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Reus LM, Jansen IE, Tijms BM, Visser PJ, Tesi N, van der Lee SJ, Vermunt L, Peeters CFW, De Groot LA, Hok-A-Hin YS, Chen-Plotkin A, Irwin DJ, Hu WT, Meeter LH, van Swieten JC, Holstege H, Hulsman M, Lemstra AW, Pijnenburg YAL, van der Flier WM, Teunissen CE, del Campo Milan M. Connecting dementia risk loci to the CSF proteome identifies pathophysiological leads for dementia. Brain 2024; 147:3522-3533. [PMID: 38527854 PMCID: PMC11449142 DOI: 10.1093/brain/awae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 03/27/2024] Open
Abstract
Genome-wide association studies have successfully identified many genetic risk loci for dementia, but exact biological mechanisms through which genetic risk factors contribute to dementia remains unclear. Integrating CSF proteomic data with dementia risk loci could reveal intermediate molecular pathways connecting genetic variance to the development of dementia. We tested to what extent effects of known dementia risk loci can be observed in CSF levels of 665 proteins [proximity extension-based (PEA) immunoassays] in a deeply-phenotyped mixed memory clinic cohort [n = 502, mean age (standard deviation, SD) = 64.1 (8.7) years, 181 female (35.4%)], including patients with Alzheimer's disease (AD, n = 213), dementia with Lewy bodies (DLB, n = 50) and frontotemporal dementia (FTD, n = 93), and controls (n = 146). Validation was assessed in independent cohorts (n = 99 PEA platform, n = 198, mass reaction monitoring-targeted mass spectroscopy and multiplex assay). We performed additional analyses stratified according to diagnostic status (AD, DLB, FTD and controls separately), to explore whether associations between CSF proteins and genetic variants were specific to disease or not. We identified four AD risk loci as protein quantitative trait loci (pQTL): CR1-CR2 (rs3818361, P = 1.65 × 10-8), ZCWPW1-PILRB (rs1476679, P = 2.73 × 10-32), CTSH-CTSH (rs3784539, P = 2.88 × 10-24) and HESX1-RETN (rs186108507, P = 8.39 × 10-8), of which the first three pQTLs showed direct replication in the independent cohorts. We identified one AD-specific association between a rare genetic variant of TREM2 and CSF IL6 levels (rs75932628, P = 3.90 × 10-7). DLB risk locus GBA showed positive trans effects on seven inter-related CSF levels in DLB patients only. No pQTLs were identified for FTD loci, either for the total sample as for analyses performed within FTD only. Protein QTL variants were involved in the immune system, highlighting the importance of this system in the pathophysiology of dementia. We further identified pQTLs in stratified analyses for AD and DLB, hinting at disease-specific pQTLs in dementia. Dissecting the contribution of risk loci to neurobiological processes aids in understanding disease mechanisms underlying dementia.
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Affiliation(s)
- Lianne M Reus
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA 90095 CA, USA
| | - Iris E Jansen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Psychiatry, Maastricht University, 6229 ET Maastricht, The Netherlands
| | - Niccoló Tesi
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Sven J van der Lee
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Lisa Vermunt
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, 1081 HZ Amsterdam, The Netherlands
| | - Carel F W Peeters
- Mathematical and Statistical Methods group (Biometris), Wageningen University and Research, Wageningen, 6708 PB Wageningen, The Netherlands
| | - Lisa A De Groot
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Yanaika S Hok-A-Hin
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, 1081 HZ Amsterdam, The Netherlands
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David J Irwin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William T Hu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Rutgers-RWJ Medical School, Institute for Health, Health Care Policy, and Aging Research, Rutgers Biomedical and Health Sciences, New Brunswick, NJ 08901, USA
| | - Lieke H Meeter
- Department of Neurology and Alzheimer Center, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GD, The Netherlands
| | - John C van Swieten
- Department of Neurology and Alzheimer Center, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GD, The Netherlands
| | - Henne Holstege
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Marc Hulsman
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081 HZ Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, 1081 HZ Amsterdam, The Netherlands
| | - Marta del Campo Milan
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, 1081 HZ Amsterdam, The Netherlands
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, 28003 Madrid, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, 08005 Barcelona, Spain
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2
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Duan RN, Liu A, Sun YQ, Xie YF, Wei SJ, Gao S, Liu YM, Li X, Sun WJ, Li JX, Yan CZ, Liu QJ. Loss of Smek1 Induces Tauopathy and Triggers Neurodegeneration by Regulating Microtubule Stability. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400584. [PMID: 39206808 DOI: 10.1002/advs.202400584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/22/2024] [Indexed: 09/04/2024]
Abstract
