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Fernandez MV, Liu M, Beric A, Johnson M, Cetin A, Patel M, Budde J, Kohlfeld P, Bergmann K, Lowery J, Flynn A, Brock W, Sanchez Montejo B, Gentsch J, Sykora N, Norton J, Gentsch J, Valdez O, Gorijala P, Sanford J, Sun Y, Wang C, Western D, Timsina J, Mangetti Goncalves T, Do AN, Sung YJ, Zhao G, Morris JC, Moulder K, Holtzman DM, Bateman RJ, Karch C, Hassenstab J, Xiong C, Schindler SE, Balls-Berry JJ, Benzinger TLS, Perrin RJ, Denny A, Snider BJ, Stark SL, Ibanez L, Cruchaga C. Genetic and multi-omic resources for Alzheimer disease and related dementia from the Knight Alzheimer Disease Research Center. Sci Data 2024; 11:768. [PMID: 38997326 PMCID: PMC11245521 DOI: 10.1038/s41597-024-03485-9] [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: 01/24/2024] [Accepted: 06/06/2024] [Indexed: 07/14/2024] Open
Abstract
The Knight-Alzheimer Disease Research Center (Knight-ADRC) at Washington University in St. Louis has pioneered and led worldwide seminal studies that have expanded our clinical, social, pathological, and molecular understanding of Alzheimer Disease. Over more than 40 years, research volunteers have been recruited to participate in cognitive, neuropsychologic, imaging, fluid biomarkers, genomic and multi-omic studies. Tissue and longitudinal data collected to foster, facilitate, and support research on dementia and aging. The Genetics and high throughput -omics core (GHTO) have collected of more than 26,000 biological samples from 6,625 Knight-ADRC participants. Samples available include longitudinal DNA, RNA, non-fasted plasma, cerebrospinal fluid pellets, and peripheral blood mononuclear cells. The GHTO has performed deep molecular profiling (genomic, transcriptomic, epigenomic, proteomic, and metabolomic) from large number of brain (n = 2,117), CSF (n = 2,012) and blood/plasma (n = 8,265) samples with the goal of identifying novel risk and protective variants, identify novel molecular biomarkers and causal and druggable targets. Overall, the resources available at GHTO support the increase of our understanding of Alzheimer Disease.
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Affiliation(s)
- Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Research Center and Memory Clinic, ACE Alzheimer Center, Barcelona, Spain
| | - Menghan Liu
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aleksandra Beric
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Matt Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Arda Cetin
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Maulik Patel
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joseph Lowery
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Allison Flynn
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - William Brock
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brenda Sanchez Montejo
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nicholas Sykora
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Olga Valdez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jessie Sanford
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yichen Sun
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ciyang Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Anh N Do
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Guoyan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Pathology and Immunology Department, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Krista Moulder
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Celeste Karch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Jason Hassenstab
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Suzanne E Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Joyce Joy Balls-Berry
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Tammie L S Benzinger
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
- Radiology Department, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Richard J Perrin
- Pathology and Immunology Department, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Andrea Denny
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - B Joy Snider
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan L Stark
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Occupational Therapy, Neurology and Social Work, St. Louis, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA.
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA.
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Sahelijo N, Rajagopalan P, Qian L, Rahman R, Priyadarshi D, Goldstein D, Thomopoulos SI, Bennett DA, Farrer LA, Stein TD, Shen L, Huang H, Nho K, Andrew SJ, Davatzikos C, Thompson PM, Tcw J, Jun GR. Brain Cell-based Genetic Subtyping and Drug Repositioning for Alzheimer Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.21.24309255. [PMID: 38947056 PMCID: PMC11213108 DOI: 10.1101/2024.06.21.24309255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Alzheimer's Disease (AD) is characterized by its complex and heterogeneous etiology and gradual progression, leading to high drug failure rates in late-stage clinical trials. In order to better stratify individuals at risk for AD and discern potential therapeutic targets we employed a novel procedure utilizing cell-based co-regulated gene networks and polygenic risk scores (cbPRSs). After defining genetic subtypes using extremes of cbPRS distributions, we evaluated correlations of the genetic subtypes with previously defined AD subtypes defined on the basis of domain-specific cognitive functioning and neuroimaging biomarkers. Employing a PageRank algorithm, we identified priority gene targets for the genetic subtypes. Pathway analysis of priority genes demonstrated associations with neurodegeneration and suggested candidate drugs currently utilized in diabetes, hypertension, and epilepsy for repositioning in AD. Experimental validation utilizing human induced pluripotent stem cell (hiPSC)-derived astrocytes demonstrated the modifying effects of estradiol, levetiracetam, and pioglitazone on expression of APOE and complement C4 genes, suggesting potential repositioning for AD.
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3
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Yap CX, Vo DD, Heffel MG, Bhattacharya A, Wen C, Yang Y, Kemper KE, Zeng J, Zheng Z, Zhu Z, Hannon E, Vellame DS, Franklin A, Caggiano C, Wamsley B, Geschwind DH, Zaitlen N, Gusev A, Pasaniuc B, Mill J, Luo C, Gandal MJ. Brain cell-type shifts in Alzheimer's disease, autism, and schizophrenia interrogated using methylomics and genetics. SCIENCE ADVANCES 2024; 10:eadn7655. [PMID: 38781333 PMCID: PMC11114225 DOI: 10.1126/sciadv.adn7655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/14/2024] [Indexed: 05/25/2024]
Abstract
Few neuropsychiatric disorders have replicable biomarkers, prompting high-resolution and large-scale molecular studies. However, we still lack consensus on a more foundational question: whether quantitative shifts in cell types-the functional unit of life-contribute to neuropsychiatric disorders. Leveraging advances in human brain single-cell methylomics, we deconvolve seven major cell types using bulk DNA methylation profiling across 1270 postmortem brains, including from individuals diagnosed with Alzheimer's disease, schizophrenia, and autism. We observe and replicate cell-type compositional shifts for Alzheimer's disease (endothelial cell loss), autism (increased microglia), and schizophrenia (decreased oligodendrocytes), and find age- and sex-related changes. Multiple layers of evidence indicate that endothelial cell loss contributes to Alzheimer's disease, with comparable effect size to APOE genotype among older people. Genome-wide association identified five genetic loci related to cell-type composition, involving plausible genes for the neurovascular unit (P2RX5 and TRPV3) and excitatory neurons (DPY30 and MEMO1). These results implicate specific cell-type shifts in the pathophysiology of neuropsychiatric disorders.
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Affiliation(s)
- Chloe X. Yap
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel D. Vo
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Lifespan Brain Institute at Penn Medicine and The Children’s Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew G. Heffel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Data Science in Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cindy Wen
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuanhao Yang
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Kathryn E. Kemper
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- The National Centre for Register-based Research, Aarhus University, Denmark
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Dorothea Seiler Vellame
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alice Franklin
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Christa Caggiano
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Brie Wamsley
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H. Geschwind
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Noah Zaitlen
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael J. Gandal
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Lifespan Brain Institute at Penn Medicine and The Children’s Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Mitra S, Bp K, C R S, Saikumar NV, Philip P, Narayanan M. Alzheimer's disease rewires gene coexpression networks coupling different brain regions. NPJ Syst Biol Appl 2024; 10:50. [PMID: 38724582 PMCID: PMC11082197 DOI: 10.1038/s41540-024-00376-y] [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: 10/21/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Connectome studies have shown how Alzheimer's disease (AD) disrupts functional and structural connectivity among brain regions. But the molecular basis of such disruptions is less studied, with most genomic/transcriptomic studies performing within-brain-region analyses. To inspect how AD rewires the correlation structure among genes in different brain regions, we performed an Inter-brain-region Differential Correlation (Inter-DC) analysis of RNA-seq data from Mount Sinai Brain Bank on four brain regions (frontal pole, superior temporal gyrus, parahippocampal gyrus and inferior frontal gyrus, comprising 264 AD and 372 control human post-mortem samples). An Inter-DC network was assembled from all pairs of genes across two brain regions that gained (or lost) correlation strength in the AD group relative to controls at FDR 1%. The differentially correlated (DC) genes in this network complemented known differentially expressed genes in AD, and likely reflects cell-intrinsic changes since we adjusted for cell compositional effects. Each brain region used a distinctive set of DC genes when coupling with other regions, with parahippocampal gyrus showing the most rewiring, consistent with its known vulnerability to AD. The Inter-DC network revealed master dysregulation hubs in AD (at genes ZKSCAN1, SLC5A3, RCC1, IL17RB, PLK4, etc.), inter-region gene modules enriched for known AD pathways (synaptic signaling, endocytosis, etc.), and candidate signaling molecules that could mediate region-region communication. The Inter-DC network generated in this study is a valuable resource of gene pairs, pathways and signaling molecules whose inter-brain-region functional coupling is disrupted in AD, thereby offering a new perspective of AD etiology.
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Affiliation(s)
- Sanga Mitra
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Kailash Bp
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Srivatsan C R
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Naga Venkata Saikumar
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Philge Philip
- Centre for Integrative Biology and Systems Medicine, IIT Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, Chennai, India
| | - Manikandan Narayanan
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India.
- Centre for Integrative Biology and Systems Medicine, IIT Madras, Chennai, India.
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, Chennai, India.
- Sudha Gopalakrishnan Brain Centre, IIT Madras, Chennai, India.
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5
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Beric A, Sun Y, Sanchez S, Martin C, Powell T, Adrian Pardo J, Sanford J, Botia JA, Cruchaga C, Ibanez L. Circulating blood circular RNA in Parkinson's Disease; a systematic study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.22.24301623. [PMID: 38343838 PMCID: PMC10854348 DOI: 10.1101/2024.01.22.24301623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
We aimed to identify circRNAs associated with Parkinson's disease (PD) by leveraging 1,848 participants and 1,789 circRNA from two of the largest publicly available studies with longitudinal clinical and blood transcriptomic data. To comprehensively understand changes in circRNAs we performed a cross-sectional study utilizing the last visit of each participant, and a longitudinal (mix model) analysis that included 1,166 participants with at least two time points. We identified 192 circRNAs differentially expressed in PD participants compared to healthy controls, with effects that were consistent in the mixed models, mutation carriers, and diverse ancestry. Finally, we included the 149 circRNA in a model with a ROC AUC of 0.825, showing that have the potential to aid the diagnosis of PD. Overall, we demonstrated that circRNAs play an important role in PD and can be leveraged as biomarkers.
