1
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Shen Y, Timsina J, Heo G, Beric A, Ali M, Wang C, Yang C, Wang Y, Western D, Liu M, Gorijala P, Budde J, Do A, Liu H, Gordon B, Llibre-Guerra JJ, Joseph-Mathurin N, Perrin RJ, Maschi D, Wyss-Coray T, Pastor P, Renton AE, Surace EI, Johnson ECB, Levey AI, Alvarez I, Levin J, Ringman JM, Allegri RF, Seyfried N, Day GS, Wu Q, Fernández MV, Tarawneh R, McDade E, Morris JC, Bateman RJ, Goate A, Ibanez L, Sung YJ, Cruchaga C. CSF proteomics identifies early changes in autosomal dominant Alzheimer's disease. Cell 2024:S0092-8674(24)00978-4. [PMID: 39332414 DOI: 10.1016/j.cell.2024.08.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/02/2024] [Accepted: 08/23/2024] [Indexed: 09/29/2024]
Abstract
In this high-throughput proteomic study of autosomal dominant Alzheimer's disease (ADAD), we sought to identify early biomarkers in cerebrospinal fluid (CSF) for disease monitoring and treatment strategies. We examined CSF proteins in 286 mutation carriers (MCs) and 177 non-carriers (NCs). The developed multi-layer regression model distinguished proteins with different pseudo-trajectories between these groups. We validated our findings with independent ADAD as well as sporadic AD datasets and employed machine learning to develop and validate predictive models. Our study identified 137 proteins with distinct trajectories between MCs and NCs, including eight that changed before traditional AD biomarkers. These proteins are grouped into three stages: early stage (stress response, glutamate metabolism, neuron mitochondrial damage), middle stage (neuronal death, apoptosis), and late presymptomatic stage (microglial changes, cell communication). The predictive model revealed a six-protein subset that more effectively differentiated MCs from NCs, compared with conventional biomarkers.
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Affiliation(s)
- Yuanyuan Shen
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Gyujin Heo
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Aleksandra Beric
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Muhammad Ali
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Ciyang Wang
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Chengran Yang
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Yueyao Wang
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Daniel Western
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Menghan Liu
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Anh Do
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA
| | - Haiyan Liu
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian Gordon
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jorge J Llibre-Guerra
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nelly Joseph-Mathurin
- Mallinckrodt Institute of Radiology, Washington University St Louis, St Louis, MO 63110, USA
| | - Richard J Perrin
- Department of Pathology and Immunology, Washington University St. Louis, St. Louis, MO 63110, USA
| | - Dario Maschi
- Department of Cell Biology and Physiology, Washington University St. Louis, St. Louis, MO 63110, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA; Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Pau Pastor
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and The Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Alan E Renton
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ezequiel I Surace
- Laboratory of Neurodegenerative Diseases, Institute of Neurosciences (INEU-Fleni-CONICET), Buenos Aires, Argentina
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30307, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Ignacio Alvarez
- Department of Neurology, University Hospital Mútua de Terrassa and Fundació Docència i Recerca Mútua de Terrassa, Terrassa 08221, Barcelona, Spain
| | - Johannes Levin
- Department of Neurology, LMU University Hospital, LMU Munich, Munich 80336, Germany; German Center for Neurodegenerative Diseases, site Munich, Munich 80336, Germany
| | - John M Ringman
- Alzheimer's Disease Research Center, Department of Neurology, Keck School of Medicine at USC, Los Angeles, CA 90033, USA
| | - Ricardo Francisco Allegri
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - Nicholas Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Gregg S Day
- Department of Neurology, Mayo Clinic in Florida, Jacksonville, FL 32224, USA
| | - Qisi Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | | | - Rawan Tarawneh
- The University of New Mexico, Albuquerque, NM 87131, USA
| | - Eric McDade
- Department of Neurology, 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
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alison Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO 63110, USA; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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2
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Reddy JS, Heath L, Linden AV, Allen M, Lopes KDP, Seifar F, Wang E, Ma Y, Poehlman WL, Quicksall ZS, Runnels A, Wang Y, Duong DM, Yin L, Xu K, Modeste ES, Shantaraman A, Dammer EB, Ping L, Oatman SR, Scanlan J, Ho C, Carrasquillo MM, Atik M, Yepez G, Mitchell AO, Nguyen TT, Chen X, Marquez DX, Reddy H, Xiao H, Seshadri S, Mayeux R, Prokop S, Lee EB, Serrano GE, Beach TG, Teich AF, Haroutunian V, Fox EJ, Gearing M, Wingo A, Wingo T, Lah JJ, Levey AI, Dickson DW, Barnes LL, De Jager P, Zhang B, Bennett D, Seyfried NT, Greenwood AK, Ertekin-Taner N. Bridging the gap: Multi-omics profiling of brain tissue in Alzheimer's disease and older controls in multi-ethnic populations. Alzheimers Dement 2024. [PMID: 39215503 DOI: 10.1002/alz.14208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Multi-omics studies in Alzheimer's disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked Black Americans (BA) and Latin Americans (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership in Alzheimer's Disease (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTS We generated multi-omics data and curated and harmonized phenotypic data from BA (n = 306), LA (n = 326), or BA and LA (n = 4) brain donors plus non-Hispanic White (n = 252) and other (n = 20) ethnic groups, to establish a foundational dataset enriched for BA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSION The inclusion of traditionally underrepresented groups in multi-omics studies is essential to discovering the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD. HIGHLIGHTS Accelerating Medicines Partnership in Alzheimer's Disease Diversity Initiative led brain tissue profiling in multi-ethnic populations. Brain multi-omics data is generated from Black American, Latin American, and non-Hispanic White donors. RNA, whole genome sequencing and tandem mass tag proteomicsis completed and shared. Multiple brain regions including caudate, temporal and dorsolateral prefrontal cortex were profiled.
