intergenerational difference in AAO of AD. Missense or frameshift variants within genes associated with AD pathogenesis were more common in participants with the greatest unexplained variability in intergenerational AAO of AD (19 of 48 participants [39.6%] vs 26 of 116 participants [22.4%]; P = .03). CONCLUSIONS AND RELEVANCE Acquired and heritable factors were associated with a substantial proportion of variability in intergenerational AAO of AD. Variants in genes associated with AD pathogenesis may contribute to unexplained variability, justifying further study.
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Affiliation(s)
- Gregory S. Day
- Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine in St Louis, St Louis, Missouri
- Department of Neurology, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - Carlos Cruchaga
- Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine in St Louis, St Louis, Missouri
- Department of Psychiatry, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - Thomas Wingo
- Department of Neurology, Emory University, Atlanta, Georgia
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Suzanne E. Schindler
- Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine in St Louis, St Louis, Missouri
- Department of Neurology, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - Dean Coble
- Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine in St Louis, St Louis, Missouri
- Department of Biostatistics, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - John C. Morris
- Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine in St Louis, St Louis, Missouri
- Department of Neurology, Washington University School of Medicine in St Louis, St Louis, Missouri
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12
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Higham JP, Malik BR, Buhl E, Dawson JM, Ogier AS, Lunnon K, Hodge JJL. Alzheimer's Disease Associated Genes Ankyrin and Tau Cause Shortened Lifespan and Memory Loss in Drosophila. Front Cell Neurosci 2019; 13:260. [PMID: 31244615 PMCID: PMC6581016 DOI: 10.3389/fncel.2019.00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia and is characterized by intracellular neurofibrillary tangles of hyperphosphorylated Tau, including the 0N4R isoform and accumulation of extracellular amyloid beta (Aβ) plaques. However, less than 5% of AD cases are familial, with many additional risk factors contributing to AD including aging, lifestyle, the environment and epigenetics. Recent epigenome-wide association studies (EWAS) of AD have identified a number of loci that are differentially methylated in the AD cortex. Indeed, hypermethylation and reduced expression of the Ankyrin 1 (ANK1) gene in AD has been reported in the cortex in numerous different post-mortem brain cohorts. Little is known about the normal function of ANK1 in the healthy brain, nor the role it may play in AD. We have generated Drosophila models to allow us to functionally characterize Drosophila Ank2, the ortholog of human ANK1 and to determine its interaction with human Tau and Aβ. We show expression of human Tau 0N4R or the oligomerizing Aβ 42 amino acid peptide caused shortened lifespan, degeneration, disrupted movement, memory loss, and decreased excitability of memory neurons with co-expression tending to make the pathology worse. We find that Drosophila with reduced neuronal Ank2 expression have shortened lifespan, reduced locomotion, reduced memory and reduced neuronal excitability similar to flies overexpressing either human Tau 0N4R or Aβ42. Therefore, we show that the mis-expression of Ank2 can drive disease relevant processes and phenocopy some features of AD. Therefore, we propose targeting human ANK1 may have therapeutic potential. This represents the first study to characterize an AD-relevant gene nominated from EWAS.
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Affiliation(s)
- James P. Higham
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Bilal R. Malik
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Edgar Buhl
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Jennifer M. Dawson
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Anna S. Ogier
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - James J. L. Hodge
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
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Filippov MA, Vorobyov VV. Detrimental and synergistic role of epilepsy - Alzheimer's disease risk factors. Neural Regen Res 2019; 14:1376-1377. [PMID: 30964059 PMCID: PMC6524520 DOI: 10.4103/1673-5374.253519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Vasily V Vorobyov
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Abstract
Vascular dementia (VaD) is a common disorder that encompasses heterogeneous entities, which creates challenges in order to reach a global consensus for diagnostic criteria. While the genetic basis for sporadic VaD remains poorly understood, the identification of causal genes in monogenic forms of VaD sheds light on the pathophysiological mechanisms of VaD. This special report describes progress in genetic research on monogenic and sporadic VaD, as well as on associated phenotypes, such as cerebral small vessel disease, stroke and Alzheimer's disease. Methodological issues (e.g., small-size studies) and strategies to overcome these problems (e.g., collaborative consortiums, endophenotypes) are discussed. Lastly, future perspectives in the field and how such work could benefit patients and clinicians are mentioned.
