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Wang JC, Ramaswami G, Geschwind DH. Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility. Sci Rep 2021; 11:5748. [PMID: 33707641 PMCID: PMC7970949 DOI: 10.1038/s41598-021-85061-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified, implicating RNA and protein metabolism and intracellular transport, among other biological mechanisms. To achieve a systems-level understanding of the mechanisms governing ALS pathophysiology, we built gene co-expression networks using RNA-sequencing data from control human spinal cord samples, identifying 13 gene co-expression modules, each of which represents a distinct biological process or cell type. Analysis of four RNA-seq datasets from a range of ALS disease-associated contexts reveal dysregulation in numerous modules related to ribosomal function, wound response, and leukocyte activation, implicating astrocytes, oligodendrocytes, endothelia, and microglia in ALS pathophysiology. To identify potentially causal processes, we partitioned heritability across the genome, finding that ALS common genetic risk is enriched within two specific modules, SC.M4, representing genes related to RNA processing and gene regulation, and SC.M2, representing genes related to intracellular transport and autophagy and enriched in oligodendrocyte markers. Top hub genes of this latter module include ALS-implicated risk genes such as KPNA3, TMED2, and NCOA4, the latter of which regulates ferritin autophagy, implicating this process in ALS pathophysiology. These unbiased, genome-wide analyses confirm the utility of a systems approach to understanding the causes and drivers of ALS.
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Affiliation(s)
- Jerry C Wang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gokul Ramaswami
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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Gordon A, Yoon SJ, Tran SS, Makinson CD, Park JY, Andersen J, Valencia AM, Horvath S, Xiao X, Huguenard JR, Pașca SP, Geschwind DH. Long-term maturation of human cortical organoids matches key early postnatal transitions. Nat Neurosci 2021; 24:331-342. [PMID: 33619405 PMCID: PMC8109149 DOI: 10.1038/s41593-021-00802-y] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023]
Abstract
Human stem-cell-derived models provide the promise of accelerating our understanding of brain disorders, but not knowing whether they possess the ability to mature beyond mid- to late-fetal stages potentially limits their utility. We leveraged a directed differentiation protocol to comprehensively assess maturation in vitro. Based on genome-wide analysis of the epigenetic clock and transcriptomics, as well as RNA editing, we observe that three-dimensional human cortical organoids reach postnatal stages between 250 and 300 days, a timeline paralleling in vivo development. We demonstrate the presence of several known developmental milestones, including switches in the histone deacetylase complex and NMDA receptor subunits, which we confirm at the protein and physiological levels. These results suggest that important components of an intrinsic in vivo developmental program persist in vitro. We further map neurodevelopmental and neurodegenerative disease risk genes onto in vitro gene expression trajectories to provide a resource and webtool (Gene Expression in Cortical Organoids, GECO) to guide disease modeling.
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Affiliation(s)
- Aaron Gordon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Se-Jin Yoon
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Stephen S Tran
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Department of Integrative Biology, University of California Los Angeles, Angeles, CA, USA
| | - Christopher D Makinson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Jin Young Park
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Jimena Andersen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Alfredo M Valencia
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Xinshu Xiao
- Department of Integrative Biology, University of California Los Angeles, Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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Jabbari E, Koga S, Valentino RR, Reynolds RH, Ferrari R, Tan MMX, Rowe JB, Dalgard CL, Scholz SW, Dickson DW, Warner TT, Revesz T, Höglinger GU, Ross OA, Ryten M, Hardy J, Shoai M, Morris HR. Genetic determinants of survival in progressive supranuclear palsy: a genome-wide association study. Lancet Neurol 2021; 20:107-116. [PMID: 33341150 PMCID: PMC7116626 DOI: 10.1016/s1474-4422(20)30394-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The genetic basis of variation in the progression of primary tauopathies has not been determined. We aimed to identify genetic determinants of survival in progressive supranuclear palsy (PSP). METHODS In stage one of this two stage genome-wide association study (GWAS), we included individuals with PSP, diagnosed according to pathological and clinical criteria, from two separate cohorts: the 2011 PSP GWAS cohort, from brain banks based at the Mayo Clinic (Jacksonville, FL, USA) and in Munich (Germany), and the University College London PSP cohort, from brain banks and the PROSPECT study, a UK-wide longitudinal study of patients with atypical parkinsonian syndromes. Individuals were included if they had clinical data available on sex, age at motor symptom onset, disease duration (from motor symptom onset to death or to the date of censoring, Dec 1, 2019, if individuals were alive), and PSP phenotype (with reference to the 2017 Movement Disorder Society criteria). Genotype data were used to do a survival GWAS using a Cox proportional hazards model. In stage two, data from additional individuals from the Mayo Clinic brain bank, which were obtained after the 2011 PSP GWAS, were used for a pooled analysis. We assessed the expression quantitative trait loci (eQTL) profile of variants that passed genome-wide significance in our GWAS using the Functional Mapping and Annotation of GWAS platform, and did colocalisation analyses using the eQTLGen and PsychENCODE datasets. FINDINGS Data were collected and analysed between Aug 1, 2016, and Feb 1, 2020. Data were available for 1001 individuals of white European ancestry with PSP in stage one. We found a genome-wide significant association with survival at chromosome 12 (lead single nucleotide polymorphism rs2242367, p=7·5 × 10-10, hazard ratio 1·42 [95% CI 1·22-1·67]). rs2242367 was associated with survival in the individuals added in stage two (n=238; p=0·049, 1·22 [1·00-1·48]) and in the pooled analysis of both stages (n=1239; p=1·3 × 10-10, 1·37 [1·25-1·51]). An eQTL database screen revealed that rs2242367 is associated with increased expression of LRRK2 and two long intergenic non-coding RNAs (lncRNAs), LINC02555 and AC079630.4, in whole blood. Although we did not detect a colocalisation signal for LRRK2, analysis of the PSP survival signal and eQTLs for LINC02555 in the eQTLGen blood dataset revealed a posterior probability of hypothesis 4 of 0·77, suggesting colocalisation due to a single shared causal variant. INTERPRETATION Genetic variation at the LRRK2 locus was associated with survival in PSP. The mechanism of this association might be through a lncRNA-regulated effect on LRRK2 expression because LINC02555 has previously been shown to regulate LRRK2 expression. LRRK2 has been associated with sporadic and familial forms of Parkinson's disease, and our finding suggests a genetic overlap with PSP. Further functional studies will be important to assess the potential of LRRK2 modulation as a disease-modifying therapy for PSP and related tauopathies. FUNDING PSP Association, CBD Solutions, Medical Research Council (UK).