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Affiliation(s)
| | | | | | | | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Fatemeh Seifar
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yiyi Ma
- Columbia University Irving Medical Center, New York, New York, USA
| | | | | | | | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Duc M Duong
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Luming Yin
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kaiming Xu
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | - Eric B Dammer
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Lingyan Ping
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Jo Scanlan
- Sage Bionetworks, Seattle, Washington, USA
| | | | | | - Merve Atik
- Mayo Clinic Florida, Jacksonville, Florida, USA
| | | | | | | | | | - David X Marquez
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- University of Illinois Chicago, Chicago, Illinois, USA
| | - Hasini Reddy
- Columbia University Irving Medical Center, New York, New York, USA
| | - Harrison Xiao
- Columbia University Irving Medical Center, New York, New York, USA
| | - Sudha Seshadri
- The Glen Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas, San Antonio, Texas, USA
| | - Richard Mayeux
- Columbia University Irving Medical Center, New York, New York, USA
| | | | - Edward B Lee
- Center for Neurodegenerative Disease Brain Bank at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Andrew F Teich
- Columbia University Irving Medical Center, New York, New York, USA
| | - Varham Haroutunian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Edward J Fox
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Marla Gearing
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Aliza Wingo
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Thomas Wingo
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - James J Lah
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Allan I Levey
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Philip De Jager
- Columbia University Irving Medical Center, New York, New York, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
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3
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Pichet Binette A, Gaiteri C, Wennström M, Kumar A, Hristovska I, Spotorno N, Salvadó G, Strandberg O, Mathys H, Tsai LH, Palmqvist S, Mattsson-Carlgren N, Janelidze S, Stomrud E, Vogel JW, Hansson O. Proteomic changes in Alzheimer's disease associated with progressive Aβ plaque and tau tangle pathologies. Nat Neurosci 2024:10.1038/s41593-024-01737-w. [PMID: 39187705 DOI: 10.1038/s41593-024-01737-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 07/23/2024] [Indexed: 08/28/2024]
Abstract
Proteomics can shed light on the dynamic and multifaceted alterations in neurodegenerative disorders like Alzheimer's disease (AD). Combining radioligands measuring β-amyloid (Aβ) plaques and tau tangles with cerebrospinal fluid proteomics, we uncover molecular events mirroring different stages of AD pathology in living humans. We found 127 differentially abundant proteins (DAPs) across the AD spectrum. The strongest Aβ-related proteins were mainly expressed in glial cells and included SMOC1 and ITGAM. A dozen proteins linked to ATP metabolism and preferentially expressed in neurons were independently associated with tau tangle load and tau accumulation. Only 20% of the DAPs were also altered in other neurodegenerative diseases, underscoring AD's distinct proteome. Two co-expression modules related, respectively, to protein metabolism and microglial immune response encompassed most DAPs, with opposing, staggered trajectories along the AD continuum. We unveil protein signatures associated with Aβ and tau proteinopathy in vivo, offering insights into complex neural responses and potential biomarkers and therapeutics targeting different disease stages.
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Affiliation(s)
- Alexa Pichet Binette
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden.
| | - Chris Gaiteri
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
- Rush University Alzheimer's Disease Center, Rush University, Chicago, IL, USA
| | - Malin Wennström
- Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Atul Kumar
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Ines Hristovska
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Nicola Spotorno
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Gemma Salvadó
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Olof Strandberg
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Hansruedi Mathys
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- University of Pittsburgh Brain Institute and Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Sebastian Palmqvist
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Niklas Mattsson-Carlgren
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Department of Neurology, Skåne University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Shorena Janelidze
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Erik Stomrud
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Rush University Alzheimer's Disease Center, Rush University, Chicago, IL, USA
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Jacob W Vogel
- Department of Clinical Sciences Malmö, SciLifeLab, Lund University, Lund, Sweden
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden.
- Memory Clinic, Skåne University Hospital, Malmö, Sweden.
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4
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Levites Y, Dammer EB, Ran Y, Tsering W, Duong D, Abreha M, Gadhavi J, Lolo K, Trejo-Lopez J, Phillips J, Iturbe A, Erquizi A, Moore BD, Ryu D, Natu A, Dillon K, Torrellas J, Moran C, Ladd T, Afroz F, Islam T, Jagirdar J, Funk CC, Robinson M, Rangaraju S, Borchelt DR, Ertekin-Taner N, Kelly JW, Heppner FL, Johnson ECB, McFarland K, Levey AI, Prokop S, Seyfried NT, Golde TE. Integrative proteomics identifies a conserved Aβ amyloid responsome, novel plaque proteins, and pathology modifiers in Alzheimer's disease. Cell Rep Med 2024; 5:101669. [PMID: 39127040 PMCID: PMC11384960 DOI: 10.1016/j.xcrm.2024.101669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/15/2024] [Accepted: 07/10/2024] [Indexed: 08/12/2024]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder that develops over decades. AD brain proteomics reveals vast alterations in protein levels and numerous altered biologic pathways. Here, we compare AD brain proteome and network changes with the brain proteomes of amyloid β (Aβ)-depositing mice to identify conserved and divergent protein networks with the conserved networks identifying an Aβ amyloid responsome. Proteins in the most conserved network (M42) accumulate in plaques, cerebrovascular amyloid (CAA), and/or dystrophic neuronal processes, and overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), increases the accumulation of Aβ in plaques and CAA. M42 proteins bind amyloid fibrils in vitro, and MDK and PTN co-accumulate with cardiac transthyretin amyloid. M42 proteins appear intimately linked to amyloid deposition and can regulate amyloid deposition, suggesting that they are pathology modifiers and thus putative therapeutic targets. We posit that amyloid-scaffolded accumulation of numerous M42+ proteins is a central mechanism mediating downstream pathophysiology in AD.
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Affiliation(s)
- Yona Levites
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Yong Ran
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Wangchen Tsering
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Duc Duong
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Measho Abreha
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshna Gadhavi
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kiara Lolo
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Jorge Trejo-Lopez
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Jennifer Phillips
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Andrea Iturbe
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Aya Erquizi
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Brenda D Moore
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Danny Ryu
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Aditya Natu
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kristy Dillon
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jose Torrellas
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Corey Moran
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Thomas Ladd
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Farhana Afroz
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Tariful Islam
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Jaishree Jagirdar
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - David R Borchelt
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Nilüfer Ertekin-Taner
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL, USA; Mayo Clinic, Department of Neurology, Jacksonville, FL, USA
| | - Jeffrey W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Frank L Heppner
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 110117 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, 110117 Berlin, Germany; Cluster of Excellence, NeuroCure, Charitéplatz, 110117 Berlin, Germany
| | - Erik C B Johnson
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen McFarland
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan Prokop
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neurology, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - Nicholas T Seyfried
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
| | - Todd E Golde
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
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5
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Daniels AJ, McDade E, Llibre-Guerra JJ, Xiong C, Perrin RJ, Ibanez L, Supnet-Bell C, Cruchaga C, Goate A, Renton AE, Benzinger TL, Gordon BA, Hassenstab J, Karch C, Popp B, Levey A, Morris J, Buckles V, Allegri RF, Chrem P, Berman SB, Chhatwal JP, Farlow MR, Fox NC, Day GS, Ikeuchi T, Jucker M, Lee JH, Levin J, Lopera F, Takada L, Sosa AL, Martins R, Mori H, Noble JM, Salloway S, Huey E, Rosa-Neto P, Sánchez-Valle R, Schofield PR, Roh JH, Bateman RJ. 15 Years of Longitudinal Genetic, Clinical, Cognitive, Imaging, and Biochemical Measures in DIAN. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.08.24311689. [PMID: 39148846 PMCID: PMC11326320 DOI: 10.1101/2024.08.08.24311689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
This manuscript describes and summarizes the Dominantly Inherited Alzheimer Network Observational Study (DIAN Obs), highlighting the wealth of longitudinal data, samples, and results from this human cohort study of brain aging and a rare monogenic form of Alzheimer's disease (AD). DIAN Obs is an international collaborative longitudinal study initiated in 2008 with support from the National Institute on Aging (NIA), designed to obtain comprehensive and uniform data on brain biology and function in individuals at risk for autosomal dominant AD (ADAD). ADAD gene mutations in the amyloid protein precursor (APP), presenilin 1 (PSEN1), or presenilin 2 (PSEN2) genes are deterministic causes of ADAD, with virtually full penetrance, and a predictable age at symptomatic onset. Data and specimens collected are derived from full clinical assessments, including neurologic and physical examinations, extensive cognitive batteries, structural and functional neuro-imaging, amyloid and tau pathological measures using positron emission tomography (PET), flurordeoxyglucose (FDG) PET, cerebrospinal fluid and blood collection (plasma, serum, and whole blood), extensive genetic and multi-omic analyses, and brain donation upon death. This comprehensive evaluation of the human nervous system is performed longitudinally in both mutation carriers and family non-carriers, providing one of the deepest and broadest evaluations of the human brain across decades and through AD progression. These extensive data sets and samples are available for researchers to address scientific questions on the human brain, aging, and AD.
