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Patel M, Pottier C, Fan KH, Cetin A, Johnson M, Ali M, Liu M, Gorijala P, Budde J, Shi R, Cohen AD, Becker JT, Snitz BE, Aizenstein H, Lopez OL, Morris JC, Kamboh MI, Cruchaga C. Whole-genome sequencing reveals the impact of lipid pathway and APOE genotype on brain amyloidosis. Hum Mol Genet 2025; 34:739-748. [PMID: 39927718 PMCID: PMC11973900 DOI: 10.1093/hmg/ddaf017] [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: 08/08/2024] [Revised: 10/11/2024] [Accepted: 01/29/2025] [Indexed: 02/11/2025] Open
Abstract
Amyloid-PET imaging tracks the accumulation of amyloid beta (Aβ) deposits in the brain. Amyloid plaques accumulation may begin 10 to 20 years before the individual experiences clinical symptoms associated with Alzheimer's diseases (ad). Recent large-scale genome-wide association studies reported common risk factors associated with brain amyloidosis, suggesting that this endophenotype is driven by genetic variants. However, these loci pinpoint to large genomic regions and the functional variants remain to be identified. To identify new risk factors associated with brain amyloid deposition, we performed whole-genome sequencing on a large cohort of European descent individuals with amyloid PET imaging data (n = 1,888). Gene-based analysis for coding variants was performed using SKAT-O for amyloid PET as a quantitative endophenotype that identified genome-wide significant association for APOE (P = 2.45 × 10-10), and 26 new candidate genes with suggestive significance association (P < 5. 0 × 10-03) including SCN7A (P = 7.31 × 10-05), SH3GL1 (P = 7.56 × 10-04), and MFSD12 (P = 8.51 × 10-04). Enrichment analysis highlighted the lipid binding pathways as associated with Aβ deposition in brain driven by PITPNM3 (P = 4.27 × 10-03), APOE (P = 2.45 × 10-10), AP2A2 (P = 1.06 × 10-03), and SH3GL1 (P = 7.56 × 10-04). Overall, our data strongly support a connection between lipid metabolism and the deposition of Aβ in the brain. Our study illuminates promising avenues for therapeutic interventions targeting lipid metabolism to address brain amyloidosis.
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Affiliation(s)
- Maulikkumar Patel
- Department of Psychiatry, Neurogenomics and Informatics, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - Cyril Pottier
- Department of Psychiatry, Neurogenomics and Informatics, Department of Neurology, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - Kang-Hsien Fan
- Department of Human Genetics, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA 15261, United States
| | - Arda Cetin
- Department of Psychiatry, Neurogenomics and Informatics, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - Matthew Johnson
- Department of Psychiatry, Neurogenomics and Informatics, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - Muhammad Ali
- Department of Psychiatry, Neurogenomics and Informatics, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - Menghan Liu
- Department of Psychiatry, Neurogenomics and Informatics, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - Priyanka Gorijala
- Department of Psychiatry, Neurogenomics and Informatics, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - John Budde
- Department of Psychiatry, Neurogenomics and Informatics, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
| | - Ruyu Shi
- Department of Human Genetics, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA 15261, United States
| | - Ann D Cohen
- Department of Psychiatry, University of Pittsburgh, 3811 O'Hara Street, Pittsburgh, PA 15213, United States
| | - James T Becker
- Department of Neurology, University of Pittsburgh, 3471 Fifth Avenue, Pittsburgh, PA 15213, United States
| | - Beth E Snitz
- Department of Neurology, University of Pittsburgh, 3471 Fifth Avenue, Pittsburgh, PA 15213, United States
| | - Howard Aizenstein
- Department of Human Genetics, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA 15261, United States
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, 3471 Fifth Avenue, Pittsburgh, PA 15213, United States
| | - John C Morris
- Department of Neurology, Hope Center for Neurologic Diseases, Section on Aging & Dementia, Institute of Clinical and Translational Sciences, Knight Alzheimer Disease Research Center Washington University School of Medicine, 4901 Forest Park Ave 4th floor, St. Louis, MO 63108, United States
| | - M Ilyas Kamboh
- Department of Human Genetics, Department of Psychiatry University of Pittsburgh, 130 De Soto St, Pittsburgh, PA 15261, United States
| | - Carlos Cruchaga
- Department of Psychiatry, Neurogenomics and Informatics, Department of Neurology, Hope Center for Neurologic Diseases, Knight Alzheimer Disease Research Center, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, United States
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De Deyn L, Sleegers K. The impact of rare genetic variants on Alzheimer disease. Nat Rev Neurol 2025; 21:127-139. [PMID: 39905212 DOI: 10.1038/s41582-025-01062-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2025] [Indexed: 02/06/2025]
Abstract
Alzheimer disease (AD) is a progressive neurodegenerative disease with a strong genetic component. Although autosomal dominant mutations and common risk variants in AD risk have been extensively studied, the genetic underpinning of polygenic AD remains incompletely understood. Rare variants could elucidate part of the missing heritability in AD. Rare variant research gained momentum with the discovery of a rare variant in TREM2, along with loss-of-function variants in ABCA7 and SORL1, and has come into full bloom in recent years. Not only has the number of rare variant discoveries increased through large-scale whole-exome and genome sequencing studies, improved imputation in genome-wide association studies and increased focus on understudied populations, the number of studies mapping the functional effects of several of these rare variants has also significantly increased, leading to insights in the pathogenesis of AD and drug development. Here we provide a comprehensive overview of the known and novel rare variants implicated in AD risk, highlighting how they shine new light on AD pathophysiology and provide new inroads for drug development. We will review their impact on individual, familial and population levels, and discuss the potential and challenges of rare variants in genetic risk prediction.
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Affiliation(s)
- Lara De Deyn
- Complex Genetics of Alzheimer's Disease group, VIB-UAntwerp Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease group, VIB-UAntwerp Center for Molecular Neurology, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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Mhatre-Winters I, Eid A, Blum N, Han Y, Sammoura FM, Wu LJ, Richardson JR. Effects of Pesticide Exposure on Neuroinflammation and Microglial Gene Expression: Relevance to Mechanisms of Alzheimer's Disease Risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.14.638293. [PMID: 40027678 PMCID: PMC11870447 DOI: 10.1101/2025.02.14.638293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Background Alzheimer's disease (AD) is characterized by the presence of amyloid-β plaques, neurofibrillary tangles, and neuroinflammation. Previously, we reported serum levels of dichlorodiphenyldichloroethylene (DDE), the primary metabolite of the pesticide dichlorodiphenyltrichloroethane (DDT), were significantly higher in AD patients compared to age-matched controls and that DDT exposure worsened AD pathology in animal models. Objective Here, we investigated the effect of DDT on neuroinflammation in primary mouse microglia (PMG) and C57BL/6J mice. Methods Effects of DDT on inflammation and disease-associated microglia were determined in primary mouse microglia and C57BL/6J mice. Results PMG exposed to DDT (0.5-5.0 µM) elicited a ∼2-3-fold increase in Il-1b mRNA levels, with similar concentration-dependent upregulation in Il-6, Nos2, and Tnfa . These effects were blocked by the sodium channel antagonist tetrodotoxin, demonstrating the role of DDT-microglial sodium channel interactions in mediating this response. Additionally, NOS2 protein levels increased by ∼1.5-2-fold, while TNFa was elevated by 2-4-fold. C57BL/6J male and female mice exposed to DDT (30 mg/kg) demonstrated significantly increased mRNA levels of Nos2 , Il-1b , and Il-6 in the frontal cortex (1.5-2.3-fold), and Nos2 , Il-1b, and Tnfa (1.5-1.8-fold) in the hippocampus. Furthermore, microglial homeostatic genes, Cx3cr1 , P2ry12, and Tmem119 , were downregulated, while stage 1 disease-associated microglia genes were upregulated both in vitro and in vivo . Notably, Apoe and Trem2 were only upregulated in the frontal cortex and hippocampus of females. Conclusion These data indicate that DDT increases neuroinflammation, which may result from direct actions of DDT on microglia, providing a novel pathway by which DDT may contribute to AD risk.
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Oatman SR, Reddy JS, Atashgaran A, Wang X, Min Y, Quicksall Z, Vanelderen F, Carrasquillo MM, Liu CC, Yamazaki Y, Nguyen TT, Heckman M, Zhao N, DeTure M, Murray ME, Bu G, Kanekiyo T, Dickson DW, Allen M, Ertekin-Taner N. Integrative Epigenomic Landscape of Alzheimer's Disease Brains Reveals Oligodendrocyte Molecular Perturbations Associated with Tau. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637140. [PMID: 40027794 PMCID: PMC11870448 DOI: 10.1101/2025.02.12.637140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Alzheimer's disease (AD) brains are characterized by neuropathologic and biochemical changes that are highly variable across individuals. Capturing epigenetic factors that associate with this variability can reveal novel biological insights into AD pathophysiology. We conducted an epigenome-wide association study of DNA methylation (DNAm) in 472 AD brains with neuropathologic measures (Braak stage, Thal phase, and cerebral amyloid angiopathy score) and brain biochemical levels of five proteins (APOE, amyloid-β (Aβ)40, Aβ42, tau, and p-tau) core to AD pathogenesis. Using a novel regional methylation (rCpGm) approach, we identified 5,478 significant associations, 99.7% of which were with brain tau biochemical measures. Of the tau-associated rCpGms, 93 had concordant associations in external datasets comprising 1,337 brain samples. Integrative transcriptome-methylome analyses uncovered 535 significant gene expression associations for these 93 rCpGms. Genes with concurrent transcriptome-methylome perturbations were enriched in oligodendrocyte marker genes, including known AD risk genes such as BIN1 , myelination genes MYRF, MBP and MAG previously implicated in AD, as well as novel genes like LDB3 . We further annotated the top oligodendrocyte genes in an additional 6 brain single cell and 2 bulk transcriptome datasets from AD and two other tauopathies, Pick's disease and progressive supranuclear palsy (PSP). Our findings support consistent rCpGm and gene expression associations with these tauopathies and tau-related phenotypes in both bulk brain tissue and oligodendrocyte clusters. In summary, we uncover the integrative epigenomic landscape of AD and demonstrate tau-related oligodendrocyte gene perturbations as a common potential pathomechanism across different tauopathies.