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Affiliation(s)
- Edwin Jabbari
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK; Movement Disorders Centre, University College London Queen Square Institute of Neurology, London, UK.
| | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Regina H Reynolds
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK; Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK
| | - Raffaele Ferrari
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK
| | - Manuela M X Tan
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK; Movement Disorders Centre, University College London Queen Square Institute of Neurology, London, UK
| | - James B Rowe
- Department of Clinical Neurosciences, University of Cambridge, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Sonja W Scholz
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA; Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Thomas T Warner
- Reta Lila Weston Institute, University College London Queen Square Institute of Neurology, London, UK; Queen Square Brain Bank for Neurological Disorders, University College London Queen Square Institute of Neurology, London, UK
| | - Tamas Revesz
- Reta Lila Weston Institute, University College London Queen Square Institute of Neurology, London, UK; Queen Square Brain Bank for Neurological Disorders, University College London Queen Square Institute of Neurology, London, UK
| | - Günter U Höglinger
- German Center for Neurodegenerative Diseases, Munich, Germany; Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mina Ryten
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK; Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK
| | - John Hardy
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK; Reta Lila Weston Institute, University College London Queen Square Institute of Neurology, London, UK; Dementia Research Institute at University College London, University College London Queen Square Institute of Neurology, London, UK; Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region, China
| | - Maryam Shoai
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK; Movement Disorders Centre, University College London Queen Square Institute of Neurology, London, UK.
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Wen Y, Zhou Y, Jiao B, Shen L. Genetics of Progressive Supranuclear Palsy: A Review. JOURNAL OF PARKINSON'S DISEASE 2021; 11:93-105. [PMID: 33104043 PMCID: PMC7990399 DOI: 10.3233/jpd-202302] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/26/2020] [Indexed: 02/06/2023]
Abstract
Progressive supranuclear palsy (PSP) is an atypical parkinsonism with prominent 4R-tau neuropathology, and the classical clinical phenotype is characterized by vertical supranuclear gaze palsy, unprovoked falls, akinetic-rigid syndrome and cognitive decline. Though PSP is generally regarded as sporadic, there is increasing evidence suggesting that a series of common and rare genetic variants impact on sporadic and familial forms of PSP. To date, more than 10 genes have been reported to show a potential association with PSP. Among these genes, the microtubule-associated protein tau (MAPT) is the risk locus with the strongest effect size on sporadic PSP in the case-control genome-wide association studies (GWAS). Additionally, MAPT mutations are the most common cause of familial PSP while the leucine-rich repeat kinase 2 (LRRK2) is a rare monogenic cause of PSP, and several other gene mutations may mimic the PSP phenotype, like the dynactin subunit 1 (DCTN1). In total, 15 MAPT mutations have been identified in cases with PSP, and the mean age at onset is much earlier than in cases carrying LRRK2 or DCTN1 mutations. GWAS have further identified several risk loci of PSP, proposing molecular pathways related to PSP. The present review focused on genetic studies on PSP and summarized genetic factors of PSP, which may help to elucidate the underlying pathogenesis and provide new perspectives for therapeutic strategies.
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Affiliation(s)
- Yafei Wen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Yafang Zhou
- Department of Geriatrics Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, PR China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, Hunan, PR China
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Wamsley B, Geschwind DH. Functional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease. Curr Opin Genet Dev 2020; 65:117-125. [PMID: 32634676 PMCID: PMC8171040 DOI: 10.1016/j.gde.2020.05.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/24/2020] [Indexed: 12/30/2022]
Abstract
Neurodegenerative and neuropsychiatric disorders are pervasive and debilitating conditions characterized by diverse clinical syndromes and comorbidities, whose origins are as complex and heterogeneous as their associated phenotypes. Risk for these disorders involves substantial genetic liability, which has fueled large-scale genetic studies that have led to a flood of discoveries. In turn, these discoveries have exposed substantial gaps in our knowledge with regards to the complicated genetic architecture of each disorder and the substantial amount of genetic overlap among disorders, which implies some degree of shared pathophysiology underlying these clinically distinct, multifactorial disorders. Understanding the role of specific genetic variants will involve resolving the connections between molecular pathways, heterogeneous cell types, specific circuits and disease pathogenesis at the tissue and patient level. We consider the current known genetic basis of these disorders and highlight the utility of molecular systems approaches that establish the function of genetic variation in the context of specific neurobiological networks, cell-types, and life stages. Beyond expanding our knowledge of disease mechanisms, understanding these relationships provides promise for early detection and potential therapeutic interventions.