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Affiliation(s)
- Alisha J. Daniels
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Eric McDade
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | | | - Chengjie Xiong
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Richard J. Perrin
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Laura Ibanez
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | | | - Carlos Cruchaga
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Alison Goate
- Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Alan E. Renton
- Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | - Brian A. Gordon
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Jason Hassenstab
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Celeste Karch
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Brent Popp
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Allan Levey
- Goizueta Alzheimer’s Disease Research Center, Emory University, Atlanta, GA, USA
| | - John Morris
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | - Virginia Buckles
- Washington University School of Medicine, St Louis, St Louis, MO, USA
| | | | - Patricio Chrem
- Institute of Neurological Research FLENI, Buenos Aires, Argentina
| | | | - Jasmeer P. Chhatwal
- Massachusetts General and Brigham & Women’s Hospitals, Harvard Medical School, Boston MA, USA
| | | | - Nick C. Fox
- UK Dementia Research Institute at University College London, London, United Kingdom
- University College London, London, United Kingdom
| | | | - Takeshi Ikeuchi
- Brain Research Institute, Niigata University, Niigata, Japan
| | - Mathias Jucker
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | | | - Johannes Levin
- DZNE, German Center for Neurodegenerative Diseases, Munich, Germany
- Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | | - Ana Luisa Sosa
- Instituto Nacional de Neurologia y Neurocirugla Innn, Mexico City, Mexico
| | - Ralph Martins
- Edith Cowan University, Western Australia, Australia
| | | | - James M. Noble
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Department of Neurology, and GH Sergievsky Center, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Edward Huey
- Brown University, Butler Hospital, Providence, RI, USA
| | - Pedro Rosa-Neto
- Centre de Recherche de L’hopital Douglas and McGill University, Montreal, Quebec
| | - Raquel Sánchez-Valle
- Hospital Clínic de Barcelona. IDIBAPS. University of Barcelona, Barcelona, Spain
| | - Peter R. Schofield
- Neuroscience Research Australia, Sydney, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jee Hoon Roh
- Korea University, Korea University Anam Hospital, Seoul, South Korea
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6
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Sun Z, Kwon JS, Ren Y, Chen S, Walker CK, Lu X, Cates K, Karahan H, Sviben S, Fitzpatrick JAJ, Valdez C, Houlden H, Karch CM, Bateman RJ, Sato C, Mennerick SJ, Diamond MI, Kim J, Tanzi RE, Holtzman DM, Yoo AS. Modeling late-onset Alzheimer's disease neuropathology via direct neuronal reprogramming. Science 2024; 385:adl2992. [PMID: 39088624 DOI: 10.1126/science.adl2992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/31/2024] [Indexed: 08/03/2024]
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common form of Alzheimer's disease (AD). However, modeling sporadic LOAD that endogenously captures hallmark neuronal pathologies such as amyloid-β (Aβ) deposition, tau tangles, and neuronal loss remains an unmet need. We demonstrate that neurons generated by microRNA (miRNA)-based direct reprogramming of fibroblasts from individuals affected by autosomal dominant AD (ADAD) and LOAD in a three-dimensional environment effectively recapitulate key neuropathological features of AD. Reprogrammed LOAD neurons exhibit Aβ-dependent neurodegeneration, and treatment with β- or γ-secretase inhibitors before (but not subsequent to) Aβ deposit formation mitigated neuronal death. Moreover inhibiting age-associated retrotransposable elements in LOAD neurons reduced both Aβ deposition and neurodegeneration. Our study underscores the efficacy of modeling late-onset neuropathology of LOAD through high-efficiency miRNA-based neuronal reprogramming.
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Affiliation(s)
- Zhao Sun
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, 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
| | - Ji-Sun Kwon
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Computational and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yudong Ren
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shawei Chen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, 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
| | - Courtney K Walker
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, 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
| | - Xinguo Lu
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kitra Cates
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hande Karahan
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sanja Sviben
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Clarissa Valdez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Henry Houlden
- UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Celeste M Karch
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Randall J Bateman
- Tracy Family SILQ Center for Neurodegenerative Biology, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chihiro Sato
- Tracy Family SILQ Center for Neurodegenerative Biology, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven J Mennerick
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jungsu Kim
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - David M Holtzman
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, 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
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7
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McDade E, Liu H, Bui Q, Hassenstab J, Gordon B, Benzinger T, Shen Y, Timsina J, Wang L, Sung YJ, Karch C, Renton A, Daniels A, Morris J, Xiong C, Ibanez L, Perrin R, Llibre-Guerra JJ, Day G, Supnet-Bell C, Xu X, Berman S, Chhatwal J, Ikeuchi T, Kasuga K, Niimi Y, Huey E, Schofield P, Brooks W, Ryan N, Jucker M, Laske C, Levin J, Vöglein J, Roh JH, Lopera F, Bateman R, Cruchaga C. Ubiquitin-Proteasome System in the Different Stages of Dominantly Inherited Alzheimer's Disease. RESEARCH SQUARE 2024:rs.3.rs-4202125. [PMID: 39108475 PMCID: PMC11302696 DOI: 10.21203/rs.3.rs-4202125/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
This study explored the role of the ubiquitin-proteasome system (UPS) in dominantly inherited Alzheimer's disease (DIAD) by examining changes in cerebrospinal fluid (CSF) levels of UPS proteins along with disease progression, AD imaging biomarkers (PiB PET, tau PET), neurodegeneration imaging measures (MRI, FDG PET), and Clinical Dementia Rating® (CDR®). Using the SOMAscan assay, we detected subtle increases in specific ubiquitin enzymes associated with proteostasis in mutation carriers (MCs) up to two decades before the estimated symptom onset. This was followed by more pronounced elevations of UPS-activating enzymes, including E2 and E3 proteins, and ubiquitin-related modifiers. Our findings also demonstrated consistent correlations between UPS proteins and CSF biomarkers such as Aβ42/40 ratio, total tau, various phosphorylated tau species to total tau ratios (ptau181/T181, ptauT205/T205, ptauS202/S202, ptauT217/T217), and MTBR-tau243, alongside Neurofilament light chain (NfL) and the CDR®. Notably, a positive association was observed with imaging markers (PiB PET, tau PET) and a negative correlation with markers of neurodegeneration (FDG PET, MRI), highlighting a significant link between UPS dysregulation and neurodegenerative processes. The correlations suggest that the increase in multiple UPS proteins with rising tau levels and tau-tangle associated markers, indicating a potential role for the UPS in relation to misfolded tau/neurofibrillary tangles (NFTs) and symptom onset. These findings indicate that elevated CSF UPS proteins in DIAD MCs could serve as early indicators of disease progression and suggest a link between UPS dysregulation and amyloid plaque, tau tangles formation, implicating the UPS as a potential therapeutic target in AD pathogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Alan Renton
- Nash Family Department of Neuroscience and Ronald Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA: Departments of Neurology and Genetics and Ge
| | | | | | | | | | | | | | | | | | | | | | - Jasmeer Chhatwal
- Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School
| | | | - Kensaku Kasuga
- Department of Molecular Genetics, Brain Research Institute, Niigata University
| | | | | | | | | | | | | | | | | | | | | | | | - Randall Bateman
- Department of Neurology, Washington University School of Medicine
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8
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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] [Key Words] [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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9
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Guo Y, Chen SD, You J, Huang SY, Chen YL, Zhang Y, Wang LB, He XY, Deng YT, Zhang YR, Huang YY, Dong Q, Feng JF, Cheng W, Yu JT. Multiplex cerebrospinal fluid proteomics identifies biomarkers for diagnosis and prediction of Alzheimer's disease. Nat Hum Behav 2024:10.1038/s41562-024-01924-6. [PMID: 38987357 DOI: 10.1038/s41562-024-01924-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Recent expansion of proteomic coverage opens unparalleled avenues to unveil new biomarkers of Alzheimer's disease (AD). Among 6,361 cerebrospinal fluid (CSF) proteins analysed from the ADNI database, YWHAG performed best in diagnosing both biologically (AUC = 0.969) and clinically (AUC = 0.857) defined AD. Four- (YWHAG, SMOC1, PIGR and TMOD2) and five- (ACHE, YWHAG, PCSK1, MMP10 and IRF1) protein panels greatly improved the accuracy to 0.987 and 0.975, respectively. Their superior performance was validated in an independent external cohort and in discriminating autopsy-confirmed AD versus non-AD, rivalling even canonical CSF ATN biomarkers. Moreover, they effectively predicted the clinical progression to AD dementia and were strongly associated with AD core biomarkers and cognitive decline. Synaptic, neurogenic and infectious pathways were enriched in distinct AD stages. Mendelian randomization did not support the significant genetic link between CSF proteins and AD. Our findings revealed promising high-performance biomarkers for AD diagnosis and prediction, with implications for clinical trials targeting different pathomechanisms.