Suppressor of Mek1 (Smek1) is a regulatory subunit of protein phosphatase 4. Genome-wide association studies have shown the protective effect of SMEK1 in Alzheimer's disease (AD). However, the physiological and pathological roles of Smek1 in AD and other tauopathies are largely unclear. Here, the role of Smek1 in preventing neurodegeneration is investigated in tauopathy. Smek1 is downregulated in the aged human brain. Through single-cell sequencing, a novel neuronal cluster is identified that possesses neurodegenerative characteristics in Smek1-/- mice. Smek1 deficiency caused markedly more severe motor and cognitive impairments in mice, as well as neuronal loss, gliosis, and tau hyperphosphorylation at major glycogen synthase kinase 3β (Gsk3β) sites. Protein-protein interaction analysis revealed that the Ran-binding domain (RanBD) in the N-terminus of Smek1 facilitated binding with kinesin family member 2A (Kif2a). Depletion of Smek1 resulted in cytoplasmic aggregation of Kif2a, axon outgrowth defects, and impaired mitochondrial axonal trafficking. Downregulation of Kif2a markedly attenuated tau hyperphosphorylation and axon outgrowth defects in shSmek1 cells. For the first time, this study demonstrates that Smek1 deficiency progressively induces neurodegeneration by exacerbating tau pathology and mitochondrial dysfunction in an age-dependent manner.
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Affiliation(s)
- Ruo-Nan Duan
- Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Ai Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Yue-Qing Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Yun-Fang Xie
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Shi-Jun Wei
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Shang Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Yi-Ming Liu
- Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Xi Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Wen-Jie Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Jiang-Xia Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Chuan-Zhu Yan
- Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China
- Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, 266000, China
| | - Qi-Ji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266071, China
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Hirakawa H, Terao T. The genetic association between bipolar disorder and dementia: a qualitative review. Front Psychiatry 2024; 15:1414776. [PMID: 39228919 PMCID: PMC11368786 DOI: 10.3389/fpsyt.2024.1414776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 08/05/2024] [Indexed: 09/05/2024] Open
Abstract
Bipolar disorder is a chronic disorder characterized by fluctuations in mood state and energy and recurrent episodes of mania/hypomania and depression. Bipolar disorder may be regarded as a neuro-progressive disorder in which repeated mood episodes may lead to cognitive decline and dementia development. In the current review, we employed genome-wide association studies to comprehensively investigate the genetic variants associated with bipolar disorder and dementia. Thirty-nine published manuscripts were identified: 20 on bipolar disorder and 19 on dementia. The results showed that the genes CACNA1C, GABBR2, SCN2A, CTSH, MSRA, and SH3PXD2A were overlapping between patients with bipolar disorder and dementia. In conclusion, the genes CACNA1C, GABBR2, SCN2A, CTSH, MSRA, and SH3PXD2A may be associated with the neuro-progression of bipolar disorder to dementia. Further genetic studies are needed to comprehensively clarify the role of genes in cognitive decline and the development of dementia in patients with bipolar disorder.
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Affiliation(s)
- Hirofumi Hirakawa
- Department of Neuropsychiatry, Oita University Faculty of Medicine, Yufu, Oita, Japan
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Jonson C, Levine KS, Lake J, Hertslet L, Jones L, Patel D, Kim J, Bandres‐Ciga S, Terry N, Mata IF, Blauwendraat C, Singleton AB, Nalls MA, Yokoyama JS, Leonard HL. Assessing the lack of diversity in genetics research across neurodegenerative diseases: A systematic review of the GWAS Catalog and literature. Alzheimers Dement 2024; 20:5740-5756. [PMID: 39030740 PMCID: PMC11350004 DOI: 10.1002/alz.13873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 07/22/2024]
Abstract
The under-representation of non-European cohorts in neurodegenerative disease genome-wide association studies (GWAS) hampers precision medicine efforts. Despite the inherent genetic and phenotypic diversity in these diseases, GWAS research consistently exhibits a disproportionate emphasis on participants of European ancestry. This study reviews GWAS up to 2022, focusing on non-European or multi-ancestry neurodegeneration studies. We conducted a systematic review of GWAS results and publications up to 2022, focusing on non-European or multi-ancestry neurodegeneration studies. Rigorous article inclusion and quality assessment methods were employed. Of 123 neurodegenerative disease (NDD) GWAS reviewed, 82% predominantly featured European ancestry participants. A single European study identified over 90 risk loci, compared to a total of 50 novel loci in identified in all non-European or multi-ancestry studies. Notably, only six of the loci have been replicated. The significant under-representation of non-European ancestries in NDD GWAS hinders comprehensive genetic understanding. Prioritizing genomic diversity in future research is crucial for advancing NDD therapies and understanding. HIGHLIGHTS: Eighty-two percent of neurodegenerative genome-wide association studies (GWAS) focus on Europeans. Only 6 of 50 novel neurodegenerative disease (NDD) genetic loci have been replicated. Lack of diversity significantly hampers understanding of NDDs. Increasing diversity in NDD genetic research is urgently required. New initiatives are aiming to enhance diversity in NDD research.