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Affiliation(s)
- Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
| | - Yichen Sun
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
| | - Santiago Sanchez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
| | - Charissa Martin
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
| | - Tyler Powell
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
| | - Jose Adrian Pardo
- Departamento de Ingeniería de la Información y las Comunicaciones; Universidad de Murcia, Murcia, Spain
| | - Jessie Sanford
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
| | - Juan A. Botia
- Departamento de Ingeniería de la Información y las Comunicaciones; Universidad de Murcia, Murcia, Spain
- Department of Neurodegenerative Diseases, Institute of Neurology, University College London, London UK
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
- Department of Neurology, Washington University in Saint Louis School of Medicine
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis
- Department of Genetics, Washington University in Saint Louis School of Medicine
| | - Laura Ibanez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine
- Department of Neurology, Washington University in Saint Louis School of Medicine
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6
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Swain PS, Panda S, Pati S, Dehury B. Computational saturation mutagenesis to explore the effect of pathogenic mutations on extra-cellular domains of TREM2 associated with Alzheimer's and Nasu-Hakola disease. J Mol Model 2023; 29:360. [PMID: 37924367 DOI: 10.1007/s00894-023-05770-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
CONTEXT The specialised family of triggering receptors expressed on myeloid cells (TREMs) plays a pivotal role in causing neurodegenerative disorders and activating microglial anti-inflammatory responses. Nasu-Hakola disease (NHD), a rare autosomal recessive disorder, has been associated with mutations in TREM2, which is also responsible for raising the risk of Alzheimer's disease (AD). Herein, we have made an endeavour to differentiate the confirmed pathogenic variants in TREM2 extra-cellular domain (ECD) linked with NHD and AD using mutation-induced fold stability change (∆∆G), with the computation of 12distinct structure-based methods through saturation mutagenesis. Correlation analysis between relative solvent accessibility (RSA) and ∆∆G expresses the discrete distributive behaviour of mutants associated with TREM2 in AD (R2 = 0.061) and NHD (R2 = 0.601). Our findings put an emphasis on W50 and V126 as major players in maintaining V-like domain in TREM2. Interestingly, we discern that both of them interact with a common residue Y108, which is dissolved upon mutation. This Y108 could have structural or functional role for TREM2 which can be an ideal candidate for further study. Furthermore, the residual interaction network highlights the importance of R47 and R62 in maintaining the CDR loops that are crucial for ligand binding. Future studies using biophysical characterisation of ligand interactions in TREM2-ECD would be helpful for the development of novel therapeutics for AD and NHD. METHODS ConSurf algorithm and ENDscript were used to determine the position and conservation of each residue in the wild-type ECD of TREM2. The mutation-induced fold stability change (∆∆G) of confirmed pathogenic mutants associated with NHD and AD was estimated using 12 state-of-the-art structure-based protein stability tools. Furthermore, we also computed the effect of random mutation on these sites using computational saturation mutagenesis. Linear regression analysis was performed using mutants ∆∆G and RSA through GraphPad software. In addition, a comprehensive non-bonded residual interaction network (RIN) of wild type and its mutants of TREM2-ECD was enumerated using RING3.0.
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Affiliation(s)
- Preety Sthutika Swain
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sunita Panda
- Mycology Laboratory, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
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7
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de Klein N, Tsai EA, Vochteloo M, Baird D, Huang Y, Chen CY, van Dam S, Oelen R, Deelen P, Bakker OB, El Garwany O, Ouyang Z, Marshall EE, Zavodszky MI, van Rheenen W, Bakker MK, Veldink J, Gaunt TR, Runz H, Franke L, Westra HJ. Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases. Nat Genet 2023; 55:377-388. [PMID: 36823318 PMCID: PMC10011140 DOI: 10.1038/s41588-023-01300-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait locus (eQTL) meta-analyses in multiple brain region- and ancestry-specific datasets (n ≤ 2,759). Many of the 16,169 cortex cis-eQTLs were tissue-dependent when compared with blood cis-eQTLs. We inferred brain cell types for 3,549 cis-eQTLs by interaction analysis. We prioritized 186 cis-eQTLs for 31 brain-related traits using Mendelian randomization and co-localization including 40 cis-eQTLs with an inferred cell type, such as a neuron-specific cis-eQTL (CYP24A1) for multiple sclerosis. We further describe 737 trans-eQTLs for 526 unique variants and 108 unique genes. We used brain-specific gene-co-regulation networks to link GWAS loci and prioritize additional genes for five central nervous system diseases. This study represents a valuable resource for post-GWAS research on central nervous system diseases.
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Affiliation(s)
- Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Ellen A Tsai
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Martijn Vochteloo
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Denis Baird
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Yunfeng Huang
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Chia-Yen Chen
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Sipko van Dam
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Ancora Health, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Omar El Garwany
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Eric E Marshall
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Maria I Zavodszky
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark K Bakker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Heiko Runz
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA.
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
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8
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Minaya MA, Mahali S, Iyer AK, Eteleeb AM, Martinez R, Huang G, Budde J, Temple S, Nana AL, Seeley WW, Spina S, Grinberg LT, Harari O, Karch CM. Conserved gene signatures shared among MAPT mutations reveal defects in calcium signaling. Front Mol Biosci 2023; 10:1051494. [PMID: 36845551 PMCID: PMC9948093 DOI: 10.3389/fmolb.2023.1051494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction: More than 50 mutations in the MAPT gene result in heterogeneous forms of frontotemporal lobar dementia with tau inclusions (FTLD-Tau). However, early pathogenic events that lead to disease and the degree to which they are common across MAPT mutations remain poorly understood. The goal of this study is to determine whether there is a common molecular signature of FTLD-Tau. Methods: We analyzed genes differentially expressed in induced pluripotent stem cell-derived neurons (iPSC-neurons) that represent the three major categories of MAPT mutations: splicing (IVS10 + 16), exon 10 (p.P301L), and C-terminal (p.R406W) compared with isogenic controls. The genes that were commonly differentially expressed in MAPT IVS10 + 16, p.P301L, and p.R406W neurons were enriched in trans-synaptic signaling, neuronal processes, and lysosomal function. Many of these pathways are sensitive to disruptions in calcium homeostasis. One gene, CALB1, was significantly reduced across the three MAPT mutant iPSC-neurons and in a mouse model of tau accumulation. We observed a significant reduction in calcium levels in MAPT mutant neurons compared with isogenic controls, pointing to a functional consequence of this disrupted gene expression. Finally, a subset of genes commonly differentially expressed across MAPT mutations were also dysregulated in brains from MAPT mutation carriers and to a lesser extent in brains from sporadic Alzheimer disease and progressive supranuclear palsy, suggesting that molecular signatures relevant to genetic and sporadic forms of tauopathy are captured in a dish. The results from this study demonstrate that iPSC-neurons capture molecular processes that occur in human brains and can be used to pinpoint common molecular pathways involving synaptic and lysosomal function and neuronal development, which may be regulated by disruptions in calcium homeostasis.
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Affiliation(s)
- Miguel A. Minaya
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Sidhartha Mahali
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Abhirami K. Iyer
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Abdallah M. Eteleeb
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Rita Martinez
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Guangming Huang
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - John Budde
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Sally Temple
- Neural Stem Cell Institute, Rensselaer, NY, United States
| | - Alissa L. Nana
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - William W. Seeley
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Salvatore Spina
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Lea T. Grinberg
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil
| | - Oscar Harari
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University in St Louis, St Louis, MO, United States
- NeuroGenomics and Informatics Center, Washington University in St Louis, St Louis, MO, United States
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University in St Louis, St Louis, MO, United States
- NeuroGenomics and Informatics Center, Washington University in St Louis, St Louis, MO, United States
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9
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You SF, Brase L, Filipello F, Iyer AK, Del-Aguila J, He J, D’Oliveira Albanus R, Budde J, Norton J, Gentsch J, Dräger NM, Sattler SM, Kampmann M, Piccio L, Morris JC, Perrin RJ, McDade E, Paul SM, Cashikar AG, Benitez BA, Harari O, Karch CM. MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia state. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23285545. [PMID: 36798226 PMCID: PMC9934804 DOI: 10.1101/2023.02.06.23285545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Genome-wide association studies (GWAS) have identified many modifiers of Alzheimer disease (AD) risk enriched in microglia. Two of these modifiers are common variants in the MS4A locus (rs1582763: protective and rs6591561: risk) and serve as major regulators of CSF sTREM2 levels. To understand their functional impact on AD, we used single nucleus transcriptomics to profile brains from carriers of these variants. We discovered a "chemokine" microglial subpopulation that is altered in MS4A variant carriers and for which MS4A4A is the major regulator. The protective variant increases MS4A4A expression and shifts the chemokine microglia subpopulation to an interferon state, while the risk variant suppresses MS4A4A expression and reduces this subpopulation of microglia. Our findings provide a mechanistic explanation for the AD variants in the MS4A locus. Further, they pave the way for future mechanistic studies of AD variants and potential therapeutic strategies for enhancing microglia resilience in AD pathogenesis.
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Affiliation(s)
- Shih-Feng You
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Logan Brase
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Fabia Filipello
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Abhirami K. Iyer
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Jorge Del-Aguila
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - June He
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | | | - John Budde
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Nina M. Dräger
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sydney M. Sattler
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Piccio
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- Charles Perkins Centre and Brain and Mind Centre, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - John C. Morris
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard J. Perrin
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eric McDade
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
| | | | - Steven M. Paul
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Anil G. Cashikar
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Bruno A. Benitez
- Department of Neurology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, USA
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10
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The Cholesteryl Ester Transfer Protein (CETP) raises Cholesterol Levels in the Brain. J Lipid Res 2022; 63:100260. [PMID: 35921880 PMCID: PMC9464954 DOI: 10.1016/j.jlr.2022.100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/28/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022] Open
Abstract
The cholesteryl ester transfer protein (CETP) is a lipid transfer protein responsible for the exchange of cholesteryl esters and triglycerides between lipoproteins. Decreased CETP activity is associated with longevity, cardiovascular health, and maintenance of good cognitive performance. Interestingly, mice lack the CETP-encoding gene and have very low levels of LDL particles compared with humans. Currently, the molecular mechanisms induced because of CETP activity are not clear. To understand how CETP activity affects the brain, we utilized CETP transgenic (CETPtg) mice that show elevated LDL levels upon induction of CETP expression through a high-cholesterol diet. CETPtg mice on a high-cholesterol diet showed up to 22% higher cholesterol levels in the brain. Using a microarray on mostly astrocyte-derived mRNA, we found that this cholesterol increase is likely not because of elevated de novo synthesis of cholesterol. However, cholesterol efflux is decreased in CETPtg mice along with an upregulation of the complement factor C1Q, which plays a role in neuronal cholesterol clearance. Our data suggest that CETP activity affects brain health through modulating cholesterol distribution and clearance. Therefore, we propose that CETPtg mice constitute a valuable research tool to investigate the impact of cholesterol metabolism on brain function.