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Alur V, Vastrad B, Raju V, Vastrad C, Kotturshetti S. The identification of key genes and pathways in polycystic ovary syndrome by bioinformatics analysis of next-generation sequencing data. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2024; 29:53. [DOI: 10.1186/s43043-024-00212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 11/17/2024] [Indexed: 01/02/2025] Open
Abstract
Abstract
Background
Polycystic ovary syndrome (PCOS) is a reproductive endocrine disorder. The specific molecular mechanism of PCOS remains unclear. The aim of this study was to apply a bioinformatics approach to reveal related pathways or genes involved in the development of PCOS.
Methods
The next-generation sequencing (NGS) dataset GSE199225 was downloaded from the gene expression omnibus (GEO) database and NGS dataset analyzed is obtained from in vitro culture of PCOS patients’ muscle cells and muscle cells of healthy lean control women. Differentially expressed gene (DEG) analysis was performed using DESeq2. The g:Profiler was utilized to analyze the gene ontology (GO) and REACTOME pathways of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed and module analysis was performed using HiPPIE and cytoscape. The miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed. The hub genes were validated by using receiver operating characteristic (ROC) curve analysis.
Results
We have identified 957 DEG in total, including 478 upregulated genes and 479 downregulated gene. GO terms and REACTOME pathways illustrated that DEG were significantly enriched in regulation of molecular function, developmental process, interferon signaling and platelet activation, signaling, and aggregation. The top 5 upregulated hub genes including HSPA5, PLK1, RIN3, DBN1, and CCDC85B and top 5 downregulated hub genes including DISC1, AR, MTUS2, LYN, and TCF4 might be associated with PCOS. The hub gens of HSPA5 and KMT2A, together with corresponding predicted miRNAs (e.g., hsa-mir-34b-5p and hsa-mir-378a-5p), and HSPA5 and TCF4 together with corresponding predicted TF (e.g., RCOR3 and TEAD4) were found to be significantly correlated with PCOS.
Conclusions
These study uses of bioinformatics analysis of NGS data to obtain hub genes and key signaling pathways related to PCOS and its associated complications. Also provides novel ideas for finding biomarkers and treatment methods for PCOS and its associated complications.
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Mei JL, Wang SF, Zhao YY, Xu T, Luo Y, Xiong LL. Identification of immune infiltration and PANoptosis-related molecular clusters and predictive model in Alzheimer's disease based on transcriptome analysis. IBRAIN 2024; 10:323-344. [PMID: 39346794 PMCID: PMC11427814 DOI: 10.1002/ibra.12179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 10/01/2024]
Abstract
This study aims to explore the expression profile of PANoptosis-related genes (PRGs) and immune infiltration in Alzheimer's disease (AD). Based on the Gene Expression Omnibus database, this study investigated the differentially expressed PRGs and immune cell infiltration in AD and explored related molecular clusters. Gene set variation analysis (GSVA) was used to analyze the expression of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes in different clusters. Weighted gene co-expression network analysis was utilized to find co-expressed gene modules and core genes in the network. By analyzing the intersection genes in random forest, support vector machine, generalized linear model, and extreme gradient boosting (XGB), the XGB model was determined. Eventually, the first five genes (Signal Transducer and Activator of Transcription 3, Tumor Necrosis Factor (TNF) Receptor Superfamily Member 1B, Interleukin 4 Receptor, Chloride Intracellular Channel 1, TNF Receptor Superfamily Member 10B) in XGB model were selected as predictive genes. This research explored the relationship between PANoptosis and AD and established an XGB learning model to evaluate and screen key genes. At the same time, immune infiltration analysis showed that there were different immune infiltration expression profiles in AD.
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Affiliation(s)
- Jin-Lin Mei
- School of Anesthesiology Zunyi Medical University Zunyi China
| | - Shi-Feng Wang
- School of Anesthesiology Zunyi Medical University Zunyi China
| | - Yang-Yang Zhao
- School of Anesthesiology Zunyi Medical University Zunyi China
| | - Ting Xu
- School of Anesthesiology Zunyi Medical University Zunyi China
| | - Yong Luo
- Department of Neurology Third Affiliated Hospital of Zunyi Medical University Zunyi China
| | - Liu-Lin Xiong
- School of Anesthesiology Zunyi Medical University Zunyi China
- Clinical and Health Sciences University of South Australia Adelaide South Australia Australia
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Malamon JS, Farrell JJ, Xia LC, Dombroski BA, Das RG, Way J, Kuzma AB, Valladares O, Leung YY, Scanlon AJ, Lopez IAB, Brehony J, Worley KC, Zhang NR, Wang LS, Farrer LA, Schellenberg GD, Lee WP, Vardarajan BN. A comparative study of structural variant calling in WGS from Alzheimer's disease families. Life Sci Alliance 2024; 7:e202302181. [PMID: 38418088 PMCID: PMC10902710 DOI: 10.26508/lsa.202302181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation for generating a high-quality SV call set in whole-genome sequencing from the Alzheimer's Disease Sequencing Project comprising 578 individuals from 111 families. Employing two complementary pipelines, Scalpel and Parliament, for SV/indel calling, we assessed sensitivity through sample replicates (N = 9) with in silico variant spike-ins. We developed a novel metric, D-score, to evaluate caller specificity for deletions. The accuracy of deletions was evaluated by Sanger sequencing. We generated a high-quality call set of 152,301 deletions of diverse sizes. Sanger sequencing validated 114 of 146 detected deletions (78.1%). Scalpel excelled in accuracy for deletions ≤100 bp, whereas Parliament was optimal for deletions >900 bp. Overall, 83.0% and 72.5% of calls by Scalpel and Parliament were validated, respectively, including all 11 deletions called by both Parliament and Scalpel between 101 and 900 bp. Our flexible protocol successfully generated a high-quality deletion call set and a truth set of Sanger sequencing-validated deletions with precise breakpoints spanning 1-17,000 bp.
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Affiliation(s)
- John S Malamon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - John J Farrell
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Li Charlie Xia
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rueben G Das
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jessica Way
- Broad Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda B Kuzma
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Otto Valladares
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison J Scanlon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Irving Antonio Barrera Lopez
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jack Brehony
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kim C Worley
- Human Genome Sequencing Center, and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lindsay A Farrer
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Epidemiology and Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Badri N Vardarajan
- Gertrude H. Sergievsky Center and Taub Institute of Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
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Li D, Farrell JJ, Mez J, Martin ER, Bush WS, Ruiz A, Boada M, de Rojas I, Mayeux R, Haines JL, Vance MAP, Wang LS, Schellenberg GD, Lunetta KL, Farrer LA. Novel loci for Alzheimer's disease identified by a genome-wide association study in Ashkenazi Jews. Alzheimers Dement 2023; 19:5550-5562. [PMID: 37260021 PMCID: PMC10689571 DOI: 10.1002/alz.13117] [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: 12/28/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Most Alzheimer's disease (AD) loci have been discovered in individuals with European ancestry (EA). METHODS We applied principal component analysis using Gaussian mixture models and an Ashkenazi Jewish (AJ) reference genome-wide association study (GWAS) data set to identify Ashkenazi Jews ascertained in GWAS (n = 42,682), whole genome sequencing (WGS, n = 16,815), and whole exome sequencing (WES, n = 20,504) data sets. The association of AD was tested genome wide (GW) in the GWAS and WGS data sets and exome wide (EW) in all three data sets (EW). Gene-based analyses were performed using aggregated rare variants. RESULTS In addition to apolipoprotein E (APOE), GW analyses (1355 cases and 1661 controls) revealed associations with TREM2 R47H (p = 9.66 × 10-9 ), rs541586606 near RAB3B (p = 5.01 × 10-8 ), and rs760573036 between SPOCK3 and ANXA10 (p = 6.32 × 10-8 ). In EW analyses (1504 cases and 2047 controls), study-wide significant association was observed with rs1003710 near SMAP2 (p = 1.91 × 10-7 ). A significant gene-based association was identified with GIPR (p = 7.34 × 10-7 ). DISCUSSION Our results highlight the efficacy of founder populations for AD genetic studies.