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Affiliation(s)
- Raquel Manso-Calderón
- Department of Neurology, University Hospital of Salamanca, Salamanca 37007, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca 37007, Spain
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15
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Transethnic meta-analysis of rare coding variants in PLCG2, ABI3, and TREM2 supports their general contribution to Alzheimer's disease. Transl Psychiatry 2019; 9:55. [PMID: 30705288 PMCID: PMC6355764 DOI: 10.1038/s41398-019-0394-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/26/2018] [Accepted: 01/01/2019] [Indexed: 11/08/2022] Open
Abstract
Rare coding variants in TREM2, PLCG2, and ABI3 were recently associated with the susceptibility to Alzheimer's disease (AD) in Caucasians. Frequencies and AD-associated effects of variants differ across ethnicities. To start filling the gap on AD genetics in South America and assess the impact of these variants across ethnicity, we studied these variants in Argentinian population in association with ancestry. TREM2 (rs143332484 and rs75932628), PLCG2 (rs72824905), and ABI3 (rs616338) were genotyped in 419 AD cases and 486 controls. Meta-analysis with European population was performed. Ancestry was estimated from genome-wide genotyping results. All variants show similar frequencies and odds ratios to those previously reported. Their association with AD reach statistical significance by meta-analysis. Although the Argentinian population is an admixture, variant carriers presented mainly Caucasian ancestry. Rare coding variants in TREM2, PLCG2, and ABI3 also modulate susceptibility to AD in populations from Argentina, and they may have a European heritage.
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Wang ZT, Tan CC, Tan L, Yu JT. Systems biology and gene networks in Alzheimer’s disease. Neurosci Biobehav Rev 2019; 96:31-44. [DOI: 10.1016/j.neubiorev.2018.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 11/18/2018] [Accepted: 11/18/2018] [Indexed: 12/25/2022]
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Li Q, Wang BL, Sun FR, Li JQ, Cao XP, Tan L. The role of UNC5C in Alzheimer's disease. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:178. [PMID: 29951500 DOI: 10.21037/atm.2018.04.43] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a chronic progressive neurodegenerative disease in adults characterized by the deposition of extracellular plaques of β-amyloid protein (Aβ), intracellular neurofibrillary tangles (NFTs), synaptic loss and neuronal apoptosis. AD has a strong and complex genetic component that involving into multiple genes. With recent advances in whole-exome sequencing (WES) and whole-genome sequencing (WGS) technology, UNC5C was identified to have association with AD. Emerging studies on cell and animal models identified that aberrant UNC5C may contribute to AD by activating death-associated protein kinase 1 (DAPK1) which is a new component involved in AD pathogenesis with an extensive involvement in aberrant tau, Aβ and neuronal apoptosis/autophagy. In this review, we briefly summarize the biochemical properties, genetics, epigenetics, and the speculative role of UNC5C in AD. We hope our review would bring comprehensive understandings of AD pathogenesis and provide new therapeutic targets for AD.
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Affiliation(s)
- Quan Li
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Bai-Ling Wang
- Department of Geriatrics, Qingdao Mental Health Center, Qingdao 266034, China
| | - Fu-Rong Sun
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Jie-Qiong Li
- 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
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
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18
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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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19
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Nam KN, Wolfe CM, Fitz NF, Letronne F, Castranio EL, Mounier A, Schug J, Lefterov I, Koldamova R. Integrated approach reveals diet, APOE genotype and sex affect immune response in APP mice. Biochim Biophys Acta Mol Basis Dis 2018; 1864:152-161. [PMID: 29038051 PMCID: PMC5714325 DOI: 10.1016/j.bbadis.2017.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/04/2017] [Accepted: 10/12/2017] [Indexed: 01/02/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder that is influenced by genetic and environmental risk factors, such as inheritance of ε4 allele of APOE (APOE4), sex and diet. Here, we examined the effect of high fat diet (HFD) on amyloid pathology and expression profile in brains of AD model mice expressing human APOE isoforms (APP/E3 and APP/E4 mice). APP/E3 and APP/E4 mice were fed HFD or Normal diet for 3months. We found that HFD significantly increased amyloid plaques in male and female APP/E4, but not in APP/E3 mice. To identify differentially expressed genes and gene-networks correlated to diet, APOE isoform and sex, we performed RNA sequencing and applied Weighted Gene Co-expression Network Analysis. We determined that the immune response network with major hubs Tyrobp/DAP12, Csf1r, Tlr2, C1qc and Laptm5 correlated significantly and positively to the phenotype of female APP/E4-HFD mice. Correspondingly, we found that in female APP/E4-HFD mice, microglia coverage around plaques, particularly of larger size, was significantly reduced. This suggests altered containment of the plaque growth and sex-dependent vulnerability in response to diet. The results of our study show concurrent impact of diet, APOE isoform and sex on the brain transcriptome and AD-like phenotype.