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Affiliation(s)
- Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Program in Neurobehavioral Genetics and Center for Autism Research and Treatment Semel Institute and Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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56
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Tau at the interface between neurodegeneration and neuroinflammation. Genes Immun 2020; 21:288-300. [PMID: 33011744 DOI: 10.1038/s41435-020-00113-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022]
Abstract
Tau is an evolutionary conserved protein that promotes the assembly and stabilization of microtubules in neuronal axons. Complex patterns of posttranslational modifications (PTMs) dynamically regulate tau biochemical properties and consequently its functions. An imbalance in tau PTMs has been connected with a broad spectrum of neurodegenerative conditions which are collectively known as tauopathies and include Alzheimer's disease (AD), progressive supranuclear palsy (PSP), and corticobasal degeneration (CBD) among others. The hallmark of these neurological disorders is the presence in the brain of fibrillary tangles constituted of misfolded species of hyper-phosphorylated tau. The pathological events leading to tau aggregation are still largely unknown but increasing evidence suggests that neuroinflammation plays a critical role in tangle formation. Moreover, tau aggregation itself could enhance inflammation through feed-forward mechanisms, amplifying the initial neurotoxic insults. Protective effects of tau against neuroinflammation have been also documented, adding another layer of complexity to this phenomenon. Here, we will review the current knowledge on tau regulation and function in health and disease. In particular, we will address its emerging role in connecting neurodegenerative and neuroinflammatory processes.
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57
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Vergouw LJM, Melhem S, Donker Kaat L, Chiu WZ, Kuipers DJS, Breedveld G, Boon AJW, Wang LS, Naj AC, Mlynarksi E, Cantwell L, Quadri M, Ross OA, Dickson DW, Schellenberg GD, van Swieten JC, Bonifati V, de Jong FJ. LRP10 variants in progressive supranuclear palsy. Neurobiol Aging 2020; 94:311.e5-311.e10. [PMID: 32527607 PMCID: PMC8281359 DOI: 10.1016/j.neurobiolaging.2020.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/31/2020] [Accepted: 04/19/2020] [Indexed: 01/29/2023]
Abstract
The aim of this study was to explore whether variants in LRP10, recently associated with Parkinson's disease and dementia with Lewy bodies, are observed in 2 large cohorts (discovery and validation cohort) of patients with progressive supranuclear palsy (PSP). A total of 950 patients with PSP were enrolled: 246 patients with PSP (n = 85 possible (35%), n = 128 probable (52%), n = 33 definite (13%)) in the discovery cohort and 704 patients with definite PSP in the validation cohort. Sanger sequencing of all LRP10 exons and exon-intron boundaries was performed in the discovery cohort, and whole-exome sequencing was performed in the validation cohort. Two patients from the discovery cohort and 8 patients from the validation cohort carried a rare, heterozygous, and possibly pathogenic LRP10 variant (p.Gly326Asp, p.Asp389Asn, and p.Arg158His, p.Cys220Tyr, p.Thr278Ala, p.Gly306Asp, p.Glu486Asp, p.Arg554∗, p.Arg661Cys). In conclusion, possibly pathogenic LRP10 variants occur in a small fraction of patients with PSP and may be overrepresented in these patients compared with controls. This suggests that possibly pathogenic LRP10 variants may play a role in the development of PSP.
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Affiliation(s)
- Leonie J M Vergouw
- Department of Neurology and Alzheimer Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Shamiram Melhem
- Department of Neurology and Alzheimer Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Laura Donker Kaat
- Department of Neurology and Alzheimer Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Wang Z Chiu
- Department of Neurology and Alzheimer Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Demy J S Kuipers
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Guido Breedveld
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Agnita J W Boon
- Department of Neurology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Adam C Naj
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Mlynarksi
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Cantwell
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marialuisa Quadri
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John C van Swieten
- Department of Neurology and Alzheimer Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vincenzo Bonifati
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Frank Jan de Jong
- Department of Neurology and Alzheimer Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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58
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Jones E, Hummerich H, Viré E, Uphill J, Dimitriadis A, Speedy H, Campbell T, Norsworthy P, Quinn L, Whitfield J, Linehan J, Jaunmuktane Z, Brandner S, Jat P, Nihat A, How Mok T, Ahmed P, Collins S, Stehmann C, Sarros S, Kovacs GG, Geschwind MD, Golubjatnikov A, Frontzek K, Budka H, Aguzzi A, Karamujić-Čomić H, van der Lee SJ, Ibrahim-Verbaas CA, van Duijn CM, Sikorska B, Golanska E, Liberski PP, Calero M, Calero O, Sanchez-Juan P, Salas A, Martinón-Torres F, Bouaziz-Amar E, Haïk S, Laplanche JL, Brandel JP, Amouyel P, Lambert JC, Parchi P, Bartoletti-Stella A, Capellari S, Poleggi A, Ladogana A, Pocchiari M, Aneli S, Matullo G, Knight R, Zafar S, Zerr I, Booth S, Coulthart MB, Jansen GH, Glisic K, Blevins J, Gambetti P, Safar J, Appleby B, Collinge J, Mead S. Identification of novel risk loci and causal insights for sporadic Creutzfeldt-Jakob disease: a genome-wide association study. Lancet Neurol 2020; 19:840-848. [PMID: 32949544 PMCID: PMC8220892 DOI: 10.1016/s1474-4422(20)30273-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Human prion diseases are rare and usually rapidly fatal neurodegenerative disorders, the most common being sporadic Creutzfeldt-Jakob disease (sCJD). Variants in the PRNP gene that encodes prion protein are strong risk factors for sCJD but, although the condition has similar heritability to other neurodegenerative disorders, no other genetic risk loci have been confirmed. We aimed to discover new genetic risk factors for sCJD, and their causal mechanisms. METHODS We did a genome-wide association study of sCJD in European ancestry populations (patients diagnosed with probable or definite sCJD identified at national CJD referral centres) with a two-stage study design using genotyping arrays