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Affiliation(s)
- Donghe Li
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Jesse Mez
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Eden R. Martin
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - William S. Bush
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Agustin Ruiz
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Mercè Boada
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Itziar de Rojas
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center Department of Neurology, Columbia University, 710 West 168th Street, New York, NY 10032, USA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Margaret A. Pericak Vance
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
- Department of Neurology, University of Miami, Miami, FL 33136, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
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Logue MW, Dasgupta S, Farrer LA. Genetics of Alzheimer's Disease in the African American Population. J Clin Med 2023; 12:5189. [PMID: 37629231 PMCID: PMC10455208 DOI: 10.3390/jcm12165189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Black/African American (AA) individuals have a higher risk of Alzheimer's disease (AD) than White non-Hispanic persons of European ancestry (EUR) for reasons that may include economic disparities, cardiovascular health, quality of education, and biases in the methods used to diagnose AD. AD is also heritable, and some of the differences in risk may be due to genetics. Many AD-associated variants have been identified by candidate gene studies, genome-wide association studies (GWAS), and genome-sequencing studies. However, most of these studies have been performed using EUR cohorts. In this paper, we review the genetics of AD and AD-related traits in AA individuals. Importantly, studies of genetic risk factors in AA cohorts can elucidate the molecular mechanisms underlying AD risk in AA and other populations. In fact, such studies are essential to enable reliable precision medicine approaches in persons with considerable African ancestry. Furthermore, genetic studies of AA cohorts allow exploration of the ways the impact of genes can vary by ancestry, culture, and economic and environmental disparities. They have yielded important gains in our knowledge of AD genetics, and increasing AA individual representation within genetic studies should remain a priority for inclusive genetic study design.
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Affiliation(s)
- Mark W. Logue
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA 02130, USA;
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Shoumita Dasgupta
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Medical Sciences and Education, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
- Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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10
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Juul Rasmussen I, Frikke-Schmidt R. Modifiable cardiovascular risk factors and genetics for targeted prevention of dementia. Eur Heart J 2023; 44:2526-2543. [PMID: 37224508 PMCID: PMC10481783 DOI: 10.1093/eurheartj/ehad293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/22/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Dementia is a major global challenge for health and social care in the 21st century. A third of individuals >65 years of age die with dementia, and worldwide incidence numbers are projected to be higher than 150 million by 2050. Dementia is, however, not an inevitable consequence of old age; 40% of dementia may theoretically be preventable. Alzheimer's disease (AD) accounts for approximately two-thirds of dementia cases and the major pathological hallmark of AD is accumulation of amyloid-β. Nevertheless, the exact pathological mechanisms of AD remain unknown. Cardiovascular disease and dementia share several risk factors and dementia often coexists with cerebrovascular disease. In a public health perspective, prevention is crucial, and it is suggested that a 10% reduction in prevalence of cardiovascular risk factors could prevent more than nine million dementia cases worldwide by 2050. Yet this assumes causality between cardiovascular risk factors and dementia and adherence to the interventions over decades for a large number of individuals. Using genome-wide association studies, the entire genome can be scanned for disease/trait associated loci in a hypothesis-free manner, and the compiled genetic information is not only useful for pinpointing novel pathogenic pathways but also for risk assessments. This enables identification of individuals at high risk, who likely will benefit the most from a targeted intervention. Further optimization of the risk stratification can be done by adding cardiovascular risk factors. Additional studies are, however, highly needed to elucidate dementia pathogenesis and potential shared causal risk factors between cardiovascular disease and dementia.
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Affiliation(s)
- Ida Juul Rasmussen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Dang Do AN, Sleat DE, Campbell K, Johnson NL, Zheng H, Wassif CA, Dale RK, Porter FD. Cerebrospinal Fluid Protein Biomarker Discovery in CLN3. J Proteome Res 2023; 22:2493-2508. [PMID: 37338096 PMCID: PMC11095826 DOI: 10.1021/acs.jproteome.3c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Syndromic CLN3-Batten is a fatal, pediatric, neurodegenerative disease caused by variants in CLN3, which encodes the endolysosomal transmembrane CLN3 protein. No approved treatment for CLN3 is currently available. The protracted and asynchronous disease presentation complicates the evaluation of potential therapies using clinical disease progression parameters. Biomarkers as surrogates to measure the progression and effect of potential therapeutics are needed. We performed proteomic discovery studies using cerebrospinal fluid (CSF) samples from 28 CLN3-affected and 32 age-similar non-CLN3 individuals. Proximal extension assay (PEA) of 1467 proteins and untargeted data-dependent mass spectrometry [MS; MassIVE FTP server (ftp://MSV000090147@massive.ucsd.edu)] were used to generate orthogonal lists of protein marker candidates. At an adjusted p-value of <0.1 and threshold CLN3/non-CLN3 fold-change ratio of 1.5, PEA identified 54 and MS identified 233 candidate biomarkers. Some of these (NEFL, CHIT1) have been previously linked with other neurologic conditions. Others (CLPS, FAM217B, QRICH2, KRT16, ZNF333) appear to be novel. Both methods identified 25 candidate biomarkers, including CHIT1, NELL1, and ISLR2 which had absolute fold-change ratios >2. NELL1 and ISLR2 regulate axonal development in neurons and are intriguing new candidates for further investigation in CLN3. In addition to identifying candidate proteins for CLN3 research, this study provides a comparison of two large-scale proteomic discovery methods in CSF.
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Affiliation(s)
- An N. Dang Do
- Unit on Cellular Stress in Development and Diseases, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
- Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Kiersten Campbell
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nicholas L. Johnson
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Christopher A. Wassif
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Forbes D. Porter
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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12
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Ossola B, Rifat A, Rowland A, Hunter H, Drinkall S, Bender C, Hamlischer M, Teall M, Burley R, Barker DF, Cadwalladr D, Dickson L, Lawrence JMK, Harvey JRM, Lizio M, Xu X, Kavanagh E, Cheung T, Sheardown S, Lawrence CB, Harte M, Brough D, Madry C, Matthews K, Doyle K, Page K, Powell J, Brice NL, Bürli RW, Carlton MB, Dawson LA. Characterisation of C101248: A novel selective THIK-1 channel inhibitor for the modulation of microglial NLRP3-inflammasome. Neuropharmacology 2023; 224:109330. [PMID: 36375694 PMCID: PMC9841576 DOI: 10.1016/j.neuropharm.2022.109330] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Neuroinflammation, specifically the NLRP3 inflammasome cascade, is a common underlying pathological feature of many neurodegenerative diseases. Evidence suggests that NLRP3 activation involves changes in intracellular K+. Nuclear Enriched Transcript Sort Sequencing (NETSseq), which allows for deep sequencing of purified cell types from human post-mortem brain tissue, demonstrated a highly specific expression of the tandem pore domain halothane-inhibited K+ channel 1 (THIK-1) in microglia compared to other glial and neuronal cell types in the human brain. NETSseq also showed a significant increase of THIK-1 in microglia isolated from cortical regions of brains with Alzheimer's disease (AD) relative to control donors. Herein, we report the discovery and pharmacological characterisation of C101248, the first selective small-molecule inhibitor of THIK-1. C101248 showed a concentration-dependent inhibition of both mouse and human THIK-1 (IC50: ∼50 nM) and was inactive against K2P family members TREK-1 and TWIK-2, and Kv2.1. Whole-cell patch-clamp recordings of microglia from mouse hippocampal slices showed that C101248 potently blocked both tonic and ATP-evoked THIK-1 K+ currents. Notably, C101248 had no effect on other constitutively active resting conductance in slices from THIK-1-depleted mice. In isolated microglia, C101248 prevented NLRP3-dependent release of IL-1β, an effect not seen in THIK-1-depleted microglia. In conclusion, we demonstrated that inhibiting THIK-1 (a microglia specific gene that is upregulated in brains from donors with AD) using a novel selective modulator attenuates the NLRP3-dependent release of IL-1β from microglia, which suggests that this channel may be a potential therapeutic target for the modulation of neuroinflammation in AD.
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Affiliation(s)
- Bernardino Ossola
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK.