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11
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Consens ME, Chen Y, Menon V, Wang Y, Schneider JA, De Jager PL, Bennett DA, Tripathy SJ, Felsky D. Bulk and Single-Nucleus Transcriptomics Highlight Intra-Telencephalic and Somatostatin Neurons in Alzheimer's Disease. Front Mol Neurosci 2022; 15:903175. [PMID: 35754708 PMCID: PMC9231610 DOI: 10.3389/fnmol.2022.903175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cortical neuron loss is a pathological hallmark of late-onset Alzheimer's disease (AD). However, it remains unclear which neuronal subtypes beyond broad excitatory and inhibitory classes are most vulnerable. Here, we analyzed cell subtype proportion differences in AD compared to non-AD controls using 1037 post-mortem brain samples from six neocortical regions. We identified the strongest associations of AD with fewer somatostatin (SST) inhibitory neurons (β = -0.48, p bonf = 8.98 × 10-9) and intra-telencephalic (IT) excitatory neurons (β = -0.45, p bonf = 4.32 × 10-7). Replication in three AD case-control single-nucleus RNAseq datasets most strongly supported the bulk tissue association of fewer SST neurons in AD. In depth analyses of cell type proportions with specific AD-related neuropathological and cognitive phenotypes revealed fewer SST neurons with greater brain-wide post-mortem tau and beta amyloid, as well as a faster rate of antemortem cognitive decline. In contrast, greater IT neuron proportions were associated with a slower rate of cognitive decline as well as greater residual cognition-a measure of cognitive resilience-but not canonical AD neuropathology. Our findings implicate somatostatin inhibitory and intra-telencephalic excitatory neuron subclasses in the pathogenesis of AD and in cognitive resilience to AD pathology, respectively.
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Affiliation(s)
- Micaela E. Consens
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Yuxiao Chen
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Vilas Menon
- The Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States
| | - Yanling Wang
- The Rush Alzheimer’s Disease Center, Rush University, Chicago, IL, United States
| | - Julie A. Schneider
- The Rush Alzheimer’s Disease Center, Rush University, Chicago, IL, United States
| | - Philip L. De Jager
- The Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States
| | - David A. Bennett
- The Rush Alzheimer’s Disease Center, Rush University, Chicago, IL, United States
| | - Shreejoy J. Tripathy
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Daniel Felsky
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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12
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Comprehensive evaluation of deconvolution methods for human brain gene expression. Nat Commun 2022; 13:1358. [PMID: 35292647 PMCID: PMC8924248 DOI: 10.1038/s41467-022-28655-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/28/2022] [Indexed: 11/08/2022] Open
Abstract
Transcriptome deconvolution aims to estimate the cellular composition of an RNA sample from its gene expression data, which in turn can be used to correct for composition differences across samples. The human brain is unique in its transcriptomic diversity, and comprises a complex mixture of cell-types, including transcriptionally similar subtypes of neurons. Here, we carry out a comprehensive evaluation of deconvolution methods for human brain transcriptome data, and assess the tissue-specificity of our key observations by comparison with human pancreas and heart. We evaluate eight transcriptome deconvolution approaches and nine cell-type signatures, testing the accuracy of deconvolution using in silico mixtures of single-cell RNA-seq data, RNA mixtures, as well as nearly 2000 human brain samples. Our results identify the main factors that drive deconvolution accuracy for brain data, and highlight the importance of biological factors influencing cell-type signatures, such as brain region and in vitro cell culturing. Transcriptome deconvolution aims to estimate cellular composition based on gene expression data. Here the authors evaluate deconvolution methods for human brain transcriptome and conclude that partial deconvolution algorithms work best, but that appropriate cell-type signatures are also important.
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13
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Chen HH, Eteleeb A, Wang C, Fernandez MV, Budde JP, Bergmann K, Norton J, Wang F, Ebl C, Morris JC, Perrin RJ, Bateman RJ, McDade E, Xiong C, Goate A, Farlow M, Chhatwal J, Schofield PR, Chui H, Harari O, Cruchaga C, Ibanez L. Circular RNA detection identifies circPSEN1 alterations in brain specific to autosomal dominant Alzheimer's disease. Acta Neuropathol Commun 2022; 10:29. [PMID: 35246267 PMCID: PMC8895634 DOI: 10.1186/s40478-022-01328-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/07/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Autosomal-dominant Alzheimer's disease (ADAD) is caused by pathogenic mutations in APP, PSEN1, and PSEN2, which usually lead to an early age at onset (< 65). Circular RNAs are a family of non-coding RNAs highly expressed in the nervous system and especially in synapses. We aimed to investigate differences in brain gene expression of linear and circular transcripts from the three ADAD genes in controls, sporadic AD, and ADAD. METHODS We obtained and sequenced RNA from brain cortex using standard protocols. Linear counts were obtained using the TOPMed pipeline; circular counts, using python package DCC. After stringent quality control (QC), we obtained the counts for PSEN1, PSEN2 and APP genes. Only circPSEN1 passed QC. We used DESeq2 to compare the counts across groups, correcting for biological and technical variables. Finally, we performed in-silico functional analyses using the Circular RNA interactome website and DIANA mirPath software. RESULTS Our results show significant differences in gene counts of circPSEN1 in ADAD individuals, when compared to sporadic AD and controls (ADAD = 21, AD = 253, Controls = 23-ADADvsCO: log2FC = 0.794, p = 1.63 × 10-04, ADADvsAD: log2FC = 0.602, p = 8.22 × 10-04). The high gene counts are contributed by two circPSEN1 species (hsa_circ_0008521 and hsa_circ_0003848). No significant differences were observed in linear PSEN1 gene expression between cases and controls, indicating that this finding is specific to the circular forms. In addition, the high circPSEN1 levels do not seem to be specific to PSEN1 mutation carriers; the counts are also elevated in APP and PSEN2 mutation carriers. In-silico functional analyses suggest that circPSEN1 is involved in several pathways such as axon guidance (p = 3.39 × 10-07), hippo signaling pathway (p = 7.38 × 10-07), lysine degradation (p = 2.48 × 10-05) or Wnt signaling pathway (p = 5.58 × 10-04) among other KEGG pathways. Additionally, circPSEN1 counts were able to discriminate ADAD from sporadic AD and controls with an AUC above 0.70. CONCLUSIONS Our findings show the differential expression of circPSEN1 is increased in ADAD. Given the biological function previously ascribed to circular RNAs and the results of our in-silico analyses, we hypothesize that this finding might be related to neuroinflammatory events that lead or that are caused by the accumulation of amyloid-beta.
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Affiliation(s)
- Hsiang-Han Chen
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Abdallah Eteleeb
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Ciyang Wang
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - John P. Budde
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Curtis Ebl
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Richard J. Perrin
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Randall J. Bateman
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Eric McDade
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Martin Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Jasmeer Chhatwal
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Peter R. Schofield
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Helena Chui
- Department of Neurology, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Dominantly Inherited Alzheimer Network
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Division of Biostatistics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
- Department of Neurology, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
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14
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Ibanez L, Heitsch L, Carrera C, Farias FHG, Del Aguila JL, Dhar R, Budde J, Bergmann K, Bradley J, Harari O, Phuah CL, Lemmens R, Viana Oliveira Souza AA, Moniche F, Cabezas-Juan A, Arenillas JF, Krupinksi J, Cullell N, Torres-Aguila N, Muiño E, Cárcel-Márquez J, Marti-Fabregas J, Delgado-Mederos R, Marin-Bueno R, Hornick A, Vives-Bauza C, Navarro RD, Tur S, Jimenez C, Obach V, Segura T, Serrano-Heras G, Chung JW, Roquer J, Soriano-Tarraga C, Giralt-Steinhauer E, Mola-Caminal M, Pera J, Lapicka-Bodzioch K, Derbisz J, Davalos A, Lopez-Cancio E, Muñoz L, Tatlisumak T, Molina C, Ribo M, Bustamante A, Sobrino T, Castillo-Sanchez J, Campos F, Rodriguez-Castro E, Arias-Rivas S, Rodríguez-Yáñez M, Herbosa C, Ford AL, Gutierrez-Romero A, Uribe-Pacheco R, Arauz A, Lopes-Cendes I, Lowenkopf T, Barboza MA, Amini H, Stamova B, Ander BP, Sharp FR, Kim GM, Bang OY, Jimenez-Conde J, Slowik A, Stribian D, Tsai EA, Burkly LC, Montaner J, Fernandez-Cadenas I, Lee JM, Cruchaga C. Multi-ancestry GWAS reveals excitotoxicity associated with outcome after ischaemic stroke. Brain 2022; 145:2394-2406. [PMID: 35213696 PMCID: PMC9890452 DOI: 10.1093/brain/awac080] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/14/2022] [Accepted: 02/06/2022] [Indexed: 02/05/2023] Open
Abstract
During the first hours after stroke onset, neurological deficits can be highly unstable: some patients rapidly improve, while others deteriorate. This early neurological instability has a major impact on long-term outcome. Here, we aimed to determine the genetic architecture of early neurological instability measured by the difference between the National Institutes of Health Stroke Scale (NIHSS) within 6 h of stroke onset and NIHSS at 24 h. A total of 5876 individuals from seven countries (Spain, Finland, Poland, USA, Costa Rica, Mexico and Korea) were studied using a multi-ancestry meta-analyses. We found that 8.7% of NIHSS at 24 h of variance was explained by common genetic variations, and also that early neurological instability has a different genetic architecture from that of stroke risk. Eight loci (1p21.1, 1q42.2, 2p25.1, 2q31.2, 2q33.3, 5q33.2, 7p21.2 and 13q31.1) were genome-wide significant and explained 1.8% of the variability suggesting that additional variants influence early change in neurological deficits. We used functional genomics and bioinformatic annotation to identify the genes driving the association from each locus. Expression quantitative trait loci mapping and summary data-based Mendelian randomization indicate that ADAM23 (log Bayes factor = 5.41) was driving the association for 2q33.3. Gene-based analyses suggested that GRIA1 (log Bayes factor = 5.19), which is predominantly expressed in the brain, is the gene driving the association for the 5q33.2 locus. These analyses also nominated GNPAT (log Bayes factor = 7.64) ABCB5 (log Bayes factor = 5.97) for the 1p21.1 and 7p21.1 loci. Human brain single-nuclei RNA-sequencing indicates that the gene expression of ADAM23 and GRIA1 is enriched in neurons. ADAM23, a presynaptic protein and GRIA1, a protein subunit of the AMPA receptor, are part of a synaptic protein complex that modulates neuronal excitability. These data provide the first genetic evidence in humans that excitotoxicity may contribute to early neurological instability after acute ischaemic stroke.