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Affiliation(s)
- Yu Guo
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi-Dong Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jia You
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Shu-Yi Huang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Lin Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lin-Bo Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Xiao-Yu He
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue-Ting Deng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Ru Zhang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Yuan Huang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiang Dong
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian-Feng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
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10
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Timsina J, Dinasarapu A, Kilic-Berkmen G, Budde J, Sung YJ, Klein AM, Cruchaga C, Jinnah HA. Blood-Based Proteomics for Adult-Onset Focal Dystonias. Ann Neurol 2024; 96:110-120. [PMID: 38578115 PMCID: PMC11186717 DOI: 10.1002/ana.26929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
OBJECTIVES The adult-onset focal dystonias are characterized by over-active muscles leading to abnormal movements. For most cases, the etiology and pathogenesis remain unknown. In the current study, unbiased proteomics methods were used to identify potential changes in blood plasma proteins. METHODS A large-scale unbiased proteomics screen was used to compare proteins (N = 6,345) in blood plasma of normal healthy controls (N = 49) with adult-onset focal dystonia (N = 143) consisting of specific subpopulations of cervical dystonia (N = 45), laryngeal dystonia (N = 49), and blepharospasm (N = 49). Pathway analyses were conducted to identify relevant biological pathways. Finally, protein changes were used to build a prediction model for dystonia. RESULTS After correction for multiple comparisons, 15 proteins were associated with adult-onset focal dystonia. Subgroup analyses revealed some proteins were shared across the dystonia subgroups while others were unique to 1 subgroup. The top biological pathways involved changes in the immune system, metal ion transport, and reactive oxygen species. A 4-protein model showed high accuracy in discriminating control individuals from dystonia cases [average area under the curve (AUC) = 0.89]. INTERPRETATION These studies provide novel insights into the etiopathogenesis of dystonia, as well as novel potential biomarkers. ANN NEUROL 2024;96:110-120.
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Affiliation(s)
- 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, USA
| | - Ashok Dinasarapu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Gamze Kilic-Berkmen
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 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, 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, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam M. Klein
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA 30322 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, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
| | - H. A. Jinnah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
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11
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Dammer EB, Shantaraman A, Ping L, Duong DM, Gerasimov ES, Ravindran SP, Gudmundsdottir V, Frick EA, Gomez GT, Walker KA, Emilsson V, Jennings LL, Gudnason V, Western D, Cruchaga C, Lah JJ, Wingo TS, Wingo AP, Seyfried NT, Levey AI, Johnson ECB. Proteomic analysis of Alzheimer's disease cerebrospinal fluid reveals alterations associated with APOE ε4 and atomoxetine treatment. Sci Transl Med 2024; 16:eadn3504. [PMID: 38924431 DOI: 10.1126/scitranslmed.adn3504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Alzheimer's disease (AD) is currently defined by the aggregation of amyloid-β (Aβ) and tau proteins in the brain. Although biofluid biomarkers are available to measure Aβ and tau pathology, few markers are available to measure the complex pathophysiology that is associated with these two cardinal neuropathologies. Here, we characterized the proteomic landscape of cerebrospinal fluid (CSF) changes associated with Aβ and tau pathology in 300 individuals using two different proteomic technologies-tandem mass tag mass spectrometry and SomaScan. Integration of both data types allowed for generation of a robust protein coexpression network consisting of 34 modules derived from 5242 protein measurements, including disease-relevant modules associated with autophagy, ubiquitination, endocytosis, and glycolysis. Three modules strongly associated with the apolipoprotein E ε4 (APOE ε4) AD risk genotype mapped to oxidant detoxification, mitogen-associated protein kinase signaling, neddylation, and mitochondrial biology and overlapped with a previously described lipoprotein module in serum. Alterations of all three modules in blood were associated with dementia more than 20 years before diagnosis. Analysis of CSF samples from an AD phase 2 clinical trial of atomoxetine (ATX) demonstrated that abnormal elevations in the glycolysis CSF module-the network module most strongly correlated to cognitive function-were reduced by ATX treatment. Clustering of individuals based on their CSF proteomic profiles revealed heterogeneity of pathological changes not fully reflected by Aβ and tau.