| | - Ali Rifat
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neurophysiology, Charitéplatz 1, 10117 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Anna Rowland
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Helen Hunter
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Samuel Drinkall
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Clare Bender
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Mayida Hamlischer
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Martin Teall
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Russell Burley
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Daneil F Barker
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - David Cadwalladr
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Louise Dickson
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Jason M K Lawrence
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Jenna R M Harvey
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Marina Lizio
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Xiao Xu
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Edel Kavanagh
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Toni Cheung
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Steve Sheardown
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Catherine B Lawrence
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK; The Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Michael Harte
- Division of Pharmacy & Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; The Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK; The Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Christian Madry
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neurophysiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Kim Matthews
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Kevin Doyle
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Keith Page
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Justin Powell
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Nicola L Brice
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Roland W Bürli
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Mark B Carlton
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
| | - Lee A Dawson
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge, CB4 0PZ, UK
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13
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Shim YJ, Shin MK, Jung J, Koo B, Jang W. An in-silico approach to studying a very rare neurodegenerative disease using a disease with higher prevalence with shared pathways and genes: Cerebral adrenoleukodystrophy and Alzheimer’s disease. Front Mol Neurosci 2022; 15:996698. [PMID: 36245924 PMCID: PMC9553843 DOI: 10.3389/fnmol.2022.996698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/22/2022] [Indexed: 11/20/2022] Open
Abstract
Cerebral adrenoleukodystrophy (cALD) is a rare neurodegenerative disease characterized by inflammatory demyelination in the central nervous system. Another neurodegenerative disease with a high prevalence, Alzheimer’s disease (AD), shares many common features with cALD such as cognitive impairment and the alleviation of symptoms by erucic acid. We investigated cALD and AD in parallel to study the shared pathological pathways between a rare disease and a more common disease. The approach may expand the biological understandings and reveal novel therapeutic targets. Gene set enrichment analysis (GSEA) and weighted gene correlation network analysis (WGCNA) were conducted to identify both the resemblance in gene expression patterns and genes that are pathologically relevant in the two diseases. Within differentially expressed genes (DEGs), GSEA identified 266 common genes with similar up- or down-regulation patterns in cALD and AD. Among the interconnected genes in AD data, two gene sets containing 1,486 genes preserved in cALD data were selected by WGCNA that may significantly affect the development and progression of cALD. WGCNA results filtered by functional correlation via protein–protein interaction analysis overlapping with GSEA revealed four genes (annexin A5, beta-2-microglobulin, CD44 molecule, and fibroblast growth factor 2) that showed robust associations with the pathogeneses of cALD and AD, where they were highly involved in inflammation, apoptosis, and the mitogen-activated protein kinase pathway. This study provided an integrated strategy to provide new insights into a rare disease with scant publicly available data (cALD) using a more prevalent disorder with some pathological association (AD), which suggests novel druggable targets and drug candidates.
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Affiliation(s)
- Yu Jeong Shim
- Department of Life Science, Dongguk University, Goyang-si, South Korea
| | - Min Kyoung Shin
- Department of Life Science, Dongguk University, Goyang-si, South Korea
| | - Junghyun Jung
- Department of Life Science, Dongguk University, Goyang-si, South Korea
| | | | - Wonhee Jang
- Department of Life Science, Dongguk University, Goyang-si, South Korea
- *Correspondence: Wonhee Jang,
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14
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Luo J, Chen L, Huang X, Xie J, Zou C, Pan M, Mo J, Zou D. REPS1 as a Potential Biomarker in Alzheimer’s Disease and Vascular Dementia. Front Aging Neurosci 2022; 14:894824. [PMID: 35813961 PMCID: PMC9257827 DOI: 10.3389/fnagi.2022.894824] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/07/2022] [Indexed: 12/31/2022] Open
Abstract
Vascular dementia (VD) and Alzheimer’s disease (AD) are common types of dementia for which no curative therapies are known. In this study, we identified hub genes associated with AD and VD in order to explore new potential therapeutic targets. Genes differentially expressed in VD and AD in all three datasets (GSE122063, GSE132903, and GSE5281) were identified and used to construct a protein–protein interaction network. We identified 10 modules containing 427 module genes in AD and VD. Module genes showing an area under the diagnostic curve > 0.60 for AD or VD were used to construct a least absolute shrinkage and selection operator model and were entered into a support vector machine-recursive feature elimination algorithm, which identified REPS1 as a hub gene in AD and VD. Furthermore, REPS1 was associated with activation of pyruvate metabolism and inhibition of Ras signaling pathway. Module genes, together with differentially expressed microRNAs from the dataset GSE46579, were used to construct a regulatory network. REPS1 was predicted to bind to the microRNA hsa_miR_5701. Single-sample gene set enrichment analysis was used to explore immune cell infiltration, which suggested a negative correlation between REPS1 expression and infiltration by plasmacytoid dendritic cells in AD and VD. In conclusion, our results suggest core pathways involved in both AD and VD, and they identify REPS1 as a potential biomarker of both diseases. This protein may aid in early diagnosis, monitoring of treatment response, and even efforts to prevent these debilitating disorders.
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Affiliation(s)
- Jiefeng Luo
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liechun Chen
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaohua Huang
- Department of Neurology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jieqiong Xie
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chun Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Mika Pan
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jingjia Mo
- Department of General Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Jingjia Mo,
| | - Donghua Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Donghua Zou,
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15
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Rajesh Y, Kanneganti TD. Innate Immune Cell Death in Neuroinflammation and Alzheimer's Disease. Cells 2022; 11:1885. [PMID: 35741014 PMCID: PMC9221514 DOI: 10.3390/cells11121885] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder molecularly characterized by the formation of amyloid β (Aβ) plaques and type 2 microtubule-associated protein (Tau) abnormalities. Multiple studies have shown that many of the brain's immunological cells, specifically microglia and astrocytes, are involved in AD pathogenesis. Cells of the innate immune system play an essential role in eliminating pathogens but also regulate brain homeostasis and AD. When activated, innate immune cells can cause programmed cell death through multiple pathways, including pyroptosis, apoptosis, necroptosis, and PANoptosis. The cell death often results in the release of proinflammatory cytokines that propagate the innate immune response and can eliminate Aβ plaques and aggregated Tau proteins. However, chronic neuroinflammation, which can result from cell death, has been linked to neurodegenerative diseases and can worsen AD. Therefore, the innate immune response must be tightly balanced to appropriately clear these AD-related structural abnormalities without inducing chronic neuroinflammation. In this review, we discuss neuroinflammation, innate immune responses, inflammatory cell death pathways, and cytokine secretion as they relate to AD. Therapeutic strategies targeting these innate immune cell death mechanisms will be critical to consider for future preventive or palliative treatments for AD.
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16
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Patel T, Carnwath TP, Wang X, Allen M, Lincoln SJ, Lewis‐Tuffin L, Quicksall ZS, Lin S, Tutor‐New FQ, Ho CC, Min Y, Malphrus KG, Nguyen TT, Martin E, Garcia CA, Alkharboosh RM, Grewal S, Chaichana K, Wharen R, Guerrero‐Cazares H, Quinones‐Hinojosa A, Ertekin‐Taner N. Transcriptional landscape of human microglia implicates age, sex, and APOE-related immunometabolic pathway perturbations. Aging Cell 2022; 21:e13606. [PMID: 35388616 PMCID: PMC9124307 DOI: 10.1111/acel.13606] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022] Open
Abstract
Microglia have fundamental roles in health and disease; however, effects of age, sex, and genetic factors on human microglia have not been fully explored. We applied bulk and single-cell approaches to comprehensively characterize human microglia transcriptomes and their associations with age, sex, and APOE. We identified a novel microglial signature, characterized its expression in bulk tissue and single-cell microglia transcriptomes. We discovered microglial co-expression network modules associated with age, sex, and APOE-ε4 that are enriched for lipid and carbohydrate metabolism genes. Integrated analyses of modules with single-cell transcriptomes revealed significant overlap between age-associated module genes and both pro-inflammatory and disease-associated microglial clusters. These modules and clusters harbor known neurodegenerative disease genes including APOE, PLCG2, and BIN1. Meta-analyses with published bulk and single-cell microglial datasets further supported our findings. Thus, these data represent a well-characterized human microglial transcriptome resource and highlight age, sex, and APOE-related microglial immunometabolism perturbations with potential relevance in neurodegeneration.
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Affiliation(s)
- Tulsi Patel
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | - Xue Wang
- Department of Quantitative Health SciencesMayo ClinicJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | - Shu Lin
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Yuhao Min
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | - Thuy T. Nguyen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Rawan M. Alkharboosh
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
- Neuroscience Graduate ProgramMayo Clinic Graduate School of Biomedical SciencesMayo ClinicRochesterMinnesotaUSA
- Regenerative Sciences Training ProgramCenter for Regenerative MedicineMayo ClinicRochesterMinnesotaUSA
| | - Sanjeet Grewal
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
| | | | - Robert Wharen
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
- Department of NeurologyMayo ClinicJacksonvilleFloridaUSA
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17
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Makarious MB, Leonard HL, Vitale D, Iwaki H, Sargent L, Dadu A, Violich I, Hutchins E, Saffo D, Bandres-Ciga S, Kim JJ, Song Y, Maleknia M, Bookman M, Nojopranoto W, Campbell RH, Hashemi SH, Botia JA, Carter JF, Craig DW, Van Keuren-Jensen K, Morris HR, Hardy JA, Blauwendraat C, Singleton AB, Faghri F, Nalls MA. Multi-modality machine learning predicting Parkinson's disease. NPJ Parkinsons Dis 2022; 8:35. [PMID: 35365675 PMCID: PMC8975993 DOI: 10.1038/s41531-022-00288-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
Personalized medicine promises individualized disease prediction and treatment. The convergence of machine learning (ML) and available multimodal data is key moving forward. We build upon previous work to deliver multimodal predictions of Parkinson's disease (PD) risk and systematically develop a model using GenoML, an automated ML package, to make improved multi-omic predictions of PD, validated in an external cohort. We investigated top features, constructed hypothesis-free disease-relevant networks, and investigated drug-gene interactions. We performed automated ML on multimodal data from the Parkinson's progression marker initiative (PPMI). After selecting the best performing algorithm, all PPMI data was used to tune the selected model. The model was validated in the Parkinson's Disease Biomarker Program (PDBP) dataset. Our initial model showed an area under the curve (AUC) of 89.72% for the diagnosis of PD. The tuned model was then tested for validation on external data (PDBP, AUC 85.03%). Optimizing thresholds for classification increased the diagnosis prediction accuracy and other metrics. Finally, networks were built to identify gene communities specific to PD. Combining data modalities outperforms the single biomarker paradigm. UPSIT and PRS contributed most to the predictive power of the model, but the accuracy of these are supplemented by many smaller effect transcripts and risk SNPs. Our model is best suited to identifying large groups of individuals to monitor within a health registry or biobank to prioritize for further testing. This approach allows complex predictive models to be reproducible and accessible to the community, with the package, code, and results publicly available.