and exome sequencing. Conditional, transcriptional, and histological analyses of implicated genes and proteins in brain tissues, and tests of the effects of risk variants on clinical phenotypes, were done using deep longitudinal clinical cohort data. Control data from healthy individuals were obtained from publicly available datasets matched for country. FINDINGS Samples from 5208 cases were obtained between 1990 and 2014. We found 41 genome-wide significant single nucleotide polymorphisms (SNPs) and independently replicated findings at three loci associated with sCJD risk; within PRNP (rs1799990; additive model odds ratio [OR] 1·23 [95% CI 1·17-1·30], p=2·68 × 10-15; heterozygous model p=1·01 × 10-135), STX6 (rs3747957; OR 1·16 [1·10-1·22], p=9·74 × 10-9), and GAL3ST1 (rs2267161; OR 1·18 [1·12-1·25], p=8·60 × 10-10). Follow-up analyses showed that associations at PRNP and GAL3ST1 are likely to be caused by common variants that alter the protein sequence, whereas risk variants in STX6 are associated with increased expression of the major transcripts in disease-relevant brain regions. INTERPRETATION We present, to our knowledge, the first evidence of statistically robust genetic associations in sporadic human prion disease that implicate intracellular trafficking and sphingolipid metabolism as molecular causal mechanisms. Risk SNPs in STX6 are shared with progressive supranuclear palsy, a neurodegenerative disease associated with misfolding of protein tau, indicating that sCJD might share the same causal mechanisms as prion-like disorders. FUNDING Medical Research Council and the UK National Institute of Health Research in part through the Biomedical Research Centre at University College London Hospitals National Health Service Foundation Trust.
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Affiliation(s)
- Emma Jones
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Holger Hummerich
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Emmanuelle Viré
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - James Uphill
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Athanasios Dimitriadis
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Helen Speedy
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Tracy Campbell
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Penny Norsworthy
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Liam Quinn
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Jerome Whitfield
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Jacqueline Linehan
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Zane Jaunmuktane
- Division of Neuropathology, University College London Hospitals National Health Service Foundation Trust, London, UK; Department of Clinical and Movement Neurosciences and Queen Square Brain Bank for Neurological Disorders, University College London Queen Square Institute of Neurology, London, UK
| | - Sebastian Brandner
- Division of Neuropathology, University College London Hospitals National Health Service Foundation Trust, London, UK; Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK
| | - Parmjit Jat
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Akin Nihat
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK; National Prion Clinic, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Tze How Mok
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK; National Prion Clinic, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Parvin Ahmed
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK
| | - Steven Collins
- Australian National Creutzfeldt-Jakob Disease Registry, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Christiane Stehmann
- Australian National Creutzfeldt-Jakob Disease Registry, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Shannon Sarros
- Australian National Creutzfeldt-Jakob Disease Registry, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Gabor G Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria; Department of Laboratory Medicine and Pathobiology and Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, ON, Canada; Laboratory Medicine Program, Krembil Brain Institute, University Health Network, Toronto, ON, Canada
| | - Michael D Geschwind
- University of California San Francisco Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Aili Golubjatnikov
- University of California San Francisco Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Herbert Budka
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland; Medical University Vienna, Vienna, Austria
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | | | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands
| | | | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands; Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Beata Sikorska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Ewa Golanska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Pawel P Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Miguel Calero
- Chronic Disease Programme (UFIEC-CROSADIS) and Network Centre for Biomedical Research in Neurodegenerative Diseases (CIBERNED), and Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Olga Calero
- Chronic Disease Programme (UFIEC-CROSADIS) and Network Centre for Biomedical Research in Neurodegenerative Diseases (CIBERNED), and Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Pascual Sanchez-Juan
- Neurology Service, University Hospital Marqués de Valdecilla, University of Cantabria, CIBERNED and IDIVAL, Santander, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Federico Martinón-Torres
- Translational Paediatrics and Infectious Diseases, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Galicia, Spain
| | - Elodie Bouaziz-Amar
- Department of Biochemistry and Molecular Biology, Lariboisière Hospital, AP-HP, University of Paris, Paris, France
| | - Stéphane Haïk
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, Paris, France; Cellule nationale de référence des maladies de Creutzfeldt-Jakob, AP-HP, University Hospital Pitié-Salpêtrière, Paris, France
| | - Jean-Louis Laplanche
- Department of Biochemistry and Molecular Biology, Lariboisière Hospital, AP-HP, University of Paris, Paris, France
| | - Jean-Phillipe Brandel
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, Paris, France; Cellule nationale de référence des maladies de Creutzfeldt-Jakob, AP-HP, University Hospital Pitié-Salpêtrière, Paris, France
| | - Phillipe Amouyel
- INSERM, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE, Labex DISTALZ, University of Lille, Lille, France
| | - Jean-Charles Lambert
- INSERM, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE, Labex DISTALZ, University of Lille, Lille, France
| | - Piero Parchi
- IRCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Sabina Capellari
- IRCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Anna Poleggi