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Affiliation(s)
- Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anantharaman Shantaraman
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lingyan Ping
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Duc M Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ekaterina S Gerasimov
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Valborg Gudmundsdottir
- Icelandic Heart Association, 201 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | | | - Gabriela T Gomez
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Keenan A Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA
| | - Valur Emilsson
- Icelandic Heart Association, 201 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Daniel Western
- Department of Psychiatry, Washington University, St. Louis, MO 63108, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO 63108, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO 63108, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO 63108, USA
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Thomas S Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Aliza P Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA 30033, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
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12
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Carraro C, Montgomery JV, Klimmt J, Paquet D, Schultze JL, Beyer MD. Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs. Front Mol Neurosci 2024; 17:1414886. [PMID: 38952421 PMCID: PMC11215216 DOI: 10.3389/fnmol.2024.1414886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024] Open
Abstract
Drug discovery is a generally inefficient and capital-intensive process. For neurodegenerative diseases (NDDs), the development of novel therapeutics is particularly urgent considering the long list of late-stage drug candidate failures. Although our knowledge on the pathogenic mechanisms driving neurodegeneration is growing, additional efforts are required to achieve a better and ultimately complete understanding of the pathophysiological underpinnings of NDDs. Beyond the etiology of NDDs being heterogeneous and multifactorial, this process is further complicated by the fact that current experimental models only partially recapitulate the major phenotypes observed in humans. In such a scenario, multi-omic approaches have the potential to accelerate the identification of new or repurposed drugs against a multitude of the underlying mechanisms driving NDDs. One major advantage for the implementation of multi-omic approaches in the drug discovery process is that these overarching tools are able to disentangle disease states and model perturbations through the comprehensive characterization of distinct molecular layers (i.e., genome, transcriptome, proteome) up to a single-cell resolution. Because of recent advances increasing their affordability and scalability, the use of omics technologies to drive drug discovery is nascent, but rapidly expanding in the neuroscience field. Combined with increasingly advanced in vitro models, which particularly benefited from the introduction of human iPSCs, multi-omics are shaping a new paradigm in drug discovery for NDDs, from disease characterization to therapeutics prediction and experimental screening. In this review, we discuss examples, main advantages and open challenges in the use of multi-omic approaches for the in vitro discovery of targets and therapies against NDDs.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jessica V. Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
| | - Julien Klimmt
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
| | - Marc D. Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
- Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
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13
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Reddy JS, Heath L, Vander Linden A, Allen M, de Paiva Lopes K, Seifar F, Wang E, Ma Y, Poehlman WL, Quicksall ZS, Runnels A, Wang Y, Duong DM, Yin L, Xu K, Modeste ES, Shantaraman A, Dammer EB, Ping L, Oatman SR, Scanlan J, Ho C, Carrasquillo MM, Atik M, Yepez G, Mitchell AO, Nguyen TT, Chen X, Marquez DX, Reddy H, Xiao H, Seshadri S, Mayeux R, Prokop S, Lee EB, Serrano GE, Beach TG, Teich AF, Haroutunian V, Fox EJ, Gearing M, Wingo A, Wingo T, Lah JJ, Levey AI, Dickson DW, Barnes LL, De Jager P, Zhang B, Bennett D, Seyfried NT, Greenwood AK, Ertekin-Taner N. Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589592. [PMID: 38659743 PMCID: PMC11042309 DOI: 10.1101/2024.04.16.589592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
INTRODUCTION Multi-omics studies in Alzheimer's disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked African Americans (AA) and Latin Americans (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership in AD (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTS We generated multi-omics data and curated and harmonized phenotypic data from AA (n=306), LA (n=326), or AA and LA (n=4) brain donors plus Non-Hispanic White (n=252) and other (n=20) ethnic groups, to establish a foundational dataset enriched for AA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSION Inclusion of traditionally underrepresented groups in multi-omics studies is essential to discover the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD.
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Affiliation(s)
- Joseph S Reddy
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Laura Heath
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | | | - Mariet Allen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Fatemeh Seifar
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - Yiyi Ma
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | | | - Alexi Runnels
- New York Genome Center, 101 6th Ave, New York, NY 10013
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Duc M Duong
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Luming Yin
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Kaiming Xu
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erica S Modeste
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Eric B Dammer
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Lingyan Ping
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Jo Scanlan
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | - Charlotte Ho
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Merve Atik
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Geovanna Yepez
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Thuy T Nguyen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Xianfeng Chen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - David X Marquez
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
- University of Illinois Chicago, 1200 West Harrison St., Chicago, Illinois 60607
| | - Hasini Reddy
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Harrison Xiao
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Sudha Seshadri
- The Glen Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas, 8300 Floyd Curl Drive, San Antonio TX 78229
| | - Richard Mayeux
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | - Edward B Lee
- Center for Neurodegenerative Disease Brain Bank at the University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104-2676
| | - Geidy E Serrano
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Thomas G Beach
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Andrew F Teich
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Varham Haroutunian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
| | - Edward J Fox
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Marla Gearing
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Aliza Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Thomas Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - James J Lah
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Allan I Levey
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Dennis W Dickson
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Philip De Jager
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
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14
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Stroh A, Schweiger S, Ramirez JM, Tüscher O. The selfish network: how the brain preserves behavioral function through shifts in neuronal network state. Trends Neurosci 2024; 47:246-258. [PMID: 38485625 DOI: 10.1016/j.tins.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 04/12/2024]
Abstract
Neuronal networks possess the ability to regulate their activity states in response to disruptions. How and when neuronal networks turn from physiological into pathological states, leading to the manifestation of neuropsychiatric disorders, remains largely unknown. Here, we propose that neuronal networks intrinsically maintain network stability even at the cost of neuronal loss. Despite the new stable state being potentially maladaptive, neural networks may not reverse back to states associated with better long-term outcomes. These maladaptive states are often associated with hyperactive neurons, marking the starting point for activity-dependent neurodegeneration. Transitions between network states may occur rapidly, and in discrete steps rather than continuously, particularly in neurodegenerative disorders. The self-stabilizing, metastable, and noncontinuous characteristics of these network states can be mathematically described as attractors. Maladaptive attractors may represent a distinct pathophysiological entity that could serve as a target for new therapies and for fostering resilience.
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Affiliation(s)
- Albrecht Stroh
- Leibniz Institute for Resilience Research, Mainz, Germany; Institute of Pathophysiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
| | - Susann Schweiger
- Leibniz Institute for Resilience Research, Mainz, Germany; Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research at the Seattle Children's Research Institute, University of Washington, Seattle, USA
| | - Oliver Tüscher
- Leibniz Institute for Resilience Research, Mainz, Germany; Institute of Molecular Biology (IMB), Mainz, Germany; Department of Psychiatry and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
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15
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Guo Q, Ping L, Dammer EB, Yin L, Xu K, Shantaraman A, Fox EJ, Golde TE, Johnson ECB, Roberts BR, Lah JJ, Levey AI, Seyfried NT. Heparin-enriched plasma proteome is significantly altered in Alzheimer's Disease. RESEARCH SQUARE 2024:rs.3.rs-3933136. [PMID: 38464223 PMCID: PMC10925398 DOI: 10.21203/rs.3.rs-3933136/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Introduction Heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to β-amyloid (Aβ) and tau pathology in Alzheimer's disease (AD) brain and cerebrospinal fluid (CSF). However, it remains challenging to detect these proteins in plasma using standard mass spectrometry-based proteomic approaches. Methods We employed heparin affinity chromatography, followed by off-line fractionation and tandem mass tag mass spectrometry (TMT-MS), to capture and enrich HBPs in plasma obtained from AD (n=62) and control (n=47) samples. These profiles were then correlated to a consensus AD brain proteome, as well as with Aβ, tau and phosphorylated tau (pTau) CSF biomarkers from the same individuals. We then leveraged published human postmortem brain proteome datasets to assess the overlap with the heparin-enriched plasma proteome. Results Heparin-enrichment from plasma was highly reproducible, enriched well-known HBPs like APOE and thrombin, and depleted high-abundance proteins such as albumin. A total of 2865 proteins, spanning 10 orders of magnitude were detectable. Utilizing a consensus AD brain protein co-expression network, we observed that specific plasma HBPs exhibited consistent direction of change in both brain and plasma, whereas others displayed divergent changes highlighting the complex interplay between the two compartments. Elevated HBPs in AD plasma, when compared to controls, included members of the matrisome module in brain that accumulate within Aβ deposits, such as SMOC1, SMOC2, SPON1, MDK, OLFML3, FRZB, GPNMB, and APOE. Additionally, heparin enriched plasma proteins demonstrated significant correlations with conventional AD CSF biomarkers, including Aβ, total tau, pTau, and plasma pTau from the same individuals. Conclusion These findings support the utility of a heparin-affinity approach for enriching amyloid-associated proteins, as well as a wide spectrum of plasma biomarkers that reflect pathological changes in the AD brain.