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Affiliation(s)
- Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Glen Echo, MD, USA
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Dan Vitale
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Glen Echo, MD, USA
| | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Glen Echo, MD, USA
| | - Lana Sargent
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
- Geriatric Pharmacotherapy Program, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Anant Dadu
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ivo Violich
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Elizabeth Hutchins
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - David Saffo
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jonggeol Jeff Kim
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, UK
| | - Yeajin Song
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Glen Echo, MD, USA
| | | | - Matt Bookman
- Verily Life Sciences, South San Francisco, CA, USA
| | | | - Roy H Campbell
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sayed Hadi Hashemi
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Juan A Botia
- Department of Molecular Neuroscience, UCL Queen Square Institute of Neurology, London, UK
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | | | - David W Craig
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | | | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - John A Hardy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong SAR, China
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA.
- Data Tecnica International LLC, Glen Echo, MD, USA.
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA.
- Data Tecnica International LLC, Glen Echo, MD, USA.
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Zhang X, Farrell JJ, Tong T, Hu J, Zhu C, Alzheimer's Disease Sequencing Project, Wang L, Mayeux R, Haines JL, Pericak‐Vance MA, Schellenberg GD, Lunetta KL, Farrer LA. Association of mitochondrial variants and haplogroups identified by whole exome sequencing with Alzheimer's disease. Alzheimers Dement 2022; 18:294-306. [PMID: 34152079 PMCID: PMC8764625 DOI: 10.1002/alz.12396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Findings regarding the association between mitochondrial DNA (mtDNA) variants and Alzheimer's disease (AD) are inconsistent. METHODS We developed a pipeline for accurate assembly and variant calling in mitochondrial genomes embedded within whole exome sequences (WES) from 10,831 participants from the Alzheimer's Disease Sequencing Project (ADSP). Association of AD risk was evaluated with each mtDNA variant and variants located in 1158 nuclear genes related to mitochondrial function using the SCORE test. Gene-based tests were performed using SKAT-O. RESULTS Analysis of 4220 mtDNA variants revealed study-wide significant association of AD with a rare MT-ND4L variant (rs28709356 C>T; minor allele frequency = 0.002; P = 7.3 × 10-5 ) as well as with MT-ND4L in a gene-based test (P = 6.71 × 10-5 ). Significant association was also observed with a MT-related nuclear gene, TAMM41, in a gene-based test (P = 2.7 × 10-5 ). The expression of TAMM41 was lower in AD cases than controls (P = .00046) or mild cognitive impairment cases (P = .03). DISCUSSION Significant findings in MT-ND4L and TAMM41 provide evidence for a role of mitochondria in AD.
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Affiliation(s)
- Xiaoling Zhang
- Department of Medicine (Biomedical Genetics)Boston University School of Medicine72 East Concord StreetBostonMassachusetts02118USA
- Department of BiostatisticsBoston University School of Public Health801 Massachusetts Avenue 3rd FloorBostonMassachusetts02118USA
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics)Boston University School of Medicine72 East Concord StreetBostonMassachusetts02118USA
| | - Tong Tong
- Department of Medicine (Biomedical Genetics)Boston University School of Medicine72 East Concord StreetBostonMassachusetts02118USA
| | - Junming Hu
- Department of Medicine (Biomedical Genetics)Boston University School of Medicine72 East Concord StreetBostonMassachusetts02118USA
| | - Congcong Zhu
- Department of Medicine (Biomedical Genetics)Boston University School of Medicine72 East Concord StreetBostonMassachusetts02118USA
| | | | - Li‐San Wang
- Department of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania19104USA
| | - Richard Mayeux
- Department of NeurologyColumbia UniversityNew YorkNew York10032USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve UniversityClevelandOhio44106USA
| | | | - Gerard D. Schellenberg
- Department of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania19104USA
| | - Kathryn L. Lunetta
- Department of BiostatisticsBoston University School of Public Health801 Massachusetts Avenue 3rd FloorBostonMassachusetts02118USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics)Boston University School of Medicine72 East Concord StreetBostonMassachusetts02118USA
- Department of BiostatisticsBoston University School of Public Health801 Massachusetts Avenue 3rd FloorBostonMassachusetts02118USA
- Department of NeurologyBoston University School of MedicineBostonMassachusetts02118USA
- Department of OphthalmologyBoston University School of MedicineBostonMassachusetts02118USA
- Department of EpidemiologyBoston University School of Public Health715 Albany StreetBostonMassachusetts02118USA
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19
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Xue D, Bush WS, Renton AE, Marcora EA, Bis JC, Kunkle BW, The Alzheimer's Disease Sequencing Project, Boerwinkle E, DeStefano AL, Farrer L, Goate A, Mayeux R, Pericak‐Vance M, Schellenberg G, Seshadri S, Wijsman E, Haines JL, Blue EE. Large-scale sequencing studies expand the known genetic architecture of Alzheimer's disease. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12255. [PMID: 35005195 PMCID: PMC8720139 DOI: 10.1002/dad2.12255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Genes implicated by genome-wide association studies and family-based studies of Alzheimer's disease (AD) are largely discordant. We hypothesized that genes identified by sequencing studies like the Alzheimer's Disease Sequencing Project (ADSP) may bridge this gap and highlight shared biological mechanisms. METHODS We performed structured literature review of genes prioritized by ADSP studies, genes underlying familial dementias, and genes nominated by genome-wide association studies. Gene set enrichment analyses of each list identified enriched pathways. RESULTS The genes prioritized by the ADSP, familial dementia studies, and genome-wide association studies minimally overlapped. Each gene set identified dozens of enriched pathways, several of which were shared (e.g., regulation of amyloid beta clearance). DISCUSSION Alternative study designs provide unique insights into AD genetics. Shared pathways enriched by different genes highlight their relevance to AD pathogenesis, while the patterns of pathway enrichment unique to each gene set provide additional targets for functional studies.
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Affiliation(s)
- Diane Xue
- Institute for Public Health GeneticsUniversity of WashingtonSeattleWashingtonUSA
| | - William S. Bush
- Department of Population and Quantitative Health Sciences and Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Cleveland Institute for Computational BiologyClevelandOhioUSA
| | - Alan E. Renton
- Department of Genetics and Genomic SciencesNash Family Department of Neuroscienceand Ronald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Edoardo A. Marcora
- Department of Genetics and Genomic SciencesNash Family Department of Neuroscienceand Ronald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Joshua C. Bis
- Cardiovascular Health Research UnitDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Brian W. Kunkle
- The John P. Hussman Institute for Human GenomicsUniversity of MiamiMiamiFloridaUSA
- Dr. John T Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | | | - Eric Boerwinkle
- Human Genome Sequencing CenterDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- School of Public HealthUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Anita L. DeStefano
- Department of BiostatisticsBoston UniversityBostonMassachusettsUSA
- Department of NeurologyBoston UniversityBostonMassachusettsUSA
| | - Lindsay Farrer
- Department of BiostatisticsBoston UniversityBostonMassachusettsUSA
- Department of NeurologyBoston UniversityBostonMassachusettsUSA
- Division of Biomedical GeneticsDepartment of MedicineDepartment of Epidemiologyand Department of OphthalmologyBoston UniversityBostonMassachusettsUSA
| | - Alison Goate
- Department of Genetics and Genomic SciencesNash Family Department of Neuroscienceand Ronald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Genetics and Genomics Sciences and Friedman Brain InstituteMount Sinai School of MedicineNew YorkNew YorkUSA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainGertrude H. Sergievsky CenterDepartment of NeurologyDepartment of Psychiatryand EpidemiologyColumbia UniversityNew YorkNew YorkUSA
| | - Margaret Pericak‐Vance
- The John P. Hussman Institute for Human GenomicsUniversity of MiamiMiamiFloridaUSA
- Dr. John T Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics CenterDepartment of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases and Department of NeurologyUniversity of Texas Health Science CenterSan AntonioTexasUSA
| | - Ellen Wijsman
- Institute for Public Health GeneticsUniversity of WashingtonSeattleWashingtonUSA
- Division of Medical GeneticsUniversity of WashingtonSeattleWashingtonUSA
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences and Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Cleveland Institute for Computational BiologyClevelandOhioUSA
| | - Elizabeth E. Blue
- Institute for Public Health GeneticsUniversity of WashingtonSeattleWashingtonUSA
- Division of Medical GeneticsUniversity of WashingtonSeattleWashingtonUSA
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Zhan L, Li J, Jew B, Sul JH. Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. PLoS Genet 2021; 17:e1009772. [PMID: 34516545 PMCID: PMC8460036 DOI: 10.1371/journal.pgen.1009772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/23/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common type of dementia causing irreversible brain damage to the elderly and presents a major public health challenge. Clinical research and genome-wide association studies have suggested a potential contribution of the endocytic pathway to AD, with an emphasis on common loci. However, the contribution of rare variants in this pathway to AD has not been thoroughly investigated. In this study, we focused on the effect of rare variants on AD by first applying a rare-variant gene-set burden analysis using genes in the endocytic pathway on over 3,000 individuals with European ancestry from three large whole-genome sequencing (WGS) studies. We identified significant associations of rare-variant burden within the endocytic pathway with AD, which were successfully replicated in independent datasets. We further demonstrated that this endocytic rare-variant enrichment is associated with neurofibrillary tangles (NFTs) and age-related phenotypes, increasing the risk of obtaining severer brain damage, earlier age-at-onset, and earlier age-of-death. Next, by aggregating rare variants within each gene, we sought to identify single endocytic genes associated with AD and NFTs. Careful examination using NFTs revealed one significantly associated gene, ANKRD13D. To identify functional associations, we integrated bulk RNA-Seq data from over 600 brain tissues and found two endocytic expression genes (eGenes), HLA-A and SLC26A7, that displayed significant influences on their gene expressions. Differential expressions between AD patients and controls of these three identified genes were further examined by incorporating scRNA-Seq data from 48 post-mortem brain samples and demonstrated distinct expression patterns across cell types. Taken together, our results demonstrated strong rare-variant effect in the endocytic pathway on AD risk and progression and functional effect of gene expression alteration in both bulk and single-cell resolution, which may bring more insight and serve as valuable resources for future AD genetic studies, clinical research, and therapeutic targeting.