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Affiliation(s)
- Caroline Jonson
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Kristin S. Levine
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
| | - Julie Lake
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Linnea Hertslet
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
| | - Lietsel Jones
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
| | - Dhairya Patel
- Integrative Neurogenomics UnitLaboratory of NeurogeneticsNational Institute on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Jeff Kim
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Sara Bandres‐Ciga
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
| | - Nancy Terry
- Division of Library ServicesOffice of Research ServicesNational Institutes of HealthBethesdaMarylandUSA
| | - Ignacio F. Mata
- Genomic Medicine Institute, Lerner Research Institute, Genomic MedicineCleveland Clinic FoundationClevelandOhioUSA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Integrative Neurogenomics UnitLaboratory of NeurogeneticsNational Institute on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Andrew B. Singleton
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Mike A. Nalls
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Jennifer S. Yokoyama
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Hampton L. Leonard
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
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Rautila OS, Kaivola K, Rautila H, Hokkanen L, Launes J, Strandberg TE, Laaksovirta H, Palmio J, Tienari PJ. The shared ancestry between the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles using haplotype sharing trees and HAPTK. Am J Hum Genet 2024; 111:383-392. [PMID: 38242117 PMCID: PMC10870140 DOI: 10.1016/j.ajhg.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The C9orf72 hexanucleotide repeat expansion (HRE) is a common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The inheritance is autosomal dominant, but a high proportion of subjects with the mutation are simplex cases. One possible explanation is de novo expansions of unstable intermediate-length alleles (IAs). Using haplotype sharing trees (HSTs) with the haplotype analysis tool kit (HAPTK), we derived majority-based ancestral haplotypes of HRE samples and discovered that IAs containing ≥18-20 repeats share large haplotypes in common with the HRE. Using HSTs of HRE and IA samples, we demonstrate that the longer IA haplotypes are largely indistinguishable from HRE haplotypes and that several ≥18-20 IA haplotypes share over 5 Mb (>600 markers) haplotypes in common with the HRE haplotypes. These analysis tools allow physical understanding of the haplotype blocks shared with the majority-based ancestral haplotype. Our results demonstrate that the haplotypes with longer IAs belong to the same pool of haplotypes as the HRE and suggest that longer IAs represent potential premutation alleles.
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Affiliation(s)
- Osma S Rautila
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland.
| | - Karri Kaivola
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Harri Rautila
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Laura Hokkanen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Jyrki Launes
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Timo E Strandberg
- University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hannu Laaksovirta
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Johanna Palmio
- Neuromuscular Research Center, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Pentti J Tienari
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland
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Jonson C, Levine KS, Lake J, Hertslet L, Jones L, Patel D, Kim J, Bandres-Ciga S, Terry N, Mata IF, Blauwendraat C, Singleton AB, Nalls MA, Yokoyama JS, Leonard HL. Assessing the lack of diversity in genetics research across neurodegenerative diseases: a systematic review of the GWAS Catalog and literature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.08.24301007. [PMID: 38260595 PMCID: PMC10802650 DOI: 10.1101/2024.01.08.24301007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Importance The under-representation of participants with non-European ancestry in genome-wide association studies (GWAS) is a critical issue that has significant implications, including hindering the progress of precision medicine initiatives. This issue is particularly significant in the context of neurodegenerative diseases (NDDs), where current therapeutic approaches have shown limited success. Addressing this under-representation is crucial to harnessing the full potential of genomic medicine in underserved communities and improving outcomes for NDD patients. Objective Our primary objective was to assess the representation of non-European ancestry participants in genetic discovery efforts related to NDDs. We aimed to quantify the extent of inclusion of diverse ancestry groups in NDD studies and determine the number of associated loci identified in more inclusive studies. Specifically, we sought to highlight the disparities in research efforts and outcomes between studies predominantly involving European ancestry participants and those deliberately targeting non-European or multi-ancestry populations across NDDs. Evidence Review We conducted a systematic review utilizing existing GWAS results and publications to assess the inclusion of diverse ancestry groups in neurodegeneration and neurogenetics studies. Our search encompassed studies published up to the end of 2022, with a focus on identifying research that deliberately included non-European or multi-ancestry cohorts. We employed rigorous methods for the inclusion of identified articles and quality assessment. Findings Our review identified a total of 123 NDD GWAS. Strikingly, 82% of these studies predominantly featured participants of European ancestry. Endeavors specifically targeting non-European or multi-ancestry populations across NDDs identified only 52 risk loci. This contrasts with predominantly European studies, which reported over 90 risk loci for a single disease. Encouragingly, over 65% of these discoveries occurred in 2020 or later, indicating a recent increase in studies deliberately including non-European cohorts. Conclusions and relevance Our findings underscore the pressing need for increased diversity in neurodegenerative research. The significant under-representation of non-European ancestry participants in NDD GWAS limits our understanding of the genetic underpinnings of these diseases. To advance the field of neurodegenerative research and develop more effective therapies, it is imperative that future investigations prioritize and harness the genomic diversity present within and across global populations.