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Ladogana
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | | | - Serena Aneli
- Department of Medical Sciences, Università degli studi di Torino, Torino, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, Università degli studi di Torino, Torino, Italy
| | - Richard Knight
- National Creutzfeldt-Jakob Disease Research and Surveillance Unit, Edinburgh, UK
| | - Saima Zafar
- Department of Neurology, Clinical Dementia Centre and National Reference Centre for Creutzfeldt-Jakob Disease Surveillance, University Medical School, Göttingen, Germany; German Centre for Neurodegenerative Diseases (DZNE), Göttingen, Germany; Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Inga Zerr
- Department of Neurology, Clinical Dementia Centre and National Reference Centre for Creutzfeldt-Jakob Disease Surveillance, University Medical School, Göttingen, Germany; German Centre for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Stephanie Booth
- Prion Disease Program, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Michael B Coulthart
- Canadian Creutzfeldt-Jakob Disease Surveillance System, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Gerard H Jansen
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Katie Glisic
- Departments of Pathology and Neurology, Case Western Reserve University, Cleveland, OH, USA; National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, USA
| | - Janis Blevins
- Departments of Pathology and Neurology, Case Western Reserve University, Cleveland, OH, USA; National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, USA
| | - Pierluigi Gambetti
- Departments of Pathology and Neurology, Case Western Reserve University, Cleveland, OH, USA; National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, USA
| | - Jiri Safar
- Departments of Pathology and Neurology, Case Western Reserve University, Cleveland, OH, USA; National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, USA
| | - Brian Appleby
- Departments of Pathology and Neurology, Case Western Reserve University, Cleveland, OH, USA; National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, USA
| | - John Collinge
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK; National Prion Clinic, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Simon Mead
- Medical Research Council Prion Unit, University College London Institute of Prion Diseases, London, UK; National Prion Clinic, University College London Hospitals National Health Service Foundation Trust, London, UK.
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Valentino RR, Tamvaka N, Heckman MG, Johnson PW, Soto-Beasley AI, Walton RL, Koga S, Uitti RJ, Wszolek ZK, Dickson DW, Ross OA. Associations of mitochondrial genomic variation with corticobasal degeneration, progressive supranuclear palsy, and neuropathological tau measures. Acta Neuropathol Commun 2020; 8:162. [PMID: 32943110 PMCID: PMC7495714 DOI: 10.1186/s40478-020-01035-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 09/06/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial health is important in ageing and dysfunctional oxidative phosphorylation (OXPHOS) accelerates ageing and influences neurodegeneration. Mitochondrial DNA (mtDNA) codes for vital OXPHOS subunits and mtDNA background has been associated with neurodegeneration; however, no study has characterised mtDNA variation in Progressive supranuclear palsy (PSP) or Corticobasal degeneration (CBD) risk or pathogenesis. In this case-control study, 910 (42.6% male) neurologically-healthy controls, 1042 (54.1% male) pathologically-confirmed PSP cases, and 171 (52.0% male) pathologically-confirmed CBD cases were assessed to determine how stable mtDNA polymorphisms, in the form of mtDNA haplogroups, were associated with risk of PSP, risk of CBD, age of PSP onset, PSP disease duration, and neuropathological tau pathology measures for neurofibrillary tangles (NFT), neuropil threads (NT), tufted astrocytes (TA), astrocytic plaques (AP), and oligodendroglial coiled bodies (CB). 764 PSP cases and 150 CBD cases had quantitative tau pathology scores. mtDNA was genotyped for 39 unique SNPs using Agena Bioscience iPlex technologies and mitochondrial haplogroups were defined to mitochondrial phylogeny. After adjustment for multiple testing, we observed an association with risk of CBD for mtDNA sub-haplogroup H4 (OR = 4.51, P = 0.001) and the HV/HV0a haplogroup was associated with a decreased severity of NT tau pathology in PSP cases (P = 0.0023). Our study reports that mitochondrial genomic background may be associated with risk of CBD and may be influencing tau pathology measures in PSP. Replication of these findings will be important.
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Affiliation(s)
| | - Nikoleta Tamvaka
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- SURF Program Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Patrick W Johnson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Ronald L Walton
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ryan J Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA.
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA.
- Neuroscience Track, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, 32224, USA.
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60
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Wu C. Multi-trait Genome-Wide Analyses of the Brain Imaging Phenotypes in UK Biobank. Genetics 2020; 215:947-958. [PMID: 32540950 PMCID: PMC7404235 DOI: 10.1534/genetics.120.303242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
Many genetic variants identified in genome-wide association studies (GWAS) are associated with multiple, sometimes seemingly unrelated, traits. This motivates multi-trait association analyses, which have successfully identified novel associated loci for many complex diseases. While appealing, most existing methods focus on analyzing a relatively small number of traits, and may yield inflated Type 1 error rates when a large number of traits need to be analyzed jointly. As deep phenotyping data are becoming rapidly available, we develop a novel method, referred to as aMAT (adaptive multi-trait association test), for multi-trait analysis of any number of traits. We applied aMAT to GWAS summary statistics for a set of 58 volumetric imaging derived phenotypes from the UK Biobank. aMAT had a genomic inflation factor of 1.04, indicating the Type 1 error rate was well controlled. More important, aMAT identified 24 distinct risk loci, 13 of which were ignored by standard GWAS. In comparison, the competing methods either had a suspicious genomic inflation factor or identified much fewer risk loci. Finally, four additional sets of traits have been analyzed and provided similar conclusions.