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Affiliation(s)
- Lingyu Zhan
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jiajin Li
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Brandon Jew
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, California, United States of America
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21
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Sinsky J, Pichlerova K, Hanes J. Tau Protein Interaction Partners and Their Roles in Alzheimer's Disease and Other Tauopathies. Int J Mol Sci 2021; 22:9207. [PMID: 34502116 PMCID: PMC8431036 DOI: 10.3390/ijms22179207] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
Tau protein plays a critical role in the assembly, stabilization, and modulation of microtubules, which are important for the normal function of neurons and the brain. In diseased conditions, several pathological modifications of tau protein manifest. These changes lead to tau protein aggregation and the formation of paired helical filaments (PHF) and neurofibrillary tangles (NFT), which are common hallmarks of Alzheimer's disease and other tauopathies. The accumulation of PHFs and NFTs results in impairment of physiological functions, apoptosis, and neuronal loss, which is reflected as cognitive impairment, and in the late stages of the disease, leads to death. The causes of this pathological transformation of tau protein haven't been fully understood yet. In both physiological and pathological conditions, tau interacts with several proteins which maintain their proper function or can participate in their pathological modifications. Interaction partners of tau protein and associated molecular pathways can either initiate and drive the tau pathology or can act neuroprotective, by reducing pathological tau proteins or inflammation. In this review, we focus on the tau as a multifunctional protein and its known interacting partners active in regulations of different processes and the roles of these proteins in Alzheimer's disease and tauopathies.
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Affiliation(s)
| | | | - Jozef Hanes
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10 Bratislava, Slovakia; (J.S.); (K.P.)
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22
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Patel S, Howard D, Chowdhury N, Derieux C, Wellslager B, Yilmaz Ö, French L. Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons. Front Immunol 2021; 12:646259. [PMID: 34194426 PMCID: PMC8236716 DOI: 10.3389/fimmu.2021.646259] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
Porphyromonas gingivalis, a bacterium associated with periodontal disease, is a suspected cause of Alzheimer's disease. This bacterium is reliant on gingipain proteases, which cleave host proteins after arginine and lysine residues. To characterize gingipain susceptibility, we performed enrichment analyses of arginine and lysine proportion proteome-wide. Genes differentially expressed in brain samples with detected P. gingivalis reads were also examined. Genes from these analyses were tested for functional enrichment and specific neuroanatomical expression patterns. Proteins in the SRP-dependent cotranslational protein targeting to membrane pathway were enriched for these residues and previously associated with periodontal and Alzheimer's disease. These ribosomal genes are up-regulated in prefrontal cortex samples with detected P. gingivalis sequences. Other differentially expressed genes have been previously associated with dementia (ITM2B, MAPT, ZNF267, and DHX37). For an anatomical perspective, we characterized the expression of the P. gingivalis associated genes in the mouse and human brain. This analysis highlighted the hypothalamus, cholinergic neurons, and the basal forebrain. Our results suggest markers of neural P. gingivalis infection and link the cholinergic and gingipain hypotheses of Alzheimer's disease.
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Affiliation(s)
- Sejal Patel
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Derek Howard
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Nityananda Chowdhury
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Casey Derieux
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Bridgette Wellslager
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Özlem Yilmaz
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States
| | - Leon French
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute for Medical Science, University of Toronto, Toronto, ON, Canada
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23
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Monk B, Rajkovic A, Petrus S, Rajkovic A, Gaasterland T, Malinow R. A Machine Learning Method to Identify Genetic Variants Potentially Associated With Alzheimer's Disease. Front Genet 2021; 12:647436. [PMID: 34194466 PMCID: PMC8238203 DOI: 10.3389/fgene.2021.647436] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/06/2021] [Indexed: 01/17/2023] Open
Abstract
There is hope that genomic information will assist prediction, treatment, and understanding of Alzheimer's disease (AD). Here, using exome data from ∼10,000 individuals, we explore machine learning neural network (NN) methods to estimate the impact of SNPs (i.e., genetic variants) on AD risk. We develop an NN-based method (netSNP) that identifies hundreds of novel potentially protective or at-risk AD-associated SNPs (along with an effect measure); the majority with frequency under 0.01. For case individuals, the number of "protective" (or "at-risk") netSNP-identified SNPs in their genome correlates positively (or inversely) with their age of AD diagnosis and inversely (or positively) with autopsy neuropathology. The effect measure increases correlations. Simulations suggest our results are not due to genetic linkage, overfitting, or bias introduced by netSNP. These findings suggest that netSNP can identify SNPs associated with AD pathophysiology that may assist with the diagnosis and mechanistic understanding of the disease.
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Affiliation(s)
- Bradley Monk
- Department of Neurosciences, Center for Neural Circuits and Behavior, School of Medicine, University of California, San Diego, San Diego, CA, United States
- Cognitive Science & Psychology IDP, University of California, San Diego, San Diego, CA, United States
| | - Andrei Rajkovic
- Department of Computer Science, Royal Holloway, University of London, Egham, United Kingdom
| | - Semar Petrus
- Institute for Genomic Medicine, Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Aleks Rajkovic
- Department of Pathology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Terry Gaasterland
- Institute for Genomic Medicine, Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Roberto Malinow
- Department of Neurosciences, Center for Neural Circuits and Behavior, School of Medicine, University of California, San Diego, San Diego, CA, United States
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
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Dehghani N, Bras J, Guerreiro R. How understudied populations have contributed to our understanding of Alzheimer's disease genetics. Brain 2021; 144:1067-1081. [PMID: 33889936 DOI: 10.1093/brain/awab028] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/30/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
The majority of genome-wide association studies have been conducted using samples with a broadly European genetic background. As a field, we acknowledge this limitation and the need to increase the diversity of populations studied. A major challenge when designing and conducting such studies is to assimilate large samples sizes so that we attain enough statistical power to detect variants associated with disease, particularly when trying to identify variants with low and rare minor allele frequencies. In this review, we aimed to illustrate the benefits to genetic characterization of Alzheimer's disease, in researching currently understudied populations. This is important for both fair representation of world populations and the translatability of findings. To that end, we conducted a literature search to understand the contributions of studies, on different populations, to Alzheimer's disease genetics. Using both PubMed and Alzforum Mutation Database, we systematically quantified the number of studies reporting variants in known disease-causing genes, in a worldwide manner, and discuss the contributions of research in understudied populations to the identification of novel genetic factors in this disease. Additionally, we compared the effects of genome-wide significant single nucleotide polymorphisms across populations by focusing on loci that show different association profiles between populations (a key example being APOE). Reports of variants in APP, PSEN1 and PSEN2 can initially determine whether patients from a country have been studied for Alzheimer's disease genetics. Most genome-wide significant associations in non-Hispanic white genome-wide association studies do not reach genome-wide significance in such studies of other populations, with some suggesting an opposite effect direction; this is likely due to much smaller sample sizes attained. There are, however, genome-wide significant associations first identified in understudied populations which have yet to be replicated. Familial studies in understudied populations have identified rare, high effect variants, which have been replicated in other populations. This work functions to both highlight how understudied populations have furthered our understanding of Alzheimer's disease genetics, and to help us gauge our progress in understanding the genetic architecture of this disease in all populations.