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Affiliation(s)
- Caroline Jonson
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
- Pharmaceutical Sciences and Pharmacogenomics, UCSF, San Francisco, CA, USA
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Kristin S. Levine
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
| | - Julie Lake
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Linnea Hertslet
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
| | - Lietsel Jones
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
| | - Dhairya Patel
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jeff Kim
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
| | - Nancy Terry
- Division of Library Services, Office of Research Services, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Ignacio F. Mata
- Genomic Medicine Institute, Lerner Research Institute, Genomic Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Mike A. Nalls
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Jennifer S. Yokoyama
- Pharmaceutical Sciences and Pharmacogenomics, UCSF, San Francisco, CA, USA
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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Holtman IR, Glass CK, Nott A. Interpretation of Neurodegenerative GWAS Risk Alleles in Microglia and their Interplay with Other Cell Types. ADVANCES IN NEUROBIOLOGY 2024; 37:531-544. [PMID: 39207711 DOI: 10.1007/978-3-031-55529-9_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Microglia have been implicated in numerous neurodegenerative and neuroinflammatory disorders; however, the causal contribution of this immune cell type is frequently debated. Genetic studies offer a unique vantage point in that they infer causality over a secondary consequence. Genome-wide association studies (GWASs) have identified hundreds of loci in the genome that are associated with susceptibility to neurodegenerative disorders. GWAS studies implicate microglia in the pathogenesis of Alzheimer's disease (AD), Parkinson's disease (PD), multiple sclerosis (MS), and to a lesser degree suggest a role for microglia in vascular dementia (VaD), frontotemporal dementia (FTD), and amyotrophic lateral sclerosis (ALS), and other neurodegenerative and neuropsychiatric disorders. The contribution and function of GWAS risk loci on disease progression is an ongoing field of study, in which large genomic datasets, and an extensive framework of computational tools, have proven to be crucial. Several GWAS risk loci are shared between disorders, pointing towards common pleiotropic mechanisms. In this chapter, we introduce key concepts in GWAS and post-GWAS interpretation of neurodegenerative disorders, with a focus on GWAS risk genes implicated in microglia, their interplay with other cell types and shared convergence of GWAS risk loci on microglia.
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Affiliation(s)
- Inge R Holtman
- Department of Biomedical Sciences, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, UC San Diego, La Jolla, CA, USA.
- Department of Medicine, School of Medicine, UC San Diego, La Jolla, CA, USA.
| | - Alexi Nott
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute, Imperial College London, London, UK
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Nassan M, Daghlas I, Piras IS, Rogalski E, Reus LM, Pijnenburg Y, Cuddy LK, Saxena R, Mesulam MM, Huentelman M. Evaluating the association between genetically proxied ACE inhibition and dementias. Alzheimers Dement 2023; 19:3894-3901. [PMID: 37023267 DOI: 10.1002/alz.13062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
INTRODUCTION Angiotensin-converting enzyme (ACE) has been implicated in the metabolism of amyloid beta; however, the causal effect of ACE inhibition on risk of Alzheimer's disease (AD) dementia and other common dementias is largely unknown. METHODS We examined the causal association of genetically proxied ACE inhibition with four types of dementias using a two-sample Mendelian randomization (MR) approach. RESULTS Genetically proxied ACE inhibition was associated with increased risk of AD dementia (odds ratio per one standard deviation reduction in serum ACE [95% confidence interval]; 1.07 [1.04-1.10], P = 5 × 10-07 ) and frontotemporal dementia (1.16 [1.04-1.29], P = 0.01) but not with Lewy body dementia or vascular dementia (P > 0.05). These findings were independently replicated and remained consistent in sensitivity analyses. DISCUSSION This comprehensive MR study provided genetic evidence for an association between ACE inhibition and the risk for AD and frontotemporal dementias. These results should encourage further studies of the neurocognitive effects of ACE inhibition. HIGHLIGHTS This study evaluated genetically proxied angiotensin-converting enzyme (ACE) inhibition association with dementias. The results suggest an association between ACE inhibition and Alzheimer's disease. The results suggest an association between ACE inhibition and frontotemporal dementia. Those associations can be interpreted as potentially causal.