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Affiliation(s)
- Laura Ibanez
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Laura Heitsch
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Department of Emergency Medicine, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Caty Carrera
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
| | - Fabiana H G Farias
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Jorge L Del Aguila
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Rajat Dhar
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - John Budde
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Joseph Bradley
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Oscar Harari
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Hope Center for Neurological Disorders, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Chia Ling Phuah
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Robin Lemmens
- Department of Neuroscience, Katholieke Universiteit Leuven, Campus Gasthuisberg O&N2, Leuven BE-3000, Belgium
| | - Alessandro A Viana Oliveira Souza
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Cidade Universitaria, Campinas 13083-887, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), R. Tessalia Viera de Camargo, Campinas 13083-887, Brazil
| | - Francisco Moniche
- Department of Neurology, Hospital Virgen del Rocio, University of Seville, Seville 41013, Spain
| | - Antonio Cabezas-Juan
- Department of Neurology, Hospital Virgen del Rocio, University of Seville, Seville 41013, Spain
- Hospital Virgen de la Macarena, University of Seville, Seville 41009, Spain
| | - Juan Francisco Arenillas
- Department of Neurology, Hospital Clinico Universitario Valladolid, Valladolid University, Valladolid 47003, Spain
| | - Jerzy Krupinksi
- Department of Neurology, Mutua Terrassa University Hospital, Universitat de Barcelona, Terrassa 08221, Spain
- Fundacio Docencia i Recerca Mutua Terrassa, Universitat de Barcelona, Terrassa 08221, Spain
| | - Natalia Cullell
- Fundacio Docencia i Recerca Mutua Terrassa, Universitat de Barcelona, Terrassa 08221, Spain
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Nuria Torres-Aguila
- Fundacio Docencia i Recerca Mutua Terrassa, Universitat de Barcelona, Terrassa 08221, Spain
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Elena Muiño
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Jara Cárcel-Márquez
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Joan Marti-Fabregas
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Raquel Delgado-Mederos
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Rebeca Marin-Bueno
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Alejandro Hornick
- Department of Neurology, Southern Illinois Healthcare Memorial Hospital of Carbondale, Carbondale 62901, IL, USA
| | | | - Rosa Diaz Navarro
- Department of Neurology, Hospital Universitari Son Espases, Universitat de les Illes Balears, Palma 07120, Spain
| | - Silvia Tur
- Department of Neurology, Hospital Universitari Son Espases, Universitat de les Illes Balears, Palma 07120, Spain
| | - Carmen Jimenez
- Department of Neurology, Hospital Universitari Son Espases, Universitat de les Illes Balears, Palma 07120, Spain
| | - Victor Obach
- Department of Neurology, Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona 08036, Spain
| | - Tomas Segura
- Research Unit, Complejo Hospitalario Universitario de Albacete, Albacete 02008, Spain
| | - Gemma Serrano-Heras
- Research Unit, Complejo Hospitalario Universitario de Albacete, Albacete 02008, Spain
| | - Jong Won Chung
- Department of Neurology, Samsung Medical Center, Seoul, South Korea
| | - Jaume Roquer
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Carol Soriano-Tarraga
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Eva Giralt-Steinhauer
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Marina Mola-Caminal
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
- Department of Surgical Sciences, Orthopedics, Uppsala University, Uppsala 75185, Sweden
| | - Joanna Pera
- Department of Neurology, Jagiellonian University, Krakow 31-007, Poland
| | | | - Justyna Derbisz
- Department of Neurology, Jagiellonian University, Krakow 31-007, Poland
| | - Antoni Davalos
- Department of Neurology, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona 08916, Spain
| | - Elena Lopez-Cancio
- Department of Neurology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Lucia Muñoz
- Department of Neurology, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona 08916, Spain
| | - Turgut Tatlisumak
- Department of Neurology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg 413 45, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Carlos Molina
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
| | - Marc Ribo
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
| | - Alejandro Bustamante
- Department of Neurology, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona 08916, Spain
| | - Tomas Sobrino
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Jose Castillo-Sanchez
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Francisco Campos
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Emilio Rodriguez-Castro
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Susana Arias-Rivas
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Manuel Rodríguez-Yáñez
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Christina Herbosa
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Andria L Ford
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Hope Center for Neurological Disorders, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Department of Radiology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | | | - Rodrigo Uribe-Pacheco
- Instituto Nacional de Neurologia y Neurocirurgia de Mexico, Ciudad de Mexico 14269, Mexico
| | - Antonio Arauz
- Instituto Nacional de Neurologia y Neurocirurgia de Mexico, Ciudad de Mexico 14269, Mexico
| | - Iscia Lopes-Cendes
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Cidade Universitaria, Campinas 13083-887, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), R. Tessalia Viera de Camargo, Campinas 13083-887, Brazil
| | - Theodore Lowenkopf
- Department of Neurology, Providence St. Vincent Medical Center, Portland 97225, OR, USA
| | - Miguel A Barboza
- Neurosciences Department, Hospital Rafael A. Calderon Guardia, Aranjuez, San José, Costa Rica
| | - Hajar Amini
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Boryana Stamova
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Bradley P Ander
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Frank R Sharp
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Gyeong Moon Kim
- Department of Neurology, Samsung Medical Center, Seoul, South Korea
| | - Oh Young Bang
- Department of Neurology, Samsung Medical Center, Seoul, South Korea
| | - Jordi Jimenez-Conde
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Agnieszka Slowik
- Department of Neurology, Jagiellonian University, Krakow 31-007, Poland
| | - Daniel Stribian
- Department of Neurology, Helsinki University Hospital, Helsinki 00290, Finland
| | - Ellen A Tsai
- Translational Biology, Biogen, Inc., Cambridge 02142, MA, USA
| | - Linda C Burkly
- Genetics and Neurodevelopmental Disease Research Unit, Biogen, Inc., Cambridge 02142, MA, USA
| | - Joan Montaner
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
- Department of Neurology, Hospital Virgen del Rocio, University of Seville, Seville 41013, Spain
- Hospital Virgen de la Macarena, University of Seville, Seville 41009, Spain
| | - Israel Fernandez-Cadenas
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Jin Moo Lee
- Correspondence may also be addressed to: Jin-Moo Lee School of Medicine, Washington University 660 South Euclid Avenue Campus Box 8111 St. Louis, MO 63110, USA E-mail:
| | - Carlos Cruchaga
- Correspondence to: Carlos Cruchaga School of Medicine, Washington University 660 South Euclid Avenue Campus Box 8134 Saint Louis, MO 63110, USA E-mail:
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15
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Bigley TM, Xiong M, Ali M, Chen Y, Wang C, Serrano JR, Eteleeb A, Harari O, Yang L, Patel SJ, Cruchaga C, Yokoyama WM, Holtzman DM. Murine roseolovirus does not accelerate amyloid-β pathology and human roseoloviruses are not over-represented in Alzheimer disease brains. Mol Neurodegener 2022; 17:10. [PMID: 35033173 PMCID: PMC8760754 DOI: 10.1186/s13024-021-00514-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/22/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The role of viral infection in Alzheimer Disease (AD) pathogenesis is an area of great interest in recent years. Several studies have suggested an association between the human roseoloviruses, HHV-6 and HHV-7, and AD. Amyloid-β (Aβ) plaques are a hallmark neuropathological finding of AD and were recently proposed to have an antimicrobial function in response to infection. Identifying a causative and mechanistic role of human roseoloviruses in AD has been confounded by limitations in performing in vivo studies. Recent -omics based approaches have demonstrated conflicting associations between human roseoloviruses and AD. Murine roseolovirus (MRV) is a natural murine pathogen that is highly-related to the human roseoloviruses, providing an opportunity to perform well-controlled studies of the impact of roseolovirus on Aβ deposition. METHODS We utilized the 5XFAD mouse model to test whether MRV induces Aβ deposition in vivo. We also evaluated viral load and neuropathogenesis of MRV infection. To evaluate Aβ interaction with MRV, we performed electron microscopy. RNA-sequencing of a cohort of AD brains compared to control was used to investigate the association between human roseolovirus and AD. RESULTS We found that 5XFAD mice were susceptible to MRV infection and developed neuroinflammation. Moreover, we demonstrated that Aβ interacts with viral particles in vitro and, subsequent to this interaction, can disrupt infection. Despite this, neither peripheral nor brain infection with MRV increased or accelerated Aβ plaque formation. Moreover, -omics based approaches have demonstrated conflicting associations between human roseoloviruses and AD. Our RNA-sequencing analysis of a cohort of AD brains compared to controls did not show an association between roseolovirus infection and AD. CONCLUSION Although MRV does infect the brain and cause transient neuroinflammation, our data do not support a role for murine or human roseoloviruses in the development of Aβ plaque formation and AD.
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Affiliation(s)
- Tarin M. Bigley
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Monica Xiong
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Division of Biology and Biomedical Sciences (DBBS), Washington University School of Medicine, St. Louis, MO 63110 USA
- Present address: Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Muhammad Ali
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
| | - Yun Chen
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Division of Biology and Biomedical Sciences (DBBS), Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Chao Wang
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Javier Remolina Serrano
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Abdallah Eteleeb
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - Oscar Harari
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - Liping Yang
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Swapneel J. Patel
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Carlos Cruchaga
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - Wayne M. Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - David M. Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
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16
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Chappus-McCendie H, Poulin MA, Chouinard-Watkins R, Vandal M, Calon F, Lauzon MA, Plourde M. A diet rich in docosahexaenoic acid enhances reactive astrogliosis and ramified microglia morphology in apolipoprotein E epsilon 4-targeted replacement mice. AGING BRAIN 2022; 2:100046. [PMID: 36908881 PMCID: PMC9997137 DOI: 10.1016/j.nbas.2022.100046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 10/16/2022] Open
Abstract
Docosahexaenoic acid (DHA) consumption reduces spatial memory impairment in mice carrying the human apolipoprotein E ε4 (APOE4) allele. The current study evaluated whether astrocyte and microglia morphology contribute to the mechanism of this result. APOE3 and APOE4 mice were fed either a DHA-enriched diet or a control diet from 4 to 12 months of age. Coronal brain sections were immunostained for GFAP, Iba1, and NeuN. Astrocytes from APOE4 mice exhibited signs of reactive astrogliosis compared to APOE3 mice. Consumption of DHA exacerbated reactive astrocyte morphology in APOE4 carriers. Microglia from APOE4-control mice exhibited characteristics of amoeboid morphology and other characteristics of ramified morphology (more processes, greater process complexity, and greater distance between neighboring microglia). DHA enhanced ramified microglia morphology in APOE4 mice. In addition, APOE4 mice fed the DHA diet had lower hippocampal concentrations of interleukin-7, lipopolysaccharide-induced CXC chemokine and monocyte chemoattractant protein 1, and higher concentration of interferon-gamma compared to APOE4-control mice. Our results indicate that a diet rich in DHA enhances reactive astrogliosis and ramified microglia morphology in APOE4 mice.