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Affiliation(s)
- Nadia Dehghani
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
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25
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Patel D, Zhang X, Farrell JJ, Lunetta KL, Farrer LA. Set-Based Rare Variant Expression Quantitative Trait Loci in Blood and Brain from Alzheimer Disease Study Participants. Genes (Basel) 2021; 12:419. [PMID: 33804025 PMCID: PMC7999141 DOI: 10.3390/genes12030419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Because studies of rare variant effects on gene expression have limited power, we investigated set-based methods to identify rare expression quantitative trait loci (eQTL) related to Alzheimer disease (AD). Gene-level and pathway-level cis rare-eQTL mapping was performed genome-wide using gene expression data derived from blood donated by 713 Alzheimer's Disease Neuroimaging Initiative participants and from brain tissues donated by 475 Religious Orders Study/Memory and Aging Project participants. The association of gene or pathway expression with a set of all cis potentially regulatory low-frequency and rare variants within 1 Mb of genes was evaluated using SKAT-O. A total of 65 genes expressed in the brain were significant targets for rare expression single nucleotide polymorphisms (eSNPs) among which 17% (11/65) included established AD genes HLA-DRB1 and HLA-DRB5. In the blood, 307 genes were significant targets for rare eSNPs. In the blood and the brain, GNMT, LDHC, RBPMS2, DUS2, and HP were targets for significant eSNPs. Pathway enrichment analysis revealed significant pathways in the brain (n = 9) and blood (n = 16). Pathways for apoptosis signaling, cholecystokinin receptor (CCKR) signaling, and inflammation mediated by chemokine and cytokine signaling were common to both tissues. Significant rare eQTLs in inflammation pathways included five genes in the blood (ALOX5AP, CXCR2, FPR2, GRB2, IFNAR1) that were previously linked to AD. This study identified several significant gene- and pathway-level rare eQTLs, which further confirmed the importance of the immune system and inflammation in AD and highlighted the advantages of using a set-based eQTL approach for evaluating the effect of low-frequency and rare variants on gene expression.
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Affiliation(s)
- Devanshi Patel
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
| | - Lindsay A. Farrer
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
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Enhancing and Complementary Mechanisms of Synergistic Action of Acori Tatarinowii Rhizoma and Codonopsis Radix for Alzheimer's Disease Based on Systems Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:6317230. [PMID: 32802132 PMCID: PMC7334796 DOI: 10.1155/2020/6317230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/20/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Materials and Methods In this study, a systems pharmacology-based strategy was used to elucidate the synergistic mechanism of Acori Tatarinowii Rhizoma and Codonopsis Radix for the treatment of AD. This novel systems pharmacology model consisted of component information, pharmacokinetic analysis, and pharmacological data. Additionally, the related pathways were compressed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the organ distributions were determined in the BioGPS bank. Results Sixty-eight active ingredients with suitable pharmacokinetic profiles and biological activities were selected through ADME screening in silico. Based on 62 AD-related targets, such as APP, CHRM1, and PTGS1, systematic analysis showed that these two herbs were mainly involved in the PI3K-Akt signaling pathway, MAPK signaling pathway, neuroactive ligand-receptor interaction, and fluid shear stress and atherosclerosis, indicating that they had a synergistic effect on AD. However, ATR acted on the KDR gene, while CR acted on IGF1R, MET, IL1B, and CHUK, showing that they also had complementary effects on AD. The ingredient contribution score involved 29 ingredients contributing 90.14% of the total contribution score of this formula for AD treatment, which emphasized that the effective therapeutic effects of these herbs for AD were derived from both ATR and CR, not a single herb. Organ distribution showed that the targets of the active ingredients were mainly located in the whole blood, the brain, and the muscle, which are associated with AD. Conclusions In sum, our findings suggest that the systems pharmacology methods successfully revealed the synergistic and complementary mechanisms of ATR and CR for the treatment of AD.
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Executive Summary of the 2019 International Conference of Korean Dementia Association: Exploring the Novel Concept of Alzheimer's Disease and Other Dementia: a Report from the Academic Committee of the Korean Dementia Association. Dement Neurocogn Disord 2020; 19:39-53. [PMID: 32602279 PMCID: PMC7326615 DOI: 10.12779/dnd.2020.19.2.39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 01/14/2023] Open
Abstract
Because of repeated failures of clinical trials, the concept of Alzheimer's disease (AD) has been changing rapidly in recent years. As suggested by the National Institute on Aging and the Alzheimer's Association Research Framework, the diagnosis and classification of AD is now based on biomarkers rather than on symptoms, allowing more accurate identification of proper candidates for clinical trials by pathogenesis and disease stage. Recent development in neuroimaging has provided a way to reveal the complex dynamics of amyloid and tau in the brain in vivo, and studies of blood biomarkers are taking another leap forward in diagnosis and treatment of AD. In the field of basic and translational research, the development of animal models and a deeper understanding of the role of neuroinflammation are taking a step closer to clarifying the pathogenesis of AD. Development of big data and the Internet of Things is also incorporating dementia care and research into other aspects. Large-scale genetic research has identified genetic abnormalities that can provide a foundation for precision medicine along with the aforementioned digital technologies. Through the first international conference of the Korean Dementia Association, experts from all over the world gathered to exchange opinions with association members on these topics. The Academic Committee of the Korean Dementia Association briefly summarizes the contents of the lectures to convey the depth of the conference and discussions. This will be an important milestone in understanding the latest trends in AD's pathogenesis, diagnostic and therapeutic research and in establishing a future direction.
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Muraoka S, DeLeo AM, Sethi MK, Yukawa‐Takamatsu K, Yang Z, Ko J, Hogan JD, Ruan Z, You Y, Wang Y, Medalla M, Ikezu S, Chen M, Xia W, Gorantla S, Gendelman HE, Issadore D, Zaia J, Ikezu T. Proteomic and biological profiling of extracellular vesicles from Alzheimer's disease human brain tissues. Alzheimers Dement 2020; 16:896-907. [PMID: 32301581 PMCID: PMC7293582 DOI: 10.1002/alz.12089] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/05/2019] [Accepted: 01/15/2020] [Indexed: 12/31/2022]
Abstract
Introduction Extracellular vesicles (EVs) from human Alzheimer's disease (AD) biospecimens contain amyloid beta (Aβ) peptide and tau. While AD EVs are known to affect brain disease pathobiology, their biochemical and molecular characterizations remain ill defined. Methods EVs were isolated from the cortical gray matter of 20 AD and 18 control brains. Tau and Aβ levels were measured by immunoassay. Differentially expressed EV proteins were assessed by quantitative proteomics and machine learning. Results Levels of pS396 tau and Aβ1–42 were significantly elevated in AD EVs. High levels of neuron‐ and glia‐specific factors are detected in control and AD EVs, respectively. Machine learning identified ANXA5, VGF, GPM6A, and ACTZ in AD EV compared to controls. They distinguished AD EVs from controls in the test sets with 88% accuracy. Discussion In addition to Aβ and tau, ANXA5, VGF, GPM6A, and ACTZ are new signature proteins in AD EVs.
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Affiliation(s)
- Satoshi Muraoka
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
| | - Annina M. DeLeo
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
| | - Manveen K. Sethi
- Department of BiochemistryBoston University School of Medicine Boston Massachusetts USA
| | - Kayo Yukawa‐Takamatsu
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
| | - Zijian Yang
- Department of BioengineeringUniversity of Pennsylvania Philadelphia Pennsylvania USA
| | - Jina Ko
- Department of BioengineeringUniversity of Pennsylvania Philadelphia Pennsylvania USA
| | - John D. Hogan
- Program in BioinformaticsBoston University Boston Massachusetts USA
| | - Zhi Ruan
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
| | - Yang You
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
| | - Yuzhi Wang
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
| | - Maria Medalla
- Department of Anatomy and NeurobiologyBoston University School of Medicine Boston Massachusetts USA
| | - Seiko Ikezu
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
| | - Mei Chen
- Geriatric ResearchEducation and Clinical CenterEdith Nourse Rogers Memorial Veterans Hospital Bedford Massachusetts USA
| | - Weiming Xia
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
- Geriatric ResearchEducation and Clinical CenterEdith Nourse Rogers Memorial Veterans Hospital Bedford Massachusetts USA
| | - Santhi Gorantla
- Department of Pharmacology and Experimental NeurosciencesUniversity of Nebraska Medical Center Omaha Nebraska USA
| | - Howard E. Gendelman
- Department of Pharmacology and Experimental NeurosciencesUniversity of Nebraska Medical Center Omaha Nebraska USA
| | - David Issadore
- Department of BioengineeringUniversity of Pennsylvania Philadelphia Pennsylvania USA
| | - Joseph Zaia
- Department of BiochemistryBoston University School of Medicine Boston Massachusetts USA
| | - Tsuneya Ikezu
- Department of Pharmacology and Experimental TherapeuticsBoston University School of Medicine Boston Massachusetts USA
- Department of NeurologyBoston University School of Medicine Boston Massachusetts USA
- Center for Systems NeuroscienceBoston University Boston Massachusetts USA
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Bellenguez C, Grenier-Boley B, Lambert JC. Genetics of Alzheimer’s disease: where we are, and where we are going. Curr Opin Neurobiol 2020; 61:40-48. [DOI: 10.1016/j.conb.2019.11.024] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
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Ma Y, Jun GR, Zhang X, Chung J, Naj AC, Chen Y, Bellenguez C, Hamilton-Nelson K, Martin ER, Kunkle BW, Bis JC, Debette S, DeStefano AL, Fornage M, Nicolas G, van Duijn C, Bennett DA, De Jager PL, Mayeux R, Haines JL, Pericak-Vance MA, Seshadri S, Lambert JC, Schellenberg GD, Lunetta KL, Farrer LA. Analysis of Whole-Exome Sequencing Data for Alzheimer Disease Stratified by APOE Genotype. JAMA Neurol 2019; 76:1099-1108. [PMID: 31180460 PMCID: PMC6563544 DOI: 10.1001/jamaneurol.2019.1456] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/22/2019] [Indexed: 12/13/2022]
Abstract
IMPORTANCE Previous genome-wide association studies of common variants identified associations for Alzheimer disease (AD) loci evident only among individuals with particular APOE alleles. OBJECTIVE To identify APOE genotype-dependent associations with infrequent and rare variants using whole-exome sequencing. DESIGN, SETTING, AND PARTICIPANTS The discovery stage included 10 441 non-Hispanic white participants in the Alzheimer Disease Sequencing Project. Replication was sought in 2 independent, whole-exome sequencing data sets (1766 patients with AD, 2906 without AD [controls]) and a chip-based genotype imputation data set (8728 patients with AD, 9808 controls). Bioinformatics and functional analyses were conducted using clinical, cognitive, neuropathologic, whole-exome sequencing, and gene expression data obtained from a longitudinal cohort sample including 402 patients with AD and 647 controls. Data were analyzed between March 2017 and September 2018. MAIN OUTCOMES AND MEASURES Score, Firth, and sequence kernel association tests were used to test the association of AD risk with individual variants and genes in subgroups of APOE ε4 carriers and noncarriers. Results with P ≤ 1 × 10-5 were further evaluated in the replication data sets and combined by meta-analysis. RESULTS Among 3145 patients with AD and 4213 controls lacking ε4 (mean [SD] age, 83.4 [7.6] years; 4363 [59.3.%] women), novel genome-wide significant associations were obtained in the discovery sample with rs536940594 in AC099552 (odds ratio [OR], 88.0; 95% CI, 9.08-852.0; P = 2.22 × 10-7) and rs138412600 in GPAA1 (OR, 1.78; 95% CI, 1.44-2.2; meta-P = 7.81 × 10-8). GPAA1 was also associated with expression in the brain of GPAA1 (β = -0.08; P = .03) and its repressive transcription factor, FOXG1 (β = 0.13; P = .003), and global cognition function (β = -0.53; P = .009). Significant gene-wide associations (threshold P ≤ 6.35 × 10-7) were observed for OR8G5 (P = 4.67 × 10-7), IGHV3-7 (P = 9.75 × 10-16), and SLC24A3 (P = 2.67 × 10-12) in 2377 patients with AD and 706 controls with ε4 (mean [SD] age, 75.2 [9.6] years; 1668 [54.1%] women). CONCLUSIONS AND RELEVANCE The study identified multiple possible novel associations for AD with individual and aggregated rare variants in groups of individuals with and without APOE ε4 alleles that reinforce known and suggest additional pathways leading to AD.
