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Melnik M, Miyoshi E, Ma R, Corrada M, Kawas C, Bohannan R, Caraway C, Miller CA, Hinman JD, John V, Bilousova T, Gylys KH. Simultaneous isolation of intact brain cells and cell-specific extracellular vesicles from cryopreserved Alzheimer's disease cortex. J Neurosci Methods 2024; 406:110137. [PMID: 38626853 DOI: 10.1016/j.jneumeth.2024.110137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND The neuronal and gliaI populations within the brain are tightly interwoven, making isolation and study of large populations of a single cell type from brain tissue a major technical challenge. Concurrently, cell-type specific extracellular vesicles (EVs) hold enormous diagnostic and therapeutic potential in neurodegenerative disorders including Alzheimer's disease (AD). NEW METHOD Postmortem AD cortical samples were thawed and gently dissociated. Following filtration, myelin and red blood cell removal, cell pellets were immunolabeled with fluorescent antibodies and analyzed by flow cytometry. The cell pellet supernatant was applied to a triple sucrose cushion for brain EV isolation. RESULTS Neuronal, astrocyte and microglial cell populations were identified. Cell integrity was demonstrated using calcein AM, which is retained by cells with esterase activity and an intact membrane. For some experiments cell pellets were fixed, permeabilized, and immunolabeled for cell-specific markers. Characterization of brain small EV fractions showed the expected size, depletion of EV negative markers, and enrichment in positive and cell-type specific markers. COMPARISON WITH EXISTING METHODS AND CONCLUSIONS We optimized and integrated established protocols, aiming to maximize information obtained from each human autopsy brain sample. The uniqueness of our method lies in its capability to isolate cells and EVs from a single cryopreserved brain sample. Our results not only demonstrate the feasibility of isolating specific brain cell subpopulations for RNA-seq but also validate these subpopulations at the protein level. The accelerated study of EVs from human samples is crucial for a better understanding of their contribution to neuron/glial crosstalk and disease progression.
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Affiliation(s)
- Mikhail Melnik
- UCLA School of Nursing, Los Angeles, CA 90095, USA; Neuroscience Interdepartmental Program, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | | | - Ricky Ma
- UCLA School of Nursing, Los Angeles, CA 90095, USA
| | - Maria Corrada
- Departments of Neurology, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Claudia Kawas
- Departments of Neurology, Irvine, CA 92697, USA; Neurobiology & Behavior, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Ryan Bohannan
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Chad Caraway
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | | | - Jason D Hinman
- Mary S. Easton Center for Alzheimer's Research at UCLA, Los Angeles, CA 90073, USA; Departments of Neurology, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | - Varghese John
- Mary S. Easton Center for Alzheimer's Research at UCLA, Los Angeles, CA 90073, USA; Departments of Neurology, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | - Tina Bilousova
- UCLA School of Nursing, Los Angeles, CA 90095, USA; Mary S. Easton Center for Alzheimer's Research at UCLA, Los Angeles, CA 90073, USA; Departments of Neurology, UCLA School of Medicine, Los Angeles, CA 90095, USA.
| | - Karen H Gylys
- UCLA School of Nursing, Los Angeles, CA 90095, USA; Mary S. Easton Center for Alzheimer's Research at UCLA, Los Angeles, CA 90073, USA; Neuroscience Interdepartmental Program, UCLA School of Medicine, Los Angeles, CA 90095, USA
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Buonfiglioli A, Kübler R, Missall R, De Jong R, Chan S, Haage V, Wendt S, Lin AJ, Mattei D, Graziani M, Latour B, Gigase F, Nygaard HB, De Jager PL, De Witte LD. A microglia-containing cerebral organoid model to study early life immune challenges. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595814. [PMID: 38826204 PMCID: PMC11142229 DOI: 10.1101/2024.05.24.595814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Prenatal infections and activation of the maternal immune system have been proposed to contribute to causing neurodevelopmental disorders (NDDs), chronic conditions often linked to brain abnormalities. Microglia are the resident immune cells of the brain and play a key role in neurodevelopment. Disruption of microglial functions can lead to brain abnormalities and increase the risk of developing NDDs. How the maternal as well as the fetal immune system affect human neurodevelopment and contribute to NDDs remains unclear. An important reason for this knowledge gap is the fact that the impact of exposure to prenatal risk factors has been challenging to study in the human context. Here, we characterized a model of cerebral organoids (CO) with integrated microglia (COiMg). These organoids express typical microglial markers and respond to inflammatory stimuli. The presence of microglia influences cerebral organoid development, including cell density and neural differentiation, and regulates the expression of several ciliated mesenchymal cell markers. Moreover, COiMg and organoids without microglia show similar but also distinct responses to inflammatory stimuli. Additionally, IFN-γ induced significant transcriptional and structural changes in the cerebral organoids, that appear to be regulated by the presence of microglia. Specifically, interferon-gamma (IFN-γ) was found to alter the expression of genes linked to autism. This model provides a valuable tool to study how inflammatory perturbations and microglial presence affect neurodevelopmental processes.