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Affiliation(s)
- Qi Guo
- Emory University School of Medicine
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16
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Cruchaga C, Ali M, Shen Y, Do A, Wang L, Western D, Liu M, Beric A, Budde J, Gentsch J, Schindler S, Morris J, Holtzman D, Fernández M, Ruiz A, Alvarez I, Aguilar M, Pastor P, Rutledge J, Oh H, Wilson E, Le Guen Y, Khalid R, Robins C, Pulford D, Ibanez L, Wyss-Coray T, Ju Sung Y. Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures for asymptomatic and symptomatic Alzheimer's disease. RESEARCH SQUARE 2024:rs.3.rs-3631708. [PMID: 38410465 PMCID: PMC10896368 DOI: 10.21203/rs.3.rs-3631708/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Changes in Amyloid-β (A), hyperphosphorylated Tau (T) in brain and cerebrospinal fluid (CSF) precedes AD symptoms, making CSF proteome a potential avenue to understand the pathophysiology and facilitate reliable diagnostics and therapies. Using the AT framework and a three-stage study design (discovery, replication, and meta-analysis), we identified 2,173 proteins dysregulated in AD, that were further validated in a third totally independent cohort. Machine learning was implemented to create and validate highly accurate and replicable (AUC>0.90) models that predict AD biomarker positivity and clinical status. These models can also identify people that will convert to AD and those AD cases with faster progression. The associated proteins cluster in four different protein pseudo-trajectories groups spanning the AD continuum and were enrichment in specific pathways including neuronal death, apoptosis and tau phosphorylation (early stages), microglia dysregulation and endolysosomal dysfuncton(mid-stages), brain plasticity and longevity (mid-stages) and late microglia-neuron crosstalk (late stages).
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Affiliation(s)
| | | | | | - Anh Do
- Washington University School of Medicine
| | - Lihua Wang
- Washington University School of Medicine
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca MútuaTerrassa, Terrassa, Barcelona, Spain
| | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
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Chatanaka MK, Prassas I, Diamandis EP. Diagnostic and progression biomarkers in cerebrospinal fluid of Alzheimer's disease patients. BMC Med 2024; 22:60. [PMID: 38331825 PMCID: PMC10854014 DOI: 10.1186/s12916-024-03270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
In this commentary, we address a paper published by Johnson et al. by assessing the robustness of their method to discover diagnostic biomarkers in Alzheimer's disease (AD). In addition, we examine how these newly discovered and previously discovered biomarkers, can play a role in assisting patients with AD and those at risk for developing AD, with an emphasis on the translational hurdles that accompany such discoveries.
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Affiliation(s)
- Miyo K Chatanaka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ioannis Prassas
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
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18
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Gorijala P, Aslam MM, Dang LT, Xicota L, Fernandez MV, Sung YJ, Fan K, Feingold E, Surace EI, Chhatwal JP, Hom CL, Hartley SL, Hassenstab J, Perrin RJ, Mapstone M, Zaman SH, Ances BM, Kamboh MI, Lee JH, Cruchaga C. Alzheimer's polygenic risk scores are associated with cognitive phenotypes in Down syndrome. Alzheimers Dement 2024; 20:1038-1049. [PMID: 37855447 PMCID: PMC10916941 DOI: 10.1002/alz.13506] [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: 05/03/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION This study aimed to investigate the influence of the overall Alzheimer's disease (AD) genetic architecture on Down syndrome (DS) status, cognitive measures, and cerebrospinal fluid (CSF) biomarkers. METHODS AD polygenic risk scores (PRS) were tested for association with DS-related traits. RESULTS The AD risk PRS was associated with disease status in several cohorts of sporadic late- and early-onset and familial late-onset AD, but not in familial early-onset AD or DS. On the other hand, lower DS Mental Status Examination memory scores were associated with higher PRS, independent of intellectual disability and APOE (PRS including APOE, PRSAPOE , p = 2.84 × 10-4 ; PRS excluding APOE, PRSnonAPOE , p = 1.60 × 10-2 ). PRSAPOE exhibited significant associations with Aβ42, tTau, pTau, and Aβ42/40 ratio in DS. DISCUSSION These data indicate that the AD genetic architecture influences cognitive and CSF phenotypes in DS adults, supporting common pathways that influence memory decline in both traits. HIGHLIGHTS Examination of the polygenic risk of AD in DS presented here is the first of its kind. AD PRS influences memory aspects in DS individuals, independently of APOE genotype. These results point to an overlap between the genes and pathways that leads to AD and those that influence dementia and memory decline in the DS population. APOE ε4 is linked to DS cognitive decline, expanding cognitive insights in adults.