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Affiliation(s)
- Yiyi Ma
- Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Center for Translational & Computational Neuroimmunology, Multiple Sclerosis Clinical Care and Research Center, Division of Neuroimmunology, Columbia University Medical Center, New York, New York
- Department of Neurology, Columbia University Medical Center, New York, New York
| | - Gyungah R. Jun
- Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Adam C. Naj
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Yuning Chen
- Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Celine Bellenguez
- Universite de Lille, INSERM UMR1167, Institute Pasteur de Lille, Lille, France
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
| | - Stéphanie Debette
- Bordeaux Population Health Research Center, UMR1219, University Bordeaux, Inserm, Bordeaux, France
- Department of Neurology, Bordeaux University Hospital, Bordeaux, France
| | - Anita L. DeStefano
- Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Department of Neurology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Myriam Fornage
- School of Public Health, University of Texas Health Science Center at Houston, Houston
| | - Gaël Nicolas
- UNIROUEN, Inserm U1245, Normandie University, Rouen, France
- Department of Genetics, Rouen University Hospital, Rouen, France
- Normandy Centre for Genomic and Personalized Medicine, Centre National de Référence pour les Malades Alzheimer Jeunes, Rouen, France
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Multiple Sclerosis Clinical Care and Research Center, Division of Neuroimmunology, Columbia University Medical Center, New York, New York
- Department of Neurology, Columbia University Medical Center, New York, New York
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Richard Mayeux
- Department of Neurology, Columbia University Medical Center, New York, New York
| | - Jonathan L Haines
- Institute for Computational Biology, Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Sudha Seshadri
- Department of Neurology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio
| | | | | | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Department of Neurology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Department of Ophthalmology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
- Department of Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
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Jiang Z, Liu G, Yang Y, Shao K, Wang Y, Liu W, Han B. N-Acetyl chitooligosaccharides attenuate amyloid β-induced damage in animal and cell models of Alzheimer’s disease. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sadlon A, Takousis P, Alexopoulos P, Evangelou E, Prokopenko I, Perneczky R. miRNAs Identify Shared Pathways in Alzheimer's and Parkinson's Diseases. Trends Mol Med 2019; 25:662-672. [PMID: 31221572 DOI: 10.1016/j.molmed.2019.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/10/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
Despite the identification of several dozens of common genetic variants associated with Alzheimer's disease (AD) and Parkinson's disease (PD), most of the genetic risk remains uncharacterised. Therefore, it is important to understand the role of regulatory elements, such as miRNAs. Dysregulated miRNAs are implicated in AD and PD, with potential value in dissecting the shared pathophysiology between the two disorders. miRNAs relevant to both neurodegenerative diseases are related to axonal guidance, apoptosis, and inflammation, therefore, AD and PD likely arise from similar underlying biological pathway defects. Furthermore, pathways regulated by APP, L1CAM, and genes of the caspase family may represent promising therapeutic miRNA targets in AD and PD since they are targeted by dysregulated miRNAs in both disorders.
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Affiliation(s)
- Angélique Sadlon
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK
| | - Petros Takousis
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK
| | - Panagiotis Alexopoulos
- Department of Psychiatry, University of Patras, Patras, Greece; Department of Psychiatry and Psychotherapy, Technische Universität München, Munich, Germany
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Inga Prokopenko
- Section of Genomics of Common Disease, Department of Medicine, Imperial College London, London, UK; Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Robert Perneczky
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK; Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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Patel D, Mez J, Vardarajan BN, Staley L, Chung J, Zhang X, Farrell JJ, Rynkiewicz MJ, Cannon-Albright LA, Teerlink CC, Stevens J, Corcoran C, Gonzalez Murcia JD, Lopez OL, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg G, Kauwe JSK, Lunetta KL, Farrer LA. Association of Rare Coding Mutations With Alzheimer Disease and Other Dementias Among Adults of European Ancestry. JAMA Netw Open 2019; 2:e191350. [PMID: 30924900 PMCID: PMC6450321 DOI: 10.1001/jamanetworkopen.2019.1350] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/01/2019] [Indexed: 12/26/2022] Open
Abstract
Importance Some of the unexplained heritability of Alzheimer disease (AD) may be due to rare variants whose effects are not captured in genome-wide association studies because very large samples are needed to observe statistically significant associations. Objective To identify genetic variants associated with AD risk using a nonstatistical approach. Design, Setting, and Participants Genetic association study in which rare variants were identified by whole-exome sequencing in unrelated individuals of European ancestry from the Alzheimer's Disease Sequencing Project (ADSP). Data were analyzed between March 2017 and September 2018. Main Outcomes and Measures Minor alleles genome-wide and in 95 genes previously associated with AD, AD-related traits, or other dementias were tabulated and filtered for predicted functional impact and occurrence in participants with AD but not controls. Support for several findings was sought in a whole-exome sequencing data set comprising 19 affected relative pairs from Utah high-risk pedigrees and whole-genome sequencing data sets from the ADSP and Alzheimer's Disease Neuroimaging Initiative. Results Among 5617 participants with AD (3202 [57.0%] women; mean [SD] age, 76.4 [9.3] years) and 4594 controls (2719 [59.0%] women; mean [SD] age, 86.5 [4.5] years), a total of 24 variants with moderate or high functional impact from 19 genes were observed in 10 or more participants with AD but not in controls. These variants included a missense mutation (rs149307620 [p.A284T], n = 10) in NOTCH3, a gene in which coding mutations are associated with cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), that was also identified in 1 participant with AD and 1 participant with mild cognitive impairment in the whole genome sequencing data sets. Four participants with AD carried the TREM2 rs104894002 (p.Q33X) high-impact mutation that, in homozygous form, causes Nasu-Hakola disease, a rare disorder characterized by early-onset dementia and multifocal bone cysts, suggesting an intermediate inheritance model for the mutation. Compared with controls, participants with AD had a significantly higher burden of deleterious rare coding variants in dementia-associated genes (2314 vs 3354 cumulative variants, respectively; P = .006). Conclusions and Relevance Different mutations in the same gene or variable dose of a mutation may be associated with result in distinct dementias. These findings suggest that minor differences in the structure or amount of protein may be associated with in different clinical outcomes. Understanding these genotype-phenotype associations may provide further insight into the pathogenic nature of the mutations, as well as offer clues for developing new therapeutic targets.
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Affiliation(s)
- Devanshi Patel
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
| | - Jesse Mez
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | | | - Lyndsay Staley
- Department of Biology, Brigham Young University, Provo, Utah
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
| | - Michael J. Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Lisa A. Cannon-Albright
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | - Craig C. Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | - Jeffery Stevens
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | | | | | - Oscar L. Lopez
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Richard Mayeux
- Department of Neurology, Columbia University, New York, New York
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia
| | | | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
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