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Affiliation(s)
- Chong Wu
- Department of Statistics, Florida State University, Tallahassee, Florida 32306
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61
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Abdolmohammadi B, Dupre A, Evers L, Mez J. Genetics of Chronic Traumatic Encephalopathy. Semin Neurol 2020; 40:420-429. [DOI: 10.1055/s-0040-1713631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractAlthough chronic traumatic encephalopathy (CTE) garners substantial attention in the media and there have been marked scientific advances in the last few years, much remains unclear about the role of genetic risk in CTE. Two athletes with comparable contact-sport exposure may have varying amounts of CTE neuropathology, suggesting that other factors, including genetics, may contribute to CTE risk and severity. In this review, we explore reasons why genetics may be important for CTE, concepts in genetic study design for CTE (including choosing controls, endophenotypes, gene by environment interaction, and epigenetics), implicated genes in CTE (including APOE, MAPT, and TMEM106B), and whether predictive genetic testing for CTE should be considered.
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Affiliation(s)
- Bobak Abdolmohammadi
- Boston University Alzheimer’s Disease Center, Boston University School of Medicine, Boston, MA
- Boston University Chronic Traumatic Encephalopathy Center, Boston University School of Medicine, Boston, MA
- Department of Neurology, Boston University School of Medicine, Boston, MA
| | - Alicia Dupre
- Boston University Alzheimer’s Disease Center, Boston University School of Medicine, Boston, MA
- Boston University Chronic Traumatic Encephalopathy Center, Boston University School of Medicine, Boston, MA
- Department of Neurology, Boston University School of Medicine, Boston, MA
| | - Laney Evers
- Boston University Alzheimer’s Disease Center, Boston University School of Medicine, Boston, MA
- Boston University Chronic Traumatic Encephalopathy Center, Boston University School of Medicine, Boston, MA
- Department of Neurology, Boston University School of Medicine, Boston, MA
| | - Jesse Mez
- Boston University Alzheimer’s Disease Center, Boston University School of Medicine, Boston, MA
- Boston University Chronic Traumatic Encephalopathy Center, Boston University School of Medicine, Boston, MA
- Department of Neurology, Boston University School of Medicine, Boston, MA
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62
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Swarup V, Chang TS, Duong DM, Dammer EB, Dai J, Lah JJ, Johnson ECB, Seyfried NT, Levey AI, Geschwind DH. Identification of Conserved Proteomic Networks in Neurodegenerative Dementia. Cell Rep 2020; 31:107807. [PMID: 32579933 PMCID: PMC8221021 DOI: 10.1016/j.celrep.2020.107807] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/27/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022] Open
Abstract
Data-driven analyses are increasingly valued in modern medicine. We integrate quantitative proteomics and transcriptomics from over 1,000 post-mortem brains from six cohorts representing Alzheimer's disease (AD), asymptomatic AD, progressive supranuclear palsy (PSP), and control patients from the Accelerating Medicines Partnership - Alzheimer's Disease consortium. We define robust co-expression trajectories related to disease progression, including early neuronal, microglial, astrocyte, and immune response modules, and later mRNA splicing and mitochondrial modules. The majority of, but not all, modules are conserved at the transcriptomic level, including module C3, which is only observed in proteome networks and enriched in mitogen-activated protein kinase (MAPK) signaling. Genetic risk enriches in modules changing early in disease and indicates that AD and PSP have distinct causal biological drivers at the pathway level, despite aspects of similar pathology, including synaptic loss and glial inflammatory changes. The conserved, high-confidence proteomic changes enriched in genetic risk represent targets for drug discovery.
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Affiliation(s)
- Vivek Swarup
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy S Chang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jingting Dai
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Erik C B Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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63
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Giagkou N, Höglinger GU, Stamelou M. Progressive supranuclear palsy. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2019; 149:49-86. [PMID: 31779824 DOI: 10.1016/bs.irn.2019.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Progressive supranuclear palsy (PSP) is a neurodegenerative disease characterized pathologically by 4 repeat tau deposition in various cell types and anatomical regions. Richardson's syndrome (RS) is the initially described and one of the clinical phenotypes associated with PSP pathology, characterized by vertical supranuclear gaze paly in particular downwards, postural instability with early falls and subcortical frontal dementia. PSP can manifest as several other clinical phenotypes, including PSP-parkinsonism, -pure akinesia with gait freezing, -frontotemporal dementia, - corticobasal syndrome, - speech/language impairment. RS can also have a pathologic diagnosis other than PSP, including corticobasal degeneration, FTD-TDP-43 and others. New clinical diagnostic criteria take into account this phenotypic variability in an attempt to diagnose the disease earlier, given the current lack of a validated biomarker. At present, therapeutic options for PSP are symptomatic and insufficient. Recent large neuroprotective trials have failed to provide a positive clinical outcome, however, have led to the design of better studies that are ongoing and hold promise for a neuroprotective treatment for PSP.