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Affiliation(s)
- Hillary Chappus-McCendie
- Centre de Recherche sur le Vieillissement, CIUSSS de l'Estrie-CHUS, Sherbrooke, QC, Canada.,Département de pharmacologie-physiologie, Université de Sherbrooke, Sherbrooke, QC, Canada.,Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Marc-Antoine Poulin
- Département de génie chimique et de génie biotechnologique, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Raphaël Chouinard-Watkins
- Centre de Recherche sur le Vieillissement, CIUSSS de l'Estrie-CHUS, Sherbrooke, QC, Canada.,Département de pharmacologie-physiologie, Université de Sherbrooke, Sherbrooke, QC, Canada.,Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de la nutrition et des aliments fonctionnels, Université Laval, Québec, QC, Canada
| | - Milène Vandal
- Institut de la nutrition et des aliments fonctionnels, Université Laval, Québec, QC, Canada.,Faculté de pharmacie et centre de recherche du CHU de Québec-Université Laval, QC, Canada
| | - Frédéric Calon
- Institut de la nutrition et des aliments fonctionnels, Université Laval, Québec, QC, Canada.,Faculté de pharmacie et centre de recherche du CHU de Québec-Université Laval, QC, Canada
| | - Marc-Antoine Lauzon
- Centre de Recherche sur le Vieillissement, CIUSSS de l'Estrie-CHUS, Sherbrooke, QC, Canada.,Département de génie chimique et de génie biotechnologique, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mélanie Plourde
- Centre de Recherche sur le Vieillissement, CIUSSS de l'Estrie-CHUS, Sherbrooke, QC, Canada.,Département de pharmacologie-physiologie, Université de Sherbrooke, Sherbrooke, QC, Canada.,Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de la nutrition et des aliments fonctionnels, Université Laval, Québec, QC, Canada.,Département de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
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17
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Saito ER, Miller JB, Harari O, Cruchaga C, Mihindukulasuriya KA, Kauwe JSK, Bikman BT. Alzheimer's disease alters oligodendrocytic glycolytic and ketolytic gene expression. Alzheimers Dement 2021; 17:1474-1486. [PMID: 33650792 PMCID: PMC8410881 DOI: 10.1002/alz.12310] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/05/2021] [Accepted: 01/17/2021] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Sporadic Alzheimer's disease (AD) is strongly correlated with impaired brain glucose metabolism, which may affect AD onset and progression. Ketolysis has been suggested as an alternative pathway to fuel the brain. METHODS RNA-seq profiles of post mortem AD brains were used to determine whether dysfunctional AD brain metabolism can be determined by impairments in glycolytic and ketolytic gene expression. Data were obtained from the Knight Alzheimer's Disease Research Center (62 cases; 13 controls), Mount Sinai Brain Bank (110 cases; 44 controls), and the Mayo Clinic Brain Bank (80 cases; 76 controls), and were normalized to cell type: astrocytes, microglia, neurons, oligodendrocytes. RESULTS In oligodendrocytes, both glycolytic and ketolytic pathways were significantly impaired in AD brains. Ketolytic gene expression was not significantly altered in neurons, astrocytes, and microglia. DISCUSSION Oligodendrocytes may contribute to brain hypometabolism observed in AD. These results are suggestive of a potential link between hypometabolism and dysmyelination in disease physiology. Additionally, ketones may be therapeutic in AD due to their ability to fuel neurons despite impaired glycolytic metabolism.
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Affiliation(s)
- Erin R. Saito
- Department of Physiology and Developmental BiologyBrigham Young UniversityProvoUtahUSA
| | | | - Oscar Harari
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Carlos Cruchaga
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
- Department of NeurologyWashington University School of MedicineSt. LouisMissouriUSA
- Hope Center for Neurological DisordersWashington University School of MedicineSt. LouisMissouriUSA
- NeuroGenomics and InformaticsWashington University School of MedicineSt. LouisMissouriUSA
| | - Kathie A. Mihindukulasuriya
- The Edison Family Center for Genome Sciences and Systems BiologyPathology and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | | | - Benjamin T. Bikman
- Department of Physiology and Developmental BiologyBrigham Young UniversityProvoUtahUSA
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18
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Ibanez L, Cruchaga C, Fernández MV. Advances in Genetic and Molecular Understanding of Alzheimer's Disease. Genes (Basel) 2021; 12:1247. [PMID: 34440421 PMCID: PMC8394321 DOI: 10.3390/genes12081247] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 01/19/2023] Open
Abstract
Alzheimer's disease (AD) has become a common disease of the elderly for which no cure currently exists. After over 30 years of intensive research, we have gained extensive knowledge of the genetic and molecular factors involved and their interplay in disease. These findings suggest that different subgroups of AD may exist. Not only are we starting to treat autosomal dominant cases differently from sporadic cases, but we could be observing different underlying pathological mechanisms related to the amyloid cascade hypothesis, immune dysfunction, and a tau-dependent pathology. Genetic, molecular, and, more recently, multi-omic evidence support each of these scenarios, which are highly interconnected but can also point to the different subgroups of AD. The identification of the pathologic triggers and order of events in the disease processes are key to the design of treatments and therapies. Prevention and treatment of AD cannot be attempted using a single approach; different therapeutic strategies at specific disease stages may be appropriate. For successful prevention and treatment, biomarker assays must be designed so that patients can be more accurately monitored at specific points during the course of the disease and potential treatment. In addition, to advance the development of therapeutic drugs, models that better mimic the complexity of the human brain are needed; there have been several advances in this arena. Here, we review significant, recent developments in genetics, omics, and molecular studies that have contributed to the understanding of this disease. We also discuss the implications that these contributions have on medicine.
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Affiliation(s)
- Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; (L.I.); (C.C.)
- Neurogenomics and Informatics Center, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; (L.I.); (C.C.)
- Neurogenomics and Informatics Center, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; (L.I.); (C.C.)
- Neurogenomics and Informatics Center, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
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19
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Perrone F, Cacace R, van der Zee J, Van Broeckhoven C. Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases. Genome Med 2021; 13:59. [PMID: 33853652 PMCID: PMC8048219 DOI: 10.1186/s13073-021-00878-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the molecular etiology of neurodegenerative brain diseases (NBD) has substantially increased over the past three decades. Early genetic studies of NBD families identified rare and highly penetrant deleterious mutations in causal genes that segregate with disease. Large genome-wide association studies uncovered common genetic variants that influenced disease risk. Major developments in next-generation sequencing (NGS) technologies accelerated gene discoveries at an unprecedented rate and revealed novel pathways underlying NBD pathogenesis. NGS technology exposed large numbers of rare genetic variants of uncertain significance (VUS) in coding regions, highlighting the genetic complexity of NBD. Since experimental studies of these coding rare VUS are largely lacking, the potential contributions of VUS to NBD etiology remain unknown. In this review, we summarize novel findings in NBD genetic etiology driven by NGS and the impact of rare VUS on NBD etiology. We consider different mechanisms by which rare VUS can act and influence NBD pathophysiology and discuss why a better understanding of rare VUS is instrumental for deriving novel insights into the molecular complexity and heterogeneity of NBD. New knowledge might open avenues for effective personalized therapies.
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Affiliation(s)
- Federica Perrone
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
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20
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Li Q, Yang MQ. Comparison of machine learning approaches for enhancing Alzheimer's disease classification. PeerJ 2021; 9:e10549. [PMID: 33665002 PMCID: PMC7916537 DOI: 10.7717/peerj.10549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 11/20/2020] [Indexed: 11/24/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder, accounting for nearly 60% of all dementia cases. The occurrence of the disease has been increasing rapidly in recent years. Presently about 46.8 million individuals suffer from AD worldwide. The current absence of effective treatment to reverse or stop AD progression highlights the importance of disease prevention and early diagnosis. Brain structural Magnetic Resonance Imaging (MRI) has been widely used for AD detection as it can display morphometric differences and cerebral structural changes. In this study, we built three machine learning-based MRI data classifiers to predict AD and infer the brain regions that contribute to disease development and progression. We then systematically compared the three distinct classifiers, which were constructed based on Support Vector Machine (SVM), 3D Very Deep Convolutional Network (VGGNet) and 3D Deep Residual Network (ResNet), respectively. To improve the performance of the deep learning classifiers, we applied a transfer learning strategy. The weights of a pre-trained model were transferred and adopted as the initial weights of our models. Transferring the learned features significantly reduced training time and increased network efficiency. The classification accuracy for AD subjects from elderly control subjects was 90%, 95%, and 95% for the SVM, VGGNet and ResNet classifiers, respectively. Gradient-weighted Class Activation Mapping (Grad-CAM) was employed to show discriminative regions that contributed most to the AD classification by utilizing the learned spatial information of the 3D-VGGNet and 3D-ResNet models. The resulted maps consistently highlighted several disease-associated brain regions, particularly the cerebellum which is a relatively neglected brain region in the present AD study. Overall, our comparisons suggested that the ResNet model provided the best classification performance as well as more accurate localization of disease-associated regions in the brain compared to the other two approaches.
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Affiliation(s)
- Qi Li
- MidSouth Bioinformatics Center and Bioinformatics Graduate Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, University of Arkansas at Little Rock, Little Rock, AR, United States of America
| | - Mary Qu Yang
- MidSouth Bioinformatics Center and Bioinformatics Graduate Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, University of Arkansas at Little Rock, Little Rock, AR, United States of America
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21
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Farias FHG, Benitez BA, Cruchaga C. Quantitative endophenotypes as an alternative approach to understanding genetic risk in neurodegenerative diseases. Neurobiol Dis 2021; 151:105247. [PMID: 33429041 DOI: 10.1016/j.nbd.2020.105247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 01/02/2023] Open
Abstract
Endophenotypes, as measurable intermediate features of human diseases, reflect underlying molecular mechanisms. The use of quantitative endophenotypes in genetic studies has improved our understanding of pathophysiological changes associated with diseases. The main advantage of the quantitative endophenotypes approach to study human diseases over a classic case-control study design is the inferred biological context that can enable the development of effective disease-modifying treatments. Here, we summarize recent progress on biomarkers for neurodegenerative diseases, including cerebrospinal fluid and blood-based, neuroimaging, neuropathological, and clinical studies. This review focuses on how endophenotypic studies have successfully linked genetic modifiers to disease risk, disease onset, or progression rate and provided biological context to genes identified in genome-wide association studies. Finally, we review critical methodological considerations for implementing this approach and future directions.
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Affiliation(s)
- Fabiana H G Farias
- Department of Psychiatry, Washington University, St. Louis, MO 63110, United States of America; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, United States of America
| | - Bruno A Benitez
- Department of Psychiatry, Washington University, St. Louis, MO 63110, United States of America; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, United States of America
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO 63110, United States of America; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, United States of America; Hope Center for Neurologic Diseases, Washington University, St. Louis, MO 63110, United States of America; The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, 63110, United States of America; Department of Genetics, Washington University School of Medicine, St Louis, MO, 63110, United States of America.