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Affiliation(s)
- Alice Buonfiglioli
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Raphael Kübler
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Human Genetics, Radboud UMC, Nijmegen, The Netherlands
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Renske De Jong
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stephanie Chan
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Verena Haage
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Stefan Wendt
- Department of Psychiatry, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Ada J. Lin
- Division of Neurology, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Daniele Mattei
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mara Graziani
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Human Genetics, Radboud UMC, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Brooke Latour
- Department of Human Genetics, Radboud UMC, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Frederieke Gigase
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Haakon B. Nygaard
- Division of Neurology, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Lot D. De Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Human Genetics, Radboud UMC, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
- Department of Psychiatry, Radboud UMC, Nijmegen, The Netherlands
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3
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Cuní-López C, Stewart R, Oikari LE, Nguyen TH, Roberts TL, Sun Y, Guo CC, Lupton MK, White AR, Quek H. Advanced patient-specific microglia cell models for pre-clinical studies in Alzheimer's disease. J Neuroinflammation 2024; 21:50. [PMID: 38365833 PMCID: PMC10870454 DOI: 10.1186/s12974-024-03037-3] [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: 12/17/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is an incurable neurodegenerative disorder with a rapidly increasing prevalence worldwide. Current approaches targeting hallmark pathological features of AD have had no consistent clinical benefit. Neuroinflammation is a major contributor to neurodegeneration and hence, microglia, the brain's resident immune cells, are an attractive target for potentially more effective therapeutic strategies. However, there is no current in vitro model system that captures AD patient-specific microglial characteristics using physiologically relevant and experimentally flexible culture conditions. METHODS To address this shortcoming, we developed novel 3D Matrigel-based monocyte-derived microglia-like cell (MDMi) mono-cultures and co-cultures with neuro-glial cells (ReNcell VM). We used single-cell RNA sequencing (scRNAseq) analysis to compare the transcriptomic signatures of MDMi between model systems (2D, 3D and 3D co-culture) and against published human microglia datasets. To demonstrate the potential of MDMi for use in personalized pre-clinical strategies, we generated and characterized MDMi models from sixteen AD patients and matched healthy controls, and profiled cytokine responses upon treatment with anti-inflammatory drugs (dasatinib and spiperone). RESULTS MDMi in 3D exhibited a more branched morphology and longer survival in culture compared to 2D. scRNAseq uncovered distinct MDMi subpopulations that exhibit higher functional heterogeneity and best resemble human microglia in 3D co-culture. AD MDMi in 3D co-culture showed altered cell-to-cell interactions, growth factor and cytokine secretion profiles and responses to amyloid-β. Drug testing assays revealed patient- and model-specific cytokine responses. CONCLUSION Our study presents a novel, physiologically relevant and AD patient-specific 3D microglia cell model that opens avenues towards improving personalized drug development strategies in AD.
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Affiliation(s)
- Carla Cuní-López
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia
| | - Romal Stewart
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- UQ Centre for Clinical Research, The University of Queensland, Brisbane City, QLD, 4029, Australia
| | - Lotta E Oikari
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane City, QLD, 4000, Australia
| | - Tam Hong Nguyen
- Scientific Services, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Tara L Roberts
- UQ Centre for Clinical Research, The University of Queensland, Brisbane City, QLD, 4029, Australia
- Ingham Institute for Applied Medical Research and School of Medicine, Western Sydney University, Liverpool, NSW, 2170, Australia
| | - Yifan Sun
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Christine C Guo
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- ActiGraph LLC, Pensacola, FL, 32502, USA
| | - Michelle K Lupton
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane City, QLD, 4000, Australia
| | - Anthony R White
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia.
- Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia.
| | - Hazel Quek
- Mental Health and Neuroscience Department, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia.
- School of Biomedical Sciences, The University of Queensland, Lucia, QLD, 4072, Australia.