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Affiliation(s)
- Nikolaos Giagkou
- Parkinson's Disease and Movement Disorders Department, HYGEIA Hospital, Athens, Greece
| | - Günter U Höglinger
- Department for Neurology Hannover Medical School (MHH), Hannover, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Maria Stamelou
- Parkinson's Disease and Movement Disorders Department, HYGEIA Hospital, Athens, Greece; Aiginiteion Hospital, First Department of Neurology, University of Athens, Greece; Clinic for Neurology, Philipps University, Marburg, Germany
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64
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Amir Mishan M, Rezaei Kanavi M, Shahpasand K, Ahmadieh H. Pathogenic Tau Protein Species: Promising Therapeutic Targets for Ocular Neurodegenerative Diseases. J Ophthalmic Vis Res 2019; 14:491-505. [PMID: 31875105 PMCID: PMC6825701 DOI: 10.18502/jovr.v14i4.5459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
Tau is a microtubule-associated protein, which is highly expressed in the central nervous system as well as ocular neurons and stabilizes microtubule structure. It is a phospho-protein being moderately phosphorylated under physiological conditions but its abnormal hyperphosphorylation or some post-phosphorylation modifications would result in a pathogenic condition, microtubule dissociation, and aggregation. The aggregates can induce neuroinflammation and trigger some pathogenic cascades, leading to neurodegeneration. Taking these together, targeting pathogenic tau employing tau immunotherapy may be a promising therapeutic strategy in fighting with cerebral and ocular neurodegenerative disorders.
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Affiliation(s)
- Mohammad Amir Mishan
- Ocular Tissue Engineering Research Center, Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mozhgan Rezaei Kanavi
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Koorosh Shahpasand
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hamid Ahmadieh
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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65
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Shoeibi A, Olfati N, Litvan I. Frontrunner in Translation: Progressive Supranuclear Palsy. Front Neurol 2019; 10:1125. [PMID: 31695675 PMCID: PMC6817677 DOI: 10.3389/fneur.2019.01125] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/08/2019] [Indexed: 12/26/2022] Open
Abstract
Progressive supranuclear palsy (PSP) is a four-repeat tau proteinopathy. Abnormal tau deposition is not unique for PSP and is the basic pathologic finding in some other neurodegenerative disorders such as Alzheimer's disease (AD), age-related tauopathy, frontotemporal degeneration, corticobasal degeneration, and chronic traumatic encephalopathy. While AD research has mostly been focused on amyloid beta pathology until recently, PSP as a prototype of a primary tauopathy with high clinical-pathologic correlation and a rapid course is a crucial candidate for tau therapeutic research. Several novel approaches to slow disease progression are being developed. It is expected that the benefits of translational research in this disease will extend beyond the PSP population. This article reviews advances in the diagnosis, epidemiology, pathology, hypothesized etiopathogenesis, and biomarkers and disease-modifying therapeutic approaches of PSP that is leading it to become a frontrunner in translation.
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Affiliation(s)
- Ali Shoeibi
- Department of Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nahid Olfati
- Department of Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Irene Litvan
- UC San Diego Department of Neurosciences, Parkinson and Other Movement Disorder Center, La Jolla, CA, United States
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66
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Stamelou M, Giagkou N, Höglinger GU. One decade ago, one decade ahead in progressive supranuclear palsy. Mov Disord 2019; 34:1284-1293. [DOI: 10.1002/mds.27788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
- Maria Stamelou
- Parkinson's disease and Movement Disorders DepartmentHYGEIA Hospital Athens Greece
- Neurology ClinicPhilipps University Marburg Germany
- First Department of Neurology, Aiginiteion HospitalUniversity of Athens Athens Greece
| | - Nikolaos Giagkou
- Parkinson's disease and Movement Disorders DepartmentHYGEIA Hospital Athens Greece
| | - Günter U Höglinger
- Department of NeurologyTechnische Universität München Munich Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich Germany
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67
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Rösler TW, Tayaranian Marvian A, Brendel M, Nykänen NP, Höllerhage M, Schwarz SC, Hopfner F, Koeglsperger T, Respondek G, Schweyer K, Levin J, Villemagne VL, Barthel H, Sabri O, Müller U, Meissner WG, Kovacs GG, Höglinger GU. Four-repeat tauopathies. Prog Neurobiol 2019; 180:101644. [PMID: 31238088 DOI: 10.1016/j.pneurobio.2019.101644] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Accepted: 06/12/2019] [Indexed: 02/08/2023]
Abstract
Tau is a microtubule-associated protein with versatile functions in the dynamic assembly of the neuronal cytoskeleton. Four-repeat (4R-) tauopathies are a group of neurodegenerative diseases defined by cytoplasmic inclusions predominantly composed of tau protein isoforms with four microtubule-binding domains. Progressive supranuclear palsy, corticobasal degeneration, argyrophilic grain disease or glial globular tauopathy belong to the group of 4R-tauopathies. The present review provides an introduction in the current concept of 4R-tauopathies, including an overview of the neuropathological and clinical spectrum of these diseases. It describes the genetic and environmental etiological factors, as well as the contemporary knowledge about the pathophysiological mechanisms, including post-translational modifications, aggregation and fragmentation of tau, as well as the role of protein degradation mechanisms. Furthermore, current theories about disease propagation are discussed, involving different extracellular tau species and their cellular release and uptake mechanisms. Finally, molecular diagnostic tools for 4R-tauopathies, including tau-PET and fluid biomarkers, and investigational therapeutic strategies are presented. In summary, we report on 4R-tauopathies as overarching disease concept based on a shared pathophysiological concept, and highlight the challenges and opportunities on the way towards a causal therapy.