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Affiliation(s)
- Priyanka Gorijala
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
- Neurogenomics and Informatics CenterWashington University School of MedicineSt. LouisMissouriUSA
| | - M. Muaaz Aslam
- Department of Human GeneticsUniversity of PittsburghSchool of Public HealthPittsburghPennsylvaniaUSA
| | - Lam‐Ha T. Dang
- Department of EpidemiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Sergievsky CenterTaub Institute for Research on Alzheimer's Disease and the Aging Brainand Department of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - L. Xicota
- Sergievsky CenterTaub Institute for Research on Alzheimer's Disease and the Aging Brainand Department of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Maria V. Fernandez
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
- Neurogenomics and Informatics CenterWashington University School of MedicineSt. LouisMissouriUSA
| | - Yun Ju Sung
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
- Neurogenomics and Informatics CenterWashington University School of MedicineSt. LouisMissouriUSA
- Division of BiostatisticsWashington University School of MedicineSt. LouisMissouriUSA
| | - Kang‐Hsien Fan
- Department of Human GeneticsUniversity of PittsburghSchool of Public HealthPittsburghPennsylvaniaUSA
| | - Eleanor Feingold
- Department of Human GeneticsUniversity of PittsburghSchool of Public HealthPittsburghPennsylvaniaUSA
| | - Ezequiel I. Surace
- Laboratory of Neurodegenerative Diseases ‐ Institute of Neurosciences (INEU‐Fleni‐ CONICET)Buenos AiresArgentina
| | - Jasmeer P Chhatwal
- Massachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Christy L. Hom
- Dept. of Psychiatry and Human BehaviorUniversity of CaliforniaIrvine School of MedicineCaliforniaUSA
| | | | | | - Sigan L. Hartley
- Waisman Center and School of Human EcologyUniversity of Wisconsin‐ MadisonMadisonWisconsinUSA
| | - Jason Hassenstab
- Department of Neurology and Psychological & Brain SciencesWashington UniversitySt. LouisMissouriUSA
| | - Richard J. Perrin
- Hope Center for Neurologic DiseasesWashington UniversitySt. LouisMissouriUSA
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
- Department of NeurologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Mark Mapstone
- Department of NeurologyUniversity of California‐IrvineIrvineCaliforniaUSA
| | - Shahid H Zaman
- Cambridge Intellectual and Developmental Disabilities Research GroupDepartment of PsychiatryUniversity of CambridgeDouglas HouseCambridgeUK
- Cambridgeshire and Peterborough NHS Foundation TrustElizabeth HouseFulbourn HospitalFulbournCambridgeUK
| | - Beau M Ances
- Department of NeurologyWashington University School of MedicineSt. LouisMissouriUSA
| | - M. Ilyas Kamboh
- Department of Human GeneticsUniversity of PittsburghSchool of Public HealthPittsburghPennsylvaniaUSA
| | - Joseph H Lee
- Department of EpidemiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Sergievsky CenterTaub Institute for Research on Alzheimer's Disease and the Aging Brainand Department of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Carlos Cruchaga
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
- Neurogenomics and Informatics CenterWashington University School of MedicineSt. LouisMissouriUSA
- Hope Center for Neurologic DiseasesWashington UniversitySt. LouisMissouriUSA
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Hobson R, Levy SH, Flaherty D, Xiao H, Ciener B, Reddy H, Singal C, Kim CY, Teich AF, Shneider NA, Bradshaw EM, Elyaman W. Clonal CD8 T Cells Accumulate in the Leptomeninges and Communicate with Microglia in Human Neurodegeneration. RESEARCH SQUARE 2024:rs.3.rs-3755733. [PMID: 38343836 PMCID: PMC10854309 DOI: 10.21203/rs.3.rs-3755733/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Murine studies have highlighted a crucial role for immune cells in the meninges in surveilling the central nervous system (CNS) and influencing neuroinflammation. However, how meningeal immunity is altered in human neurodegeneration and its effects on CNS inflammation is understudied. We performed the first single-cell analysis of the transcriptomes and T cell receptor (TCR) repertoire of 104,635 immune cells from 55 postmortem human brain and leptomeningeal tissues from donors with neurodegenerative diseases including amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease. RNA and TCR sequencing from paired leptomeninges and brain allowed us to perform lineage tracing to identify the spatial trajectory of clonal T cells in the CNS and its borders. We propose that T cells activated in the brain emigrate to and establish residency in the leptomeninges where they likely contribute to impairments in lymphatic drainage and remotely to CNS inflammation by producing IFNγ and other cytokines. We identified regulatory networks local to the meninges including NK cell-mediated CD8 T cell killing which likely help to control meningeal inflammation. Collectively, these findings provide not only a foundation for future studies into brain border immune surveillance but also highlight important intercellular dynamics that could be leveraged to modulate neuroinflammation.
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Affiliation(s)
- Ryan Hobson
- Division of Translational Neurobiology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Samuel H.S. Levy
- Division of Translational Neurobiology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Delaney Flaherty
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Harrison Xiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Benjamin Ciener
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Hasini Reddy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Chitra Singal
- Division of Translational Neurobiology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Christine Y. Kim
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Andrew F. Teich
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Neil A. Shneider
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Eleanor and Lou Gehrig ALS Center, Columbia University Irving Medical Center, New York, 10032, USA
- The Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, 10032, USA
| | - Elizabeth M. Bradshaw
- Division of Translational Neurobiology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Carol and Gene Ludwig Center for Research on Neurodegeneration, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Wassim Elyaman
- Division of Translational Neurobiology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, 10032, USA
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Bhalala OG, Watson R, Yassi N. Multi-Omic Blood Biomarkers as Dynamic Risk Predictors in Late-Onset Alzheimer's Disease. Int J Mol Sci 2024; 25:1231. [PMID: 38279230 PMCID: PMC10816901 DOI: 10.3390/ijms25021231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Late-onset Alzheimer's disease is the leading cause of dementia worldwide, accounting for a growing burden of morbidity and mortality. Diagnosing Alzheimer's disease before symptoms are established is clinically challenging, but would provide therapeutic windows for disease-modifying interventions. Blood biomarkers, including genetics, proteins and metabolites, are emerging as powerful predictors of Alzheimer's disease at various timepoints within the disease course, including at the preclinical stage. In this review, we discuss recent advances in such blood biomarkers for determining disease risk. We highlight how leveraging polygenic risk scores, based on genome-wide association studies, can help stratify individuals along their risk profile. We summarize studies analyzing protein biomarkers, as well as report on recent proteomic- and metabolomic-based prediction models. Finally, we discuss how a combination of multi-omic blood biomarkers can potentially be used in memory clinics for diagnosis and to assess the dynamic risk an individual has for developing Alzheimer's disease dementia.
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Affiliation(s)
- Oneil G. Bhalala
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia; (R.W.); (N.Y.)
- Department of Neurology, Melbourne Brain Centre at The Royal Melbourne Hospital, University of Melbourne, Parkville 3050, Australia
| | - Rosie Watson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia; (R.W.); (N.Y.)
- Department of Medicine, The Royal Melbourne Hospital, University of Melbourne, Parkville 3050, Australia
| | - Nawaf Yassi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia; (R.W.); (N.Y.)
- Department of Neurology, Melbourne Brain Centre at The Royal Melbourne Hospital, University of Melbourne, Parkville 3050, Australia
- Department of Medicine, The Royal Melbourne Hospital, University of Melbourne, Parkville 3050, Australia
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Shen Y, Ali M, Timsina J, Wang C, Do A, Western D, Liu M, Gorijala P, Budde J, Liu H, Gordon B, McDade E, Morris JC, Llibre-Guerra JJ, Bateman RJ, Joseph-Mathurin N, Perrin RJ, Maschi D, Wyss-Coray T, Pastor P, Goate A, Renton AE, Surace EI, Johnson ECB, Levey AI, Alvarez I, Levin J, Ringman JM, Allegri RF, Seyfried N, Day GS, Wu Q, Fernández MV, Ibanez L, Sung YJ, Cruchaga C. Systematic proteomics in Autosomal dominant Alzheimer's disease reveals decades-early changes of CSF proteins in neuronal death, and immune pathways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.12.24301242. [PMID: 38260583 PMCID: PMC10802763 DOI: 10.1101/2024.01.12.24301242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background To date, there is no high throughput proteomic study in the context of Autosomal Dominant Alzheimer's disease (ADAD). Here, we aimed to characterize early CSF proteome changes in ADAD and leverage them as potential biomarkers for disease monitoring and therapeutic strategies. Methods We utilized Somascan® 7K assay to quantify protein levels in the CSF from 291 mutation carriers (MCs) and 185 non-carriers (NCs). We employed a multi-layer regression model to identify proteins with different pseudo-trajectories between MCs and NCs. We replicated the results using publicly available ADAD datasets as well as proteomic data from sporadic Alzheimer's disease (sAD). To biologically contextualize the results, we performed network and pathway enrichment analyses. Machine learning was applied to create and validate predictive models. Findings We identified 125 proteins with significantly different pseudo-trajectories between MCs and NCs. Twelve proteins showed changes even before the traditional AD biomarkers (Aβ42, tau, ptau). These 125 proteins belong to three different modules that are associated with age at onset: 1) early stage module associated with stress response, glutamate metabolism, and mitochondria damage; 2) the middle stage module, enriched in neuronal death and apoptosis; and 3) the presymptomatic stage module was characterized by changes in microglia, and cell-to-cell communication processes, indicating an attempt of rebuilding and establishing new connections to maintain functionality. Machine learning identified a subset of nine proteins that can differentiate MCs from NCs better than traditional AD biomarkers (AUC>0.89). Interpretation Our findings comprehensively described early proteomic changes associated with ADAD and captured specific biological processes that happen in the early phases of the disease, fifteen to five years before clinical onset. We identified a small subset of proteins with the potentials to become therapy-monitoring biomarkers of ADAD MCs. Funding Proteomic data generation was supported by NIH: RF1AG044546.