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Affiliation(s)
- Kyong Nyon Nam
- Department of Environmental and Occupational Health, University of Pittsburgh, United States
| | - Cody M Wolfe
- Department of Environmental and Occupational Health, University of Pittsburgh, United States
| | - Nicholas F Fitz
- Department of Environmental and Occupational Health, University of Pittsburgh, United States
| | - Florent Letronne
- Department of Environmental and Occupational Health, University of Pittsburgh, United States
| | - Emilie L Castranio
- Department of Environmental and Occupational Health, University of Pittsburgh, United States
| | - Anais Mounier
- Department of Environmental and Occupational Health, University of Pittsburgh, United States
| | - Jonathan Schug
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Iliya Lefterov
- Department of Environmental and Occupational Health, University of Pittsburgh, United States.
| | - Radosveta Koldamova
- Department of Environmental and Occupational Health, University of Pittsburgh, United States.
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20
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Fernández MV, Kim JH, Budde JP, Black K, Medvedeva A, Saef B, Deming Y, Del-Aguila J, Ibañez L, Dube U, Harari O, Norton J, Chasse R, Morris JC, Goate A, Cruchaga C. Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. PLoS Genet 2017; 13:e1007045. [PMID: 29091718 PMCID: PMC5683650 DOI: 10.1371/journal.pgen.1007045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/13/2017] [Accepted: 09/27/2017] [Indexed: 12/12/2022] Open
Abstract
Alzheimer disease (AD), Frontotemporal lobar degeneration (FTD), Amyotrophic lateral sclerosis (ALS) and Parkinson disease (PD) have a certain degree of clinical, pathological and molecular overlap. Previous studies indicate that causative mutations in AD and FTD/ALS genes can be found in clinical familial AD. We examined the presence of causative and low frequency coding variants in the AD, FTD, ALS and PD Mendelian genes, in over 450 families with clinical history of AD and over 11,710 sporadic cases and cognitive normal participants from North America. Known pathogenic mutations were found in 1.05% of the sporadic cases, in 0.69% of the cognitively normal participants and in 4.22% of the families. A trend towards enrichment, albeit non-significant, was observed for most AD, FTD and PD genes. Only PSEN1 and PINK1 showed consistent association with AD cases when we used ExAC as the control population. These results suggest that current study designs may contain heterogeneity and contamination of the control population, and that current statistical methods for the discovery of novel genes with real pathogenic variants in complex late onset diseases may be inadequate or underpowered to identify genes carrying pathogenic mutations.
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Affiliation(s)
- Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jong Hun Kim
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Neurology, Dementia Center, Ilsan hospital, National Health Insurance Service, Goyang, South Korea
| | - John P. Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alexandra Medvedeva
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Ben Saef
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jorge Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Laura Ibañez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Medical Scientist Training Program, Division of Biology and Biomedical sciences, School of Medicine, Washington University in Saint Louis, St. Louis, MO, United States of America
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Rachel Chasse
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alison Goate
- Ronald M. Loeb Center for Alzheimer’s disease, Dept of Neuroscience, Icahn School of Medicine at Mount Sinai, ICAHN 10–52, New York, NY, United States of America
| | | | | | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- * E-mail:
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Walter J, Kemmerling N, Wunderlich P, Glebov K. γ-Secretase in microglia - implications for neurodegeneration and neuroinflammation. J Neurochem 2017; 143:445-454. [PMID: 28940294 DOI: 10.1111/jnc.14224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 12/13/2022]
Abstract
γ-Secretase is an intramembrane cleaving protease involved in the generation of the Alzheimer's disease (AD)-associated amyloid β peptide (Aβ). γ-Secretase is ubiquitously expressed in different organs, and also in different cell types of the human brain. Besides the involvement in the proteolytic generation of Aβ from the amyloid precursor protein, γ-secretase cleaves many additional protein substrates, suggesting pleiotropic functions under physiological and pathophysiological conditions. Microglia exert important functions during brain development and homeostasis in adulthood, and accumulating evidence indicates that microglia and neuroinflammatory processes contribute to the pathogenesis of neurodegenerative diseases. Recent studies demonstrate functional implications of γ-secretase in microglia, suggesting that alterations in γ-secretase activity could contribute to AD pathogenesis by modulation of microglia and related neuroinflammatory processes during neurodegeneration. In this review, we discuss the involvement of γ-secretase in the regulation of microglial functions, and the potential relevance of these processes under physiological and pathophysiological conditions. This article is part of the series "Beyond Amyloid".