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Affiliation(s)
- Thomas W Rösler
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Dept. of Neurology, Technical University of Munich, School of Medicine, 81675 Munich, Germany
| | - Amir Tayaranian Marvian
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Dept. of Neurology, Technical University of Munich, School of Medicine, 81675 Munich, Germany
| | - Matthias Brendel
- Dept. of Nuclear Medicine, University of Munich, 81377 Munich, Germany
| | - Niko-Petteri Nykänen
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Matthias Höllerhage
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Dept. of Neurology, Technical University of Munich, School of Medicine, 81675 Munich, Germany
| | - Sigrid C Schwarz
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | | | - Thomas Koeglsperger
- Dept. of Neurology, University of Munich, 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Gesine Respondek
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Dept. of Neurology, Technical University of Munich, School of Medicine, 81675 Munich, Germany
| | - Kerstin Schweyer
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Dept. of Neurology, Technical University of Munich, School of Medicine, 81675 Munich, Germany
| | - Johannes Levin
- Dept. of Neurology, University of Munich, 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Victor L Villemagne
- Dept. of Molecular Imaging and Therapy, Austin Health, Heidelberg, VIC, 3084, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia; Dept. of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | - Henryk Barthel
- Dept. of Nuclear Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Osama Sabri
- Dept. of Nuclear Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Ulrich Müller
- Institute for Human Genetics, University of Giessen, 35392 Giessen, Germany
| | - Wassilios G Meissner
- Service de Neurologie, CHU Bordeaux, 33000 Bordeaux, France; Université de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; Dept. of Medicine, University of Otago, Christchurch, New Zealand; New Zealand Brain Research Institute, Christchurch, New Zealand
| | - Gabor G Kovacs
- Institute of Neurology, Medical University of Vienna, 1090 Vienna, Austria; Dept. of Laboratory Medicine and Pathobiology, University of Toronto, Laboratory Medicine Program, University Health Network, Toronto, Canada; Tanz Centre for Research in Neurodegenerative Disease, Krembil Brain Institute, Toronto, Canada
| | - Günter U Höglinger
- Dept. of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Dept. of Neurology, Technical University of Munich, School of Medicine, 81675 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany; Dept. of Neurology, Hannover Medical School, 30625 Hannover, Germany.
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Chen Z, Chen JA, Shatunov A, Jones AR, Kravitz SN, Huang AY, Lawrence L, Lowe JK, Lewis CM, Payan CAM, Lieb W, Franke A, Deloukas P, Amouyel P, Tzourio C, Dartigues JF, Ludolph A, Bensimon G, Leigh PN, Bronstein JM, Coppola G, Geschwind DH, Al-Chalabi A. Genome-wide survey of copy number variants finds MAPT duplications in progressive supranuclear palsy. Mov Disord 2019; 34:1049-1059. [PMID: 31059154 DOI: 10.1002/mds.27702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/01/2019] [Accepted: 02/26/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Progressive supranuclear palsy is a neurodegenerative tauopathy manifesting clinically as a progressive akinetic-rigid syndrome. In this study, we sought to identify genetic variants influencing PSP susceptibility through a genome-wide association analysis of a cohort of well-characterized patients who had participated in the Neuroprotection and Natural History in Parkinson Plus Syndromes and Blood Brain Barrier in Parkinson Plus Syndromes studies. METHODS We genotyped single-nucleotide polymorphisms in 283 PSP cases from the United Kingdom, Germany, and France and compared these with genotypes from 4472 controls. Copy number variants were identified from genotyping data. RESULTS We observed associations on chromosome 17 within or close to the MAPT gene and explored the genetic architecture at this locus. We confirmed the previously reported association of rs1768208 in the MOBP gene (P = 3.29 × 10-13 ) and rs1411478 in STX6 (P = 3.45 × 10-10 ). The population-attributable risk from the MAPT, MOBP, and STX6 single-nucleotide polymorphisms was found to be 0.37, 0.26, and 0.08, respectively. In addition, we found 2 instances of copy number variants spanning the MAPT gene in patients with PSP. These copy number variants include tau but few other genes within the chromosome 17 haplotype region, providing additional support for the direct pathogenicity of MAPT in PSP. CONCLUSIONS Clinicians should also be aware of MAPT duplication as a possible genetic cause of PSP, especially in patients presenting with young age at onset. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Zhongbo Chen
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Jason A Chen
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Stephanie N Kravitz
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Alden Y Huang
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Lauren Lawrence
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jennifer K Lowe
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
| | - Christine A M Payan
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factor and Molecular Determinants of Aging Diseases, Labex-Distalz, Lille, France
| | - Christophe Tzourio
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Jean-François Dartigues
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Oberer Eselsberg, Ulm, Germany
| | - Gilbert Bensimon
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - P Nigel Leigh
- Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, UK
| | - Jeff M Bronstein
- Program in Movement Disorders, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Giovanni Coppola
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
- Department of Human Genetics, University of California, Los Angeles, California, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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Abstract
Purpose of review In this review we highlight recent advances in the human genetics of frontotemporal dementia (FTD). In addition to providing a broad survey of genes implicated in FTD in the last several years, we also discuss variation in genes implicated in both hereditary leukodystrophies and risk for FTD (e.g., TREM2, TMEM106B, CSF1R, AARS2, NOTCH3). Recent findings Over the past five years, genetic variation in approximately 50 genes has been confirmed or suggested to cause or influence risk for FTD and FTD-spectrum disorders. We first give background and discuss recent findings related to C9ORF72, GRN and MAPT, the genes most commonly implicated in FTD. We then provide a broad overview of other FTD-associated genes and go on to discuss new findings in FTD genetics in East Asian populations, including pathogenic variation in CHCHD10, which may represent a frequent cause of disease in Chinese populations. Finally, we consider recent insights gleaned from genome-wide association and genetic pleiotropy studies. Summary Recent genetic discoveries highlight cellular pathways involving autophagy, the endolysosomal system and neuroinflammation, and reveal an intriguing overlap between genes that confer risk for leukodystrophy and FTD.
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