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22
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Patel R, Aschner M. Commonalities between Copper Neurotoxicity and Alzheimer's Disease. TOXICS 2021; 9:4. [PMID: 33430181 PMCID: PMC7825595 DOI: 10.3390/toxics9010004] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease, a highly prevalent form of dementia, targets neuron function beginning from the hippocampal region and expanding outwards. Alzheimer's disease is caused by elevated levels of heavy metals, such as lead, zinc, and copper. Copper is found in many areas of daily life, raising a concern as to how this metal and Alzheimer's disease are related. Previous studies have not identified the common pathways between excess copper and Alzheimer's disease etiology. Our review corroborates that both copper and Alzheimer's disease target the hippocampus, cerebral cortex, cerebellum, and brainstem, affecting motor skills and critical thinking. Additionally, Aβ plaque formation was analyzed beginning from synthesis at the APP parent protein site until Aβ plaque formation was completed. Structural changes were also noted. Further analysis revealed a relationship between amyloid-beta plaques and copper ion concentration. As copper ion levels increased, it bound to the Aβ monomer, expediting the plaque formation process, and furthering neurodegeneration. These conclusions can be utilized in the medical community to further research on the etiology of Alzheimer's disease and its relationships to copper and other metal-induced neurotoxicity.
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Affiliation(s)
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA;
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23
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Multi-ancestry genetic study in 5,876 patients identifies an association between excitotoxic genes and early outcomes after acute ischemic stroke. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.10.29.20222257. [PMID: 33173895 PMCID: PMC7654887 DOI: 10.1101/2020.10.29.20222257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
During the first hours after stroke onset neurological deficits can be highly unstable: some patients rapidly improve, while others deteriorate. This early neurological instability has a major impact on long-term outcome. Here, we aimed to determine the genetic architecture of early neurological instability measured by the difference between NIH stroke scale (NIHSS) within six hours of stroke onset and NIHSS at 24h (ΔNIHSS). A total of 5,876 individuals from seven countries (Spain, Finland, Poland, United States, Costa Rica, Mexico and Korea) were studied using a multi-ancestry meta-analyses. We found that 8.7% of ΔNIHSS variance was explained by common genetic variations, and also that early neurological instability has a different genetic architecture than that of stroke risk. Seven loci (2p25.1, 2q31.2, 2q33.3, 4q34.3, 5q33.2, 6q26 and 7p21.1) were genome-wide significant and explained 2.1% of the variability suggesting that additional variants influence early change in neurological deficits. We used functional genomics and bioinformatic annotation to identify the genes driving the association from each loci. eQTL mapping and SMR indicate that ADAM23 (log Bayes Factor (LBF)=6.34) was driving the association for 2q33.3. Gene based analyses suggested that GRIA1 (LBF=5.26), which is predominantly expressed in brain, is the gene driving the association for the 5q33.2 locus. These analyses also nominated PARK2 (LBF=5.30) and ABCB5 (LBF=5.70) for the 6q26 and 7p21.1 loci. Human brain single nuclei RNA-seq indicates that the gene expression of ADAM23 and GRIA1 is enriched in neurons. ADAM23 , a pre-synaptic protein, and GRIA1 , a protein subunit of the AMPA receptor, are part of a synaptic protein complex that modulates neuronal excitability. These data provides the first evidence in humans that excitotoxicity may contribute to early neurological instability after acute ischemic stroke. RESEARCH INTO CONTEXT Evidence before this study: No previous genome-wide association studies have investigated the genetic architecture of early outcomes after ischemic stroke.Added Value of this study: This is the first study that investigated genetic influences on early outcomes after ischemic stroke using a genome-wide approach, revealing seven genome-wide significant loci. A unique aspect of this genetic study is the inclusion of all of the major ethnicities by recruiting from participants throughout the world. Most genetic studies to date have been limited to populations of European ancestry.Implications of all available evidence: The findings provide the first evidence that genes implicating excitotoxicity contribute to human acute ischemic stroke, and demonstrates proof of principle that GWAS of acute ischemic stroke patients can reveal mechanisms involved in ischemic brain injury.
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24
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Wang X, Allen M, Li S, Quicksall ZS, Patel TA, Carnwath TP, Reddy JS, Carrasquillo MM, Lincoln SJ, Nguyen TT, Malphrus KG, Dickson DW, Crook JE, Asmann YW, Ertekin-Taner N. Deciphering cellular transcriptional alterations in Alzheimer's disease brains. Mol Neurodegener 2020; 15:38. [PMID: 32660529 PMCID: PMC7359236 DOI: 10.1186/s13024-020-00392-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/27/2020] [Indexed: 02/06/2023] Open
Abstract
Large-scale brain bulk-RNAseq studies identified molecular pathways implicated in Alzheimer's disease (AD), however these findings can be confounded by cellular composition changes in bulk-tissue. To identify cell intrinsic gene expression alterations of individual cell types, we designed a bioinformatics pipeline and analyzed three AD and control bulk-RNAseq datasets of temporal and dorsolateral prefrontal cortex from 685 brain samples. We detected cell-proportion changes in AD brains that are robustly replicable across the three independently assessed cohorts. We applied three different algorithms including our in-house algorithm to identify cell intrinsic differentially expressed genes in individual cell types (CI-DEGs). We assessed the performance of all algorithms by comparison to single nucleus RNAseq data. We identified consensus CI-DEGs that are common to multiple brain regions. Despite significant overlap between consensus CI-DEGs and bulk-DEGs, many CI-DEGs were absent from bulk-DEGs. Consensus CI-DEGs and their enriched GO terms include genes and pathways previously implicated in AD or neurodegeneration, as well as novel ones. We demonstrated that the detection of CI-DEGs through computational deconvolution methods is promising and highlight remaining challenges. These findings provide novel insights into cell-intrinsic transcriptional changes of individual cell types in AD and may refine discovery and modeling of molecular targets that drive this complex disease.
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Affiliation(s)
- Xue Wang
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA.
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Shaoyu Li
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary S Quicksall
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tulsi A Patel
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Troy P Carnwath
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Sarah J Lincoln
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Thuy T Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA.
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25
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Yu B, Zhang J, Li H, Sun X. Silencing of aquaporin1 activates the Wnt signaling pathway to improve cognitive function in a mouse model of Alzheimer's disease. Gene 2020; 755:144904. [PMID: 32540373 DOI: 10.1016/j.gene.2020.144904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/28/2020] [Accepted: 06/10/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Aquaporins (AQPs) are water channel proteins robustly presenting in the central nervous system (CNS). Increasing evidence suggests the crucial role of AQP1 in the pathogenesis of CNS injury but scarce data are provided for the potential role of AQP1 in Alzheimer's disease (AD). Thus, the present study aimed to investigate the effects of AQP1 on cognitive function in a mouse model of AD. METHODS A mouse model of AD was established by using the β-amyloid isoform Aβ1-42, and then assessed by the step-through test and water maze experiment. The expression of AQP1 was quantified in the AD model. The effects of AQP1 on the cognitive function of AD mice and the Wnt signaling pathway were elucidated using gain- and loss-of-function approaches. Furthermore, hippocampal neurons were isolated and treated with Aβ1-42 for in vitro experiments and the effects of the Wnt signaling pathway on hippocampal neuron apoptosis were analyzed with the use of inhibitor or activator of this pathway. RESULTS AQP1 was highly-expressed in the AD mouse model while AQP1 silencing improved cognitive function in AD mice. Besides, silencing of AQP1 exhibited protective effects on hippocampal neurons in AD mice. Furthermore, AQP1 inhibited the Wnt signaling pathway while AQP1 promoted neuronal apoptosis by inhibiting the Wnt signaling pathway, thereby damaging the cognitive function. CONCLUSIONS AQP1 silencing attenuates the cognitive impairment in AD through activation of the Wnt signaling pathway, highlighting a novel therapeutic target against AD.
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Affiliation(s)
- Benshuai Yu
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 117000, PR China; Department of Neurosurgery, Benxi Central Hospital, Benxi 117000, PR China
| | - Junzhu Zhang
- Department of Occupational Medicine, Benxi Central Hospital, Benxi 117000, PR China
| | - Hai Li
- Department of Urology Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, PR China
| | - Xiaohong Sun
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 117000, PR China.
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26
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Dube U, Ibanez L, Budde JP, Benitez BA, Davis AA, Harari O, Iles MM, Law MH, Brown KM, Cruchaga C. Overlapping genetic architecture between Parkinson disease and melanoma. Acta Neuropathol 2020; 139:347-364. [PMID: 31845298 PMCID: PMC7379325 DOI: 10.1007/s00401-019-02110-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022]
Abstract
Epidemiologic studies have reported inconsistent results regarding an association between Parkinson disease (PD) and cutaneous melanoma (melanoma). Identifying shared genetic architecture between these diseases can support epidemiologic findings and identify common risk genes and biological pathways. Here, we apply polygenic, linkage disequilibrium-informed methods to the largest available case-control, genome-wide association study summary statistic data for melanoma and PD. We identify positive and significant genetic correlation (correlation: 0.17, 95% CI 0.10-0.24; P = 4.09 × 10-06) between melanoma and PD. We further demonstrate melanoma and PD-inferred gene expression to overlap across tissues (correlation: 0.14, 95% CI 0.06 to 0.22; P = 7.87 × 10-04) and highlight seven genes including PIEZO1, TRAPPC2L, and SOX6 as potential mediators of the genetic correlation between melanoma and PD. These findings demonstrate specific, shared genetic architecture between PD and melanoma that manifests at the level of gene expression.
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Affiliation(s)
- Umber Dube
- Medical Scientist Training Program, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Albert A Davis
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA.
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA.
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27
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Li Z, Farias FHG, Dube U, Del-Aguila JL, Mihindukulasuriya KA, Fernandez MV, Ibanez L, Budde JP, Wang F, Lake AM, Deming Y, Perez J, Yang C, Bahena JA, Qin W, Bradley JL, Davenport R, Bergmann K, Morris JC, Perrin RJ, Benitez BA, Dougherty JD, Harari O, Cruchaga C. The TMEM106B FTLD-protective variant, rs1990621, is also associated with increased neuronal proportion. Acta Neuropathol 2020; 139:45-61. [PMID: 31456032 PMCID: PMC6942643 DOI: 10.1007/s00401-019-02066-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/03/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022]
Abstract
Apart from amyloid β deposition and tau neurofibrillary tangles, Alzheimer's disease (AD) is a neurodegenerative disorder characterized by neuronal loss and astrocytosis in the cerebral cortex. The goal of this study is to investigate genetic factors associated with the neuronal proportion in health and disease. To identify cell-autonomous genetic variants associated with neuronal proportion in cortical tissues, we inferred cellular population structure from bulk RNA-Seq derived from 1536 individuals. We identified the variant rs1990621 located in the TMEM106B gene region as significantly associated with neuronal proportion (p value = 6.40 × 10-07) and replicated this finding in an independent dataset (p value = 7.41 × 10-04) surpassing the genome-wide threshold in the meta-analysis (p value = 9.42 × 10-09). This variant is in high LD with the TMEM106B non-synonymous variant p.T185S (rs3173615; r2 = 0.98) which was previously identified as a protective variant for frontotemporal lobar degeneration (FTLD). We stratified the samples by disease status, and discovered that this variant modulates neuronal proportion not only in AD cases, but also several neurodegenerative diseases and in elderly cognitively healthy controls. Furthermore, we did not find a significant association in younger controls or schizophrenia patients, suggesting that this variant might increase neuronal survival or confer resilience to the neurodegenerative process. The single variant and gene-based analyses also identified an overall genetic association between neuronal proportion, AD and FTLD risk. These results suggest that common pathways are implicated in these neurodegenerative diseases, that implicate neuronal survival. In summary, we identified a protective variant in the TMEM106B gene that may have a neuronal protection effect against general aging, independent of disease status, which could help elucidate the relationship between aging and neuronal survival in the presence or absence of neurodegenerative disorders. Our findings suggest that TMEM106B could be a potential target for neuronal protection therapies to ameliorate cognitive and functional deficits.