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Affiliation(s)
- Jochen Walter
- Department of Neurology, University of Bonn, Bonn, Germany
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22
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Analysis of population-specific pharmacogenomic variants using next-generation sequencing data. Sci Rep 2017; 7:8416. [PMID: 28871186 PMCID: PMC5583360 DOI: 10.1038/s41598-017-08468-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/11/2017] [Indexed: 02/03/2023] Open
Abstract
Functional rare variants in drug-related genes are believed to be highly differentiated between ethnic- or racial populations. However, knowledge of population differentiation (PD) of rare single-nucleotide variants (SNVs), remains widely lacking, with the highest fixation indices, (Fst values), from both rare and common variants annotated to specific genes, having only been marginally used to understand PD at the gene level. In this study, we suggest a new, gene-based PD method, PD of Rare and Common variants (PDRC), for analyzing rare variants, as inspired by Generalized Cochran-Mantel-Haenszel (GCMH) statistics, to identify highly population-differentiated drug response-related genes (“pharmacogenes”). Through simulation studies, we reveal that PDRC adequately summarizes rare and common variants, due to PD, over a specific gene. We also applied the proposed method to a real whole-exome sequencing dataset, consisting of 10,000 datasets, from the Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples (T2D-GENES) initiative, and 3,000 datasets from the Genetics of Type 2 diabetes (Go-T2D) repository. Among the 48 genes annotated with Very Important Pharmacogenetic summaries (VIPgenes), in the PharmGKB database, our PD method successfully identified candidate genes with high PD, including ACE, CYP2B6, DPYD, F5, MTHFR, and SCN5A.
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23
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Jennings CG, Landman R, Zhou Y, Sharma J, Hyman J, Movshon JA, Qiu Z, Roberts AC, Roe AW, Wang X, Zhou H, Wang L, Zhang F, Desimone R, Feng G. Opportunities and challenges in modeling human brain disorders in transgenic primates. Nat Neurosci 2017; 19:1123-30. [PMID: 27571191 DOI: 10.1038/nn.4362] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022]
Abstract
Molecular genetic tools have had a profound impact on neuroscience, but until recently their application has largely been confined to a few model species, most notably mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. With the development of new genome engineering technologies such as CRISPR, it is becoming increasingly feasible to apply these molecular tools in a wider range of species, including nonhuman primates. This will lead to many opportunities for brain research, but it will also pose challenges. Here we identify some of these opportunities and challenges in light of recent and foreseeable technological advances and offer some suggestions. Our main focus is on the creation of new primate disease models for understanding the pathological mechanisms of brain disorders and for developing new approaches to effective treatment. However, we also emphasize that primate genetic models have great potential to address many fundamental questions about brain function, providing an essential foundation for future progress in disease research.
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Affiliation(s)
- Charles G Jennings
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rogier Landman
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yang Zhou
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jitendra Sharma
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Julia Hyman
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - J Anthony Movshon
- Center for Neural Science, New York University, New York, New York, USA
| | - Zilong Qiu
- Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Angela C Roberts
- Department of Physiology, Development and Neuroscience, Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Anna Wang Roe
- Interdisciplinary Institute of Neuroscience and Technology, Zhejiang University, Hangzhou, China
| | - Xiaoqin Wang
- Laboratory of Auditory Neurophysiology, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Huihui Zhou
- The Brain Cognition and Brain Disease Institute (BCBDI) for Collaboration Research of SIAT at CAS and McGovern Institute at MIT, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Science, Shenzhen, China
| | - Liping Wang
- Shenzhen Key Lab of Neuropsychiatric Modulation and Collaborative Innovation Center for Brain Science, CAS Center for Excellence in Brain Science and Intelligence Technology, The Brain Cognition and Brain Disease Institute (BCBDI) for Collaboration Research of SIAT at CAS and McGovern Institute at MIT, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Science, Shenzhen, China
| | - Feng Zhang
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Robert Desimone
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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24
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Effect of high fat diet on phenotype, brain transcriptome and lipidome in Alzheimer's model mice. Sci Rep 2017; 7:4307. [PMID: 28655926 PMCID: PMC5487356 DOI: 10.1038/s41598-017-04412-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/15/2017] [Indexed: 02/01/2023] Open
Abstract
We examined the effect of chronic high fat diet (HFD) on amyloid deposition and cognition of 12-months old APP23 mice, and correlated the phenotype to brain transcriptome and lipidome. HFD significantly increased amyloid plaques and worsened cognitive performance compared to mice on normal diet (ND). RNA-seq results revealed that in HFD mice there was an increased expression of genes related to immune response, such as Trem2 and Tyrobp. We found a significant increase of TREM2 immunoreactivity in the cortex in response to HFD, most pronounced in female mice that correlated to the amyloid pathology. Down-regulated by HFD were genes related to neuron projections and synaptic transmission in agreement to the significantly deteriorated neurite morphology and cognition in these mice. To examine the effect of the diet on the brain lipidome, we performed Shotgun Lipidomics. While there was no difference in the total amounts of phospholipids of each class, we revealed that the levels of 24 lipid sub-species in the brain were significantly modulated by HFD. Network visualization of correlated lipids demonstrated overall imbalance with most prominent effect on cardiolipin molecular sub-species. This integrative approach demonstrates that HFD elicits a complex response at molecular, cellular and system levels in the CNS.