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22
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Levites Y, Dammer EB, Ran Y, Tsering W, Duong D, Abreha M, Gadhavi J, Lolo K, Trejo-Lopez J, Phillips JL, Iturbe A, Erqiuzi A, Moore BD, Ryu D, Natu A, Dillon KD, Torrellas J, Moran C, Ladd TB, Afroz KF, Islam T, Jagirdar J, Funk CC, Robinson M, Borchelt DR, Ertekin-Taner N, Kelly JW, Heppner FL, Johnson EC, McFarland K, Levey AL, Prokop S, Seyfried NT, Golde TE. Aβ Amyloid Scaffolds the Accumulation of Matrisome and Additional Proteins in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.568318. [PMID: 38076912 PMCID: PMC10705437 DOI: 10.1101/2023.11.29.568318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
We report a highly significant correlation in brain proteome changes between Alzheimers disease (AD) and CRND8 APP695NL/F transgenic mice. However, integrating protein changes observed in the CRND8 mice with co-expression networks derived from human AD, reveals both conserved and divergent module changes. For the most highly conserved module (M42, matrisome) we find many proteins accumulate in plaques, cerebrovascular amyloid (CAA), dystrophic processes, or a combination thereof. Overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), in CRND8 mice brains leads to increased accumulation of A β ; in plaques and in CAA; further, recombinant MDK and PTN enhance A β ; aggregation into amyloid. Multiple M42 proteins, annotated as heparan sulfate binding proteins, bind to fibrillar A β 42 and a non-human amyloid fibril in vitro. Supporting this binding data, MDK and PTN co-accumulate with transthyretin (TTR) amyloid in the heart and islet amyloid polypeptide (IAPP) amyloid in the pancreas. Our findings establish several critical insights. Proteomic changes in modules observed in human AD brains define an A β ; amyloid responsome that is well conserved from mouse model to human. Further, distinct amyloid structures may serve as scaffolds, facilitating the co-accumulation of proteins with signaling functions. We hypothesize that this co-accumulation may contribute to downstream pathological sequalae. Overall, this contextualized understanding of proteomic changes and their interplay with amyloid deposition provides valuable insights into the complexity of AD pathogenesis and potential biomarkers and therapeutic targets.
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23
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Dammer EB, Shantaraman A, Ping L, Duong DM, Gerasimov ES, Ravindran SP, Gudmundsdottir V, Frick EA, Gomez GT, Walker KA, Emilsson V, Jennings LL, Gudnason V, Western D, Cruchaga C, Lah JJ, Wingo TS, Wingo AP, Seyfried NT, Levey AI, Johnson EC. Proteomic Network Analysis of Alzheimer's Disease Cerebrospinal Fluid Reveals Alterations Associated with APOE ε4 Genotype and Atomoxetine Treatment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.29.23297651. [PMID: 37961720 PMCID: PMC10635242 DOI: 10.1101/2023.10.29.23297651] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Alzheimer's disease (AD) is currently defined at the research level by the aggregation of amyloid-β (Aβ) and tau proteins in brain. While biofluid biomarkers are available to measure Aβ and tau pathology, few biomarkers are available to measure the complex pathophysiology that is associated with these two cardinal neuropathologies. Here we describe the proteomic landscape of cerebrospinal fluid (CSF) changes associated with Aβ and tau pathology in 300 individuals as assessed by two different proteomic technologies-tandem mass tag (TMT) mass spectrometry and SomaScan. Harmonization and integration of both data types allowed for generation of a robust protein co-expression network consisting of 34 modules derived from 5242 protein measurements, including disease-relevant modules associated with autophagy, ubiquitination, endocytosis, and glycolysis. Three modules strongly associated with the apolipoprotein E ε4 (APOE ε4) AD risk genotype mapped to oxidant detoxification, mitogen associated protein kinase (MAPK) signaling, neddylation, and mitochondrial biology, and overlapped with a previously described lipoprotein module in serum. Neddylation and oxidant detoxification/MAPK signaling modules had a negative association with APOE ε4 whereas the mitochondrion module had a positive association with APOE ε4. The directions of association were consistent between CSF and blood in two independent longitudinal cohorts, and altered levels of all three modules in blood were associated with dementia over 20 years prior to diagnosis. Dual-proteomic platform analysis of CSF samples from an AD phase 2 clinical trial of atomoxetine (ATX) demonstrated that abnormal elevations in the glycolysis CSF module-the network module most strongly correlated to cognitive function-were reduced by ATX treatment. Individuals who had more severe glycolytic changes at baseline responded better to ATX. Clustering of individuals based on their CSF proteomic network profiles revealed ten groups that did not cleanly stratify by Aβ and tau status, underscoring the heterogeneity of pathological changes not fully reflected by Aβ and tau. AD biofluid proteomics holds promise for the development of biomarkers that reflect diverse pathologies for use in clinical trials and precision medicine.
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Affiliation(s)
- Eric B. Dammer
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Anantharaman Shantaraman
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lingyan Ping
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M. Duong
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Valborg Gudmundsdottir
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Gabriela T. Gomez
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Keenan A. Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Valur Emilsson
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daniel Western
- Department of Psychiatry, Washington University, St. Louis, MO, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, USA
| | - James J. Lah
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas S. Wingo
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Aliza P. Wingo
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
- Division of Mental Health, Atlanta VA Medical Center, GA, USA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I. Levey
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C.B. Johnson
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
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Hobson R, Levy SHS, Flaherty D, Xiao H, Ciener B, Reddy H, Singal C, Teich AF, Shneider NA, Bradshaw EM, Elyaman W. Clonal CD8 T cells in the leptomeninges are locally controlled and influence microglia in human neurodegeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548931. [PMID: 37503131 PMCID: PMC10369982 DOI: 10.1101/2023.07.13.548931] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Recent murine studies have highlighted a crucial role for the meninges in surveilling the central nervous system (CNS) and influencing CNS inflammation. However, how meningeal immunity is altered in human neurodegeneration and its potential effects on neuroinflammation is understudied. In the present study, we performed single-cell analysis of the transcriptomes and T cell receptor repertoire of 72,576 immune cells from 36 postmortem human brain and leptomeninges tissues from donors with neurodegenerative diseases including amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease. We identified the meninges as an important site of antigen presentation and CD8 T cell activation and clonal expansion and found that T cell activation in the meninges is a requirement for infiltration into the CNS. We further found that natural killer cells have the potential to negatively regulate T cell activation locally in the meninges through direct killing and are one of many regulatory mechanisms that work to control excessive neuroinflammation.
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