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Affiliation(s)
- Zeran Li
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Fabiana H G Farias
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Umber Dube
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathie A Mihindukulasuriya
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Fengxian Wang
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Allison M Lake
- Vanderbilt University Medical Scientist Training Program, Nashville, TN, USA
| | - Yuetiva Deming
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - James Perez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Chengran Yang
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Jorge A Bahena
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Qin
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Joseph L Bradley
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard Davenport
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John C Morris
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard J Perrin
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruno A Benitez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph D Dougherty
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
| | - Oscar Harari
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA.
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
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28
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Dube U, Del-Aguila JL, Li Z, Budde JP, Jiang S, Hsu S, Ibanez L, Fernandez MV, Farias F, Norton J, Gentsch J, Wang F, Salloway S, Masters CL, Lee JH, Graff-Radford NR, Chhatwal JP, Bateman RJ, Morris JC, Karch CM, Harari O, Cruchaga C. An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations. Nat Neurosci 2019; 22:1903-1912. [PMID: 31591557 PMCID: PMC6858549 DOI: 10.1038/s41593-019-0501-5] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 08/20/2019] [Indexed: 01/05/2023]
Abstract
We generated parietal cortex RNA-seq data from individuals with and without Alzheimer disease (AD; ncontrol = 13; nAD = 83) from the Knight-ADRC. Using this and an independent (MSBB) AD RNA-seq dataset, we quantified cortical circular RNA (circRNA) expression in the context of AD. We identified significant associations between circRNA expression and AD diagnosis, clinical dementia severity, and neuropathological severity. We demonstrated that a majority of circRNA AD-associations are independent from changes in cognate linear mRNA expression or brain cell-type proportions. We provided evidence for circRNA expression changes occurring early in pre-symptomatic AD, and in autosomal dominant AD. We also observed AD-associated circRNAs co-expressing with known AD genes. Finally, we identified potential microRNA binding sites in AD-associated circRNAs for microRNAs predicted to target AD genes. Together, these results highlight the importance of analyzing non-linear RNAs and support future studies exploring the potential roles of circRNAs in AD pathogenesis.
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Affiliation(s)
- Umber Dube
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA.,Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA.,Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Shan Jiang
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Simon Hsu
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Fabiana Farias
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | | | - Stephen Salloway
- Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, USA
| | - Colin L Masters
- The Florey Institute, the University of Melbourne. Level 1, Howard Florey Laboratories, Royal Parade, Parkville, VIC, Australia
| | - Jae-Hong Lee
- Department of Neurology, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Jasmeer P Chhatwal
- Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA.,Hope Center for Neurological Disorders. Washington University School of Medicine, St. Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA. .,Department of Neurology, Washington University School of Medicine, St Louis, MO, USA. .,Hope Center for Neurological Disorders. Washington University School of Medicine, St. Louis, MO, USA. .,NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA.
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29
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Deming Y, Filipello F, Cignarella F, Cantoni C, Hsu S, Mikesell R, Li Z, Del-Aguila JL, Dube U, Farias FG, Bradley J, Budde J, Ibanez L, Fernandez MV, Blennow K, Zetterberg H, Heslegrave A, Johansson PM, Svensson J, Nellgård B, Lleo A, Alcolea D, Clarimon J, Rami L, Molinuevo JL, Suárez-Calvet M, Morenas-Rodríguez E, Kleinberger G, Ewers M, Harari O, Haass C, Brett TJ, Benitez BA, Karch CM, Piccio L, Cruchaga C. The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer's disease risk. Sci Transl Med 2019; 11:eaau2291. [PMID: 31413141 PMCID: PMC6697053 DOI: 10.1126/scitranslmed.aau2291] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 04/05/2019] [Indexed: 12/13/2022]
Abstract
Soluble triggering receptor expressed on myeloid cells 2 (sTREM2) in cerebrospinal fluid (CSF) has been associated with Alzheimer's disease (AD). TREM2 plays a critical role in microglial activation, survival, and phagocytosis; however, the pathophysiological role of sTREM2 in AD is not well understood. Understanding the role of sTREM2 in AD may reveal new pathological mechanisms and lead to the identification of therapeutic targets. We performed a genome-wide association study (GWAS) to identify genetic modifiers of CSF sTREM2 obtained from the Alzheimer's Disease Neuroimaging Initiative. Common variants in the membrane-spanning 4-domains subfamily A (MS4A) gene region were associated with CSF sTREM2 concentrations (rs1582763; P = 1.15 × 10-15); this was replicated in independent datasets. The variants associated with increased CSF sTREM2 concentrations were associated with reduced AD risk and delayed age at onset of disease. The single-nucleotide polymorphism rs1582763 modified expression of the MS4A4A and MS4A6A genes in multiple tissues, suggesting that one or both of these genes are important for modulating sTREM2 production. Using human macrophages as a proxy for microglia, we found that MS4A4A and TREM2 colocalized on lipid rafts at the plasma membrane, that sTREM2 increased with MS4A4A overexpression, and that silencing of MS4A4A reduced sTREM2 production. These genetic, molecular, and cellular findings suggest that MS4A4A modulates sTREM2. These findings also provide a mechanistic explanation for the original GWAS signal in the MS4A locus for AD risk and indicate that TREM2 may be involved in AD pathogenesis not only in TREM2 risk-variant carriers but also in those with sporadic disease.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Fabia Filipello
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Francesca Cignarella
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Claudia Cantoni
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Simon Hsu
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Mikesell
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fabiana Geraldo Farias
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph Bradley
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
| | - Amanda Heslegrave
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Per M Johansson
- Department of Clinical Sciences Helsingborg, Lund University, Lund, Sweden
| | - Johan Svensson
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden
| | - Bengt Nellgård
- Department of Anesthesiology, Sahlgrenska University Hospital, Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden
| | - Alberto Lleo
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Daniel Alcolea
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Jordi Clarimon
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Lorena Rami
- IDIBAPS, Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, ICN Hospital Clinic, Barcelona, Spain
| | - José Luis Molinuevo
- IDIBAPS, Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, ICN Hospital Clinic, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
| | - Marc Suárez-Calvet
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Estrella Morenas-Rodríguez
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Gernot Kleinberger
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- ISAR Bioscience GmbH, 2152 Planegg, Germany
| | - Michael Ewers
- Institute for Stroke and Dementia Research, University Hospital, LMU, Munich, Germany
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Chair of Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Thomas J Brett
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Brain and Mind Centre, University of Sydney, Sydney, NSW 2050, Australia
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
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30
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Del-Aguila JL, Li Z, Dube U, Mihindukulasuriya KA, Budde JP, Fernandez MV, Ibanez L, Bradley J, Wang F, Bergmann K, Davenport R, Morris JC, Holtzman DM, Perrin RJ, Benitez BA, Dougherty J, Cruchaga C, Harari O. A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain. ALZHEIMERS RESEARCH & THERAPY 2019; 11:71. [PMID: 31399126 PMCID: PMC6689177 DOI: 10.1186/s13195-019-0524-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022]
Abstract
Background Alzheimer’s disease (AD) is the most common form of dementia. This neurodegenerative disorder is associated with neuronal death and gliosis heavily impacting the cerebral cortex. AD has a substantial but heterogeneous genetic component, presenting both Mendelian and complex genetic architectures. Using bulk RNA-seq from the parietal lobes and deconvolution methods, we previously reported that brains exhibiting different AD genetic architecture exhibit different cellular proportions. Here, we sought to directly investigate AD brain changes in cell proportion and gene expression using single-cell resolution. Methods We generated unsorted single-nuclei RNA sequencing data from brain tissue. We leveraged the tissue donated from a carrier of a Mendelian genetic mutation, PSEN1 p.A79V, and two family members who suffer from sporadic AD, but do not carry any autosomal mutations. We evaluated alternative alignment approaches to maximize the titer of reads, genes, and cells with high quality. In addition, we employed distinct clustering strategies to determine the best approach to identify cell clusters that reveal neuronal and glial cell types and avoid artifacts such as sample and batch effects. We propose an approach to cluster cells that reduces biases and enable further analyses. Results We identified distinct types of neurons, both excitatory and inhibitory, and glial cells, including astrocytes, oligodendrocytes, and microglia, among others. In particular, we identified a reduced proportion of excitatory neurons in the Mendelian mutation carrier, but a similar distribution of inhibitory neurons. Furthermore, we investigated whether single-nuclei RNA-seq from the human brains recapitulate the expression profile of disease-associated microglia (DAM) discovered in mouse models. We also determined that when analyzing human single-nuclei data, it is critical to control for biases introduced by donor-specific expression profiles. Conclusion We propose a collection of best practices to generate a highly detailed molecular cell atlas of highly informative frozen tissue stored in brain banks. Importantly, we have developed a new web application to make this unique single-nuclei molecular atlas publicly available. Electronic supplementary material The online version of this article (10.1186/s13195-019-0524-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Kathie A Mihindukulasuriya
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Joseph Bradley
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard Davenport
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John C Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA.,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - David M Holtzman
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA.,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard J Perrin
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Joseph Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA. .,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA. .,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA. .,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA. .,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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31
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Del-Aguila JL, Benitez BA, Li Z, Dube U, Mihindukulasuriya KA, Budde JP, Farias FHG, Fernández MV, Ibanez L, Jiang S, Perrin RJ, Cairns NJ, Morris JC, Harari O, Cruchaga C. TREM2 brain transcript-specific studies in AD and TREM2 mutation carriers. Mol Neurodegener 2019; 14:18. [PMID: 31068200 PMCID: PMC6505298 DOI: 10.1186/s13024-019-0319-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Low frequency coding variants in TREM2 are associated with Alzheimer disease (AD) risk and cerebrospinal fluid (CSF) TREM2 protein levels are different between AD cases and controls. Similarly, TREM2 risk variant carriers also exhibit differential CSF TREM2 levels. TREM2 has three different alternative transcripts, but most of the functional studies only model the longest transcript. No studies have analyzed TREM2 expression levels or alternative splicing in brains from AD and cognitively normal individuals. We wanted to determine whether there was differential expression of TREM2 in sporadic-AD cases versus AD-TREM2 carriers vs sex- and aged-matched normal controls; and if this differential expression was due to a particular TREM2 transcript. METHODS We analyzed RNA-Seq data from parietal lobe brain tissue from AD cases with TREM2 variants (n = 33), AD cases (n = 195) and healthy controls (n = 118), from three independent datasets using Kallisto and the R package tximport to determine the read count for each transcript and quantified transcript abundance as transcripts per million. RESULTS The three TREM2 transcripts were expressed in brain cortex in the three datasets. We demonstrate for the first time that the transcript that lacks the transmembrane domain and encodes a soluble form of TREM2 (sTREM2) has an expression level around 60% of the canonical transcript, suggesting that around 25% of the sTREM2 protein levels could be explained by this transcript. We did not observe a difference in the overall TREM2 expression level between cases and controls. However, the isoform which lacks the 5' exon, but includes the transmembrane domain, was significantly lower in TREM2- p.R62H carriers than in AD cases (p = 0.007). CONCLUSION Using bulk RNA-Seq data from three different cohorts, we were able to quantify the expression level of the three TREM2 transcripts, demonstrating: (1) all three transcripts of them are highly expressed in the human cortex, (2) that up to 25% of the sTREM2 may be due to the expression of a specific isoform and not TREM2 cleavage; and (3) that TREM2 risk variants do not affect expression levels, suggesting that the effect of the TREM2 variants on CSF levels occurs at post-transcriptional level.