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25
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van der Harg JM, Eggels L, Bangel FN, Ruigrok SR, Zwart R, Hoozemans JJM, la Fleur SE, Scheper W. Insulin deficiency results in reversible protein kinase A activation and tau phosphorylation. Neurobiol Dis 2017; 103:163-173. [PMID: 28400135 DOI: 10.1016/j.nbd.2017.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 03/13/2017] [Accepted: 04/05/2017] [Indexed: 12/25/2022] Open
Abstract
Alzheimer's disease (AD) is a highly prevalent multifactorial disease for which Diabetes Mellitus (DM) is a risk factor. Abnormal phosphorylation and aggregation of tau is a key hallmark of AD. In animal models, DM induces or exacerbates the phosphorylation of tau, suggesting that DM may influence the risk at AD by directly facilitating tau pathology. Previously we reported that tau phosphorylation induced in response to metabolic stress is reversible. Since identification and understanding of early players in tau pathology is pivotal for therapeutic intervention, we here investigated the mechanism underlying tau phosphorylation in the diabetic brain and its potential for reversibility. To model DM we used streptozotocin-treatment to induce insulin deficiency in rats. Insulin depletion leads to increased tau phosphorylation in the brain and we investigated the activation status of known tau kinases and phosphatases in this model. We identified protein kinase A (PKA) as a tau kinase activated by DM in the brain. The potential relevance of this signaling pathway to AD pathogenesis is indicated by the increased level of active PKA in temporal cortex of early stage AD patients. Our data indicate that activation of PKA and tau phosphorylation are associated with insulin deficiency per se, rather than the downstream energy deprivation. In vitro studies confirm that insulin deficiency results in PKA activation and tau phosphorylation. Strikingly, both active PKA and induced tau phosphorylation are reversed upon insulin treatment in the steptozotocin animal model. Our data identify insulin deficiency as a direct trigger that induces the activity of the tau kinase PKA and results in tau phosphorylation. The reversibility upon insulin treatment underscores the potential of insulin as an early disease-modifying intervention in AD and other tauopathies.
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Affiliation(s)
- Judith M van der Harg
- Dept. of Genome Analysis, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Dept. of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience VU University, Amsterdam, The Netherlands.
| | - Leslie Eggels
- Dept. Endocrinology and Metabolism, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Fabian N Bangel
- Dept. of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience VU University, Amsterdam, The Netherlands; Dept. of Clinical Genetics and Alzheimer Center, VU University Medical Center, Amsterdam, The Netherlands.
| | - Silvie R Ruigrok
- Dept. of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience VU University, Amsterdam, The Netherlands.
| | - Rob Zwart
- Dept. of Genome Analysis, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | | | - Susanne E la Fleur
- Dept. Endocrinology and Metabolism, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Wiep Scheper
- Dept. of Genome Analysis, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Dept. of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience VU University, Amsterdam, The Netherlands; Dept. of Clinical Genetics and Alzheimer Center, VU University Medical Center, Amsterdam, The Netherlands.