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Affiliation(s)
- Malik Nassan
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Chicago, Illinois, USA
| | - Iyas Daghlas
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Tgen, Phoenix, Arizona, USA
| | - Emily Rogalski
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Chicago, Illinois, USA
| | - Lianne M Reus
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California, USA
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Yolande Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Leah K Cuddy
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Richa Saxena
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - M-Marsel Mesulam
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Chicago, Illinois, USA
| | - Matt Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Tgen, Phoenix, Arizona, USA
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Kaivola K, Pirinen M, Laaksovirta H, Jansson L, Rautila O, Launes J, Hokkanen L, Lahti J, Eriksson JG, Strandberg TE, FinnGen, Tienari PJ. C9orf72 hexanucleotide repeat allele tagging SNPs: Associations with ALS risk and longevity. Front Genet 2023; 14:1087098. [PMID: 36936421 PMCID: PMC10014923 DOI: 10.3389/fgene.2023.1087098] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/23/2023] [Indexed: 03/05/2023] Open
Abstract
C9orf72 hexanucleotide repeat expansion is a common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The C9orf72 locus may harbor residual risk outside the hexanucleotide repeat expansion, but the evidence is conflicting. Here, we first compared 683 unrelated amyotrophic lateral sclerosis cases and 3,196 controls with Finnish ancestry to find best single nucleotide polymorphisms that tag the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles. Rs2814707 was the best tagging single nucleotide polymorphisms for intermediate-length alleles with ≥7 repeats (p = 5 × 10-307) and rs139185008 for the hexanucleotide repeat expansion (p = 7 × 10-114) as well as alleles with ≥20 repeats. rs139185008*C associated with amyotrophic lateral sclerosis after removing cases with the hexanucleotide repeat expansion, especially in the subpopulation homozygous for the rs2814707*T (p = 0.0002, OR = 5.06), which supports the concept of residual amyotrophic lateral sclerosis risk at the C9orf72 haplotypes other than the hexanucleotide repeat expansion. We then leveraged Finnish biobank data to test the effects of rs2814707*T and rs139185008*C on longevity after removing individuals with amyotrophic lateral sclerosis / frontotemporal dementia diagnoses. In the discovery cohort (n = 230,006), the frequency of rs139185008*C heterozygotes decreased significantly with age in the comparisons between 50 and 80 years vs. >80 years (p = 0.0005) and <50 years vs. >80 years (p = 0.0001). The findings were similar but less significant in a smaller replication cohort (2-sided p = 0.037 in 50-80 years vs. >80 years and 0.061 in <50 years vs. >80 years). Analysis of the allele frequencies in 5-year bins demonstrated that the decrease of rs139185008*C started after the age of 70 years. The hexanucleotide repeat expansion tagging single nucleotide polymorphisms decreasing frequency with age suggests its' association with age-related diseases probably also outside amyotrophic lateral sclerosis / frontotemporal dementia.
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Affiliation(s)
- Karri Kaivola
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- *Correspondence: Karri Kaivola,
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Hannu Laaksovirta
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Lilja Jansson
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Osma Rautila
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Jyrki Launes
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Laura Hokkanen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Johan G. Eriksson
- Folkhälsan Research Center, Helsinki, Finland
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of General Practice and Primary Healthcare, University of Helsinki, Helsinki, Finland
| | - Timo E. Strandberg
- University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- University of Oulu, Center for Life Course Health Research, Oulu, Finland
| | | | - Pentti J. Tienari
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
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Letter to the editor on a paper by Kaivola et al. (2020): carriership of two copies of C9orf72 hexanucleotide repeat intermediate-length alleles is not associated with amyotrophic lateral sclerosis or frontotemporal dementia. Acta Neuropathol Commun 2022; 10:141. [PMID: 36131298 PMCID: PMC9494883 DOI: 10.1186/s40478-022-01438-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
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