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Affiliation(s)
- Jorge L. Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Bruno A. Benitez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Kathie A. Mihindukulasuriya
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - John P. Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Fabiana H. G. Farias
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Shan Jiang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Richard J. Perrin
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO USA
| | - Nigel J. Cairns
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO USA
| | - John C. Morris
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO USA
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32
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Chen J, Huang W, Cheng CH, Zhou L, Jiang GB, Hu YY. Association Between Aldehyde dehydrogenase-2 Polymorphisms and Risk of Alzheimer's Disease and Parkinson's Disease: A Meta-Analysis Based on 5,315 Individuals. Front Neurol 2019; 10:290. [PMID: 30984100 PMCID: PMC6448532 DOI: 10.3389/fneur.2019.00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/06/2019] [Indexed: 11/21/2022] Open
Abstract
Objective: A number of studies have reported that aldehyde dehydrogenase-2 (ALDH2) polymorphisms maybe associated with the risk of Alzheimer's disease (AD) and Parkinson's disease (PD). However, the results of such studies are inconsistent. We therefore conducted a meta-analysis to clarify the association between ALDH2 polymorphisms and the risk of AD and PD. Methods: Five online databases were searched and the relevant studies were reviewed from inception through May 10, 2018. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were calculated in each genetic model of the general population and various subgroups. Furthermore, we simultaneously performed heterogeneity, cumulative, sensitivity, and publication bias analyses. Results: Overall, nine case-control studies involving 5,315 subjects were included in this meta-analysis. Potential associations were found between the ALDH2 rs671 G>A polymorphism and the risk of AD (A vs. G: OR = 1.46, 95%CI = 1.01–2.11, P = 0.05, I2 = 84.2%; AA vs. GG: OR = 2.22, 95%CI = 1.03–4.77, P = 0.04, I2 = 79.2%; AA vs. GG+GA: OR = 1.94, 95%CI = 1.03–3.64, P =0.04, I2 = 71.1%). In addition, some similar results were observed in other subgroups. Moreover, no significant association between ALDH2 polymorphisms and PD risk. Conclusions: In conclusion, our meta-analysis indicated that the ALDH2 rs671 G>A polymorphism plays an important role in AD development.
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Affiliation(s)
- Jun Chen
- Department of Neurology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Wei Huang
- Department of Neurology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chao-Hui Cheng
- Department of Neurology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Lan Zhou
- Department of Neurology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Guang-Bin Jiang
- Department of Radiology, Suizhou Central Hospital, Suizhou, China
| | - Yuan-Yuan Hu
- Department of Stomatology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
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33
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Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism. Transl Psychiatry 2019; 9:89. [PMID: 30765688 PMCID: PMC6376002 DOI: 10.1038/s41398-019-0384-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023] Open
Abstract
Alcohol exposure triggers changes in gene expression and biological pathways in human brain. We explored alterations in gene expression in the Pre-Frontal Cortex (PFC) of 65 alcoholics and 73 controls of European descent, and identified 129 genes that showed altered expression (FDR < 0.05) in subjects with alcohol dependence. Differentially expressed genes were enriched for pathways related to interferon signaling and Growth Arrest and DNA Damage-inducible 45 (GADD45) signaling. A coexpression module (thistle2) identified by weighted gene co-expression network analysis (WGCNA) was significantly correlated with alcohol dependence, alcohol consumption, and AUDIT scores. Genes in the thistle2 module were enriched with genes related to calcium signaling pathways and showed significant downregulation of these pathways, as well as enrichment for biological processes related to nicotine response and opioid signaling. A second module (brown4) showed significant upregulation of pathways related to immune signaling. Expression quantitative trait loci (eQTLs) for genes in the brown4 module were also enriched for genetic associations with alcohol dependence and alcohol consumption in large genome-wide studies included in the Psychiatric Genetic Consortium and the UK Biobank's alcohol consumption dataset. By leveraging multi-omics data, this transcriptome analysis has identified genes and biological pathways that could provide insight for identifying therapeutic targets for alcohol dependence.
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34
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Dai J, Johnson ECB, Dammer EB, Duong DM, Gearing M, Lah JJ, Levey AI, Wingo TS, Seyfried NT. Effects of APOE Genotype on Brain Proteomic Network and Cell Type Changes in Alzheimer's Disease. Front Mol Neurosci 2018; 11:454. [PMID: 30618606 PMCID: PMC6305300 DOI: 10.3389/fnmol.2018.00454] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
Polymorphic alleles in the apolipoprotein E (APOE) gene are the main genetic determinants of late-onset Alzheimer's disease (AD) risk. Individuals carrying the APOE E4 allele are at increased risk to develop AD compared to those carrying the more common E3 allele, whereas those carrying the E2 allele are at decreased risk for developing AD. How ApoE isoforms influence risk for AD remains unclear. To help fill this gap in knowledge, we performed a comparative unbiased mass spectrometry-based proteomic analysis of post-mortem brain cortical tissues from pathologically-defined AD or control cases of different APOE genotypes. Control cases (n = 10) were homozygous for the common E3 allele, whereas AD cases (n = 24) were equally distributed among E2/3, E3/3, and E4/4 genotypes. We used differential protein expression and co-expression analytical approaches to assess how changes in the brain proteome are related to APOE genotype. We observed similar levels of amyloid-β, but reduced levels of neurofibrillary tau, in E2/3 brains compared to E3/3 and E4/4 AD brains. Weighted co-expression network analysis revealed 33 modules of co-expressed proteins, 12 of which were significantly different by APOE genotype in AD. The modules that were significantly different by APOE genotype were associated with synaptic transmission and inflammation, among other biological processes. Deconvolution and analysis of brain cell type changes revealed that the E2 allele suppressed homeostatic and disease-associated cell type changes in astrocytes, microglia, oligodendroglia, and endothelia. The E2 allele-specific effect on brain cell type changes was validated in a separate cohort of 130 brains. Our systems-level proteomic analyses of AD brain reveal alterations in the brain proteome and brain cell types associated with allelic variants in APOE, and suggest further areas for investigation into the upstream mechanisms that drive ApoE-associated risk for AD.
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Affiliation(s)
- Jingting Dai
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Erik C B Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Eric B Dammer
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Marla Gearing
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States.,Division of Neurology, Atlanta VA Medical Center, Decatur, GA, United States.,Department of Human Genetics, Emory University School of Medicine,Atlanta, GA, United States
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
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35
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Jiang S, Wen N, Li Z, Dube U, Del Aguila J, Budde J, Martinez R, Hsu S, Fernandez MV, Cairns NJ, Harari O, Cruchaga C, Karch CM. Integrative system biology analyses of CRISPR-edited iPSC-derived neurons and human brains reveal deficiencies of presynaptic signaling in FTLD and PSP. Transl Psychiatry 2018; 8:265. [PMID: 30546007 PMCID: PMC6293323 DOI: 10.1038/s41398-018-0319-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 01/12/2023] Open
Abstract
Mutations in the microtubule-associated protein tau (MAPT) gene cause autosomal dominant frontotemporal lobar degeneration with tau inclusions (FTLD-tau). MAPT p.R406W carriers present clinically with progressive memory loss and neuropathologically with neuronal and glial tauopathy. However, the pathogenic events triggered by the expression of the mutant tau protein remain poorly understood. To identify the genes and pathways that are dysregulated in FTLD-tau, we performed transcriptomic analyses in induced pluripotent stem cell (iPSC)-derived neurons carrying MAPT p.R406W and CRISPR/Cas9-corrected isogenic controls. We found that the expression of the MAPT p.R406W mutation was sufficient to create a significantly different transcriptomic profile compared with that of the isogeneic controls and to cause the differential expression of 328 genes. Sixty-one of these genes were also differentially expressed in the same direction between MAPT p.R406W carriers and pathology-free human control brains. We found that genes differentially expressed in the stem cell models and human brains were enriched for pathways involving gamma-aminobutyric acid (GABA) receptors and pre-synaptic function. The expression of GABA receptor genes, including GABRB2 and GABRG2, were consistently reduced in iPSC-derived neurons and brains from MAPT p.R406W carriers. Interestingly, we found that GABA receptor genes, including GABRB2 and GABRG2, are significantly lower in symptomatic mouse models of tauopathy, as well as in brains with progressive supranuclear palsy. Genome wide association analyses reveal that common variants within GABRB2 are associated with increased risk for frontotemporal dementia (P < 1 × 10-3). Thus, our systems biology approach, which leverages molecular data from stem cells, animal models, and human brain tissue can reveal novel disease mechanisms. Here, we demonstrate that MAPT p.R406W is sufficient to induce changes in GABA-mediated signaling and synaptic function, which may contribute to the pathogenesis of FTLD-tau and other primary tauopathies.
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Affiliation(s)
- Shan Jiang
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Natalie Wen
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Zeran Li
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Umber Dube
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Jorge Del Aguila
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - John Budde
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Rita Martinez
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Simon Hsu
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Maria V. Fernandez
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Nigel J. Cairns
- 0000 0001 2355 7002grid.4367.6Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, 660S. Euclid Ave, Campus Box 8118, Saint Louis, MO 63110 USA
| | | | | | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Celeste M. Karch
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
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