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26
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He Z, Zhang D, Renton AE, Li B, Zhao L, Wang GT, Goate AM, Mayeux R, Leal SM. The Rare-Variant Generalized Disequilibrium Test for Association Analysis of Nuclear and Extended Pedigrees with Application to Alzheimer Disease WGS Data. Am J Hum Genet 2017; 100:193-204. [PMID: 28065470 PMCID: PMC5294711 DOI: 10.1016/j.ajhg.2016.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/06/2016] [Indexed: 01/10/2023] Open
Abstract
Whole-genome and exome sequence data can be cost-effectively generated for the detection of rare-variant (RV) associations in families. Causal variants that aggregate in families usually have larger effect sizes than those found in sporadic cases, so family-based designs can be a more powerful approach than population-based designs. Moreover, some family-based designs are robust to confounding due to population admixture or substructure. We developed a RV extension of the generalized disequilibrium test (GDT) to analyze sequence data obtained from nuclear and extended families. The GDT utilizes genotype differences of all discordant relative pairs to assess associations within a family, and the RV extension combines the single-variant GDT statistic over a genomic region of interest. The RV-GDT has increased power by efficiently incorporating information beyond first-degree relatives and allows for the inclusion of covariates. Using simulated genetic data, we demonstrated that the RV-GDT method has well-controlled type I error rates, even when applied to admixed populations and populations with substructure. It is more powerful than existing family-based RV association methods, particularly for the analysis of extended pedigrees and pedigrees with missing data. We analyzed whole-genome sequence data from families affected by Alzheimer disease to illustrate the application of the RV-GDT. Given the capability of the RV-GDT to adequately control for population admixture or substructure and analyze pedigrees with missing genotype data and its superior power over other family-based methods, it is an effective tool for elucidating the involvement of RVs in the etiology of complex traits.
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Affiliation(s)
- Zongxiao He
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Di Zhang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alan E. Renton
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Biao Li
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Linhai Zhao
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gao T. Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alison M. Goate
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Richard Mayeux
- Department of Neurology, Taub Institute on Alzheimer’s Disease and the Aging Brain and Gertrude H. Sergievsky Center, Columbia University, New York, NY 10027, USA
| | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Corresponding author
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28
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SORL1 variants across Alzheimer's disease European American cohorts. Eur J Hum Genet 2016; 24:1828-1830. [PMID: 27650968 DOI: 10.1038/ejhg.2016.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/27/2016] [Accepted: 08/05/2016] [Indexed: 11/08/2022] Open
Abstract
The accumulation of the toxic Aβ peptide in Alzheimer's disease (AD) largely relies upon an efficient recycling of amyloid precursor protein (APP). Recent genetic association studies have described rare variants in SORL1 with putative pathogenic consequences in the recycling of APP. In this work, we examine the presence of rare coding variants in SORL1 in three different European American cohorts: early-onset, late-onset AD (LOAD) and familial LOAD.
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29
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Yeh FL, Wang Y, Tom I, Gonzalez LC, Sheng M. TREM2 Binds to Apolipoproteins, Including APOE and CLU/APOJ, and Thereby Facilitates Uptake of Amyloid-Beta by Microglia. Neuron 2016; 91:328-40. [DOI: 10.1016/j.neuron.2016.06.015] [Citation(s) in RCA: 466] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/14/2016] [Accepted: 06/07/2016] [Indexed: 11/30/2022]
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30
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What is Your Risk of Contracting Alzheimer's Disease? A Telematics Tool Helps you to Predict it. J Med Syst 2015; 40:3. [PMID: 26573640 DOI: 10.1007/s10916-015-0369-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
Abstract
Alzheimer's disease (AD) is the most common dementia in developed countries. Between the identified risk factors, one of the most important is the age. Its prevalence reaches 24 % in men and 33 % in women over 85 years. Increase in life expectancy, making it a serious public health problem. Prevention of Alzheimer's disease represents a major challenge to health. Given that Alzheimer's disease is largely dependent on the genetics of each person and uninterrupted progress of the age, which is try to make people aware that there are other factors that can alter your chance of developing the Alzheimer disease and although currently not reduce, help is not increased in the near or distant future.The aim of this paper is to develop and evaluate a Web-Mobile application (Alzhe Alert) used to calculate the risk of Alzheimer's from a short questionnaire using a computer or mobile device, so that any user, without requiring computer skills, can access the website to estimate their risk of developing the disease in the coming years depending on their habits and daily basis activities. The users who have realized the questionnaire can to observe in a graph the result, and they will know which is at risk for Alzheimer's at present and over the next 50 years if they continue with the same habits and lifestyle. The objective is that the users can be aware of the risk they have different habits of life about their health. Currently, 243 users (84 women and 159 men) of white race have completed the questionnaire. 76 % of the users have got a risk below the average.
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