- School of Biomedical Sciences, Queensland University of Technology, Brisbane City, QLD, 4000, Australia.
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4
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Michaud SA, Pětrošová H, Sinclair NJ, Kinnear AL, Jackson AM, McGuire JC, Hardie DB, Bhowmick P, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Smith D, Mohammed Y, Schibli D, Sickmann A, Borchers CH. Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues. Commun Biol 2024; 7:6. [PMID: 38168632 PMCID: PMC10762018 DOI: 10.1038/s42003-023-05687-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomic profiling in mice by measuring normal protein abundances in tissues from three mouse strains: C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. Sex- and strain-specific differences in protein abundances are identified and described, and the measured values are freely accessible via our MouseQuaPro database: http://mousequapro.proteincentre.com . Together, this large library of quantitative MRM-MS assays established in mice and the measured baseline protein abundances represent an important resource for research involving mouse models.
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Affiliation(s)
- Sarah A Michaud
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada.
| | - Helena Pětrošová
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Nicholas J Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Andrea L Kinnear
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Angela M Jackson
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Jamie C McGuire
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Pallab Bhowmick
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Milan Ganguly
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann M Flenniken
- The Center for Phenogenomics, Toronto, ON, Canada
- Sinai Health Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Derek Smith
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - David Schibli
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Department of Pathology, McGill University, Montreal, QC, Canada.
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5
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Fiorito AM, Fakra E, Sescousse G, Ibrahim EC, Rey R. Molecular mapping of a core transcriptional signature of microglia-specific genes in schizophrenia. Transl Psychiatry 2023; 13:386. [PMID: 38092734 PMCID: PMC10719376 DOI: 10.1038/s41398-023-02677-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Besides playing a central role in neuroinflammation, microglia regulate synaptic development and is involved in plasticity. Converging lines of evidence suggest that these different processes play a critical role in schizophrenia. Furthermore, previous studies reported altered transcription of microglia genes in schizophrenia, while microglia itself seems to be involved in the etiopathology of the disease. However, the regional specificity of these brain transcriptional abnormalities remains unclear. Moreover, it is unknown whether brain and peripheral expression of microglia genes are related. Thus, we investigated the expression of a pre-registered list of 10 genes from a core signature of human microglia both at brain and peripheral levels. We included 9 independent Gene Expression Omnibus datasets (764 samples obtained from 266 individuals with schizophrenia and 237 healthy controls) from 8 different brain regions and 3 peripheral tissues. We report evidence of a widespread transcriptional alteration of microglia genes both in brain tissues (we observed a decreased expression in the cerebellum, associative striatum, hippocampus, and parietal cortex of individuals with schizophrenia compared with healthy controls) and whole blood (characterized by a mixed altered expression pattern). Our results suggest that brain underexpression of microglia genes may represent a candidate transcriptional signature for schizophrenia. Moreover, the dual brain-whole blood transcriptional alterations of microglia/macrophage genes identified support the model of schizophrenia as a whole-body disorder and lend weight to the use of blood samples as a potential source of biological peripheral biomarkers.
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Affiliation(s)
- Anna M Fiorito
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Centre Hospitalier Le Vinatier, Bron, France
| | - Eric Fakra
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Department of Psychiatry, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Guillaume Sescousse
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Centre Hospitalier Le Vinatier, Bron, France
| | - El Chérif Ibrahim
- Aix-Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, Marseille, France
| | - Romain Rey
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France.
- Centre Hospitalier Le Vinatier, Bron, France.
- Fondation FondaMental, Créteil, France.
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6
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Chen C, Bao Y, Xing L, Jiang C, Guo Y, Tong S, Zhang J, Chen L, Mao Y. Exosomes Derived from M2 Microglial Cells Modulated by 1070-nm Light Improve Cognition in an Alzheimer's Disease Mouse Model. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304025. [PMID: 37702115 PMCID: PMC10646245 DOI: 10.1002/advs.202304025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Indexed: 09/14/2023]
Abstract
Near-infrared photobiomodulation has been identified as a potential strategy for Alzheimer's disease (AD). However, the mechanisms underlying this therapeutic effect remain poorly characterize. Herein, it is illustrate that 1070-nm light induces the morphological alteration of microglia from an M1 to M2 phenotype that secretes exosomes, which alleviates the β-amyloid burden to improve cognitive function by ameliorating neuroinflammation and promoting neuronal dendritic spine plasticity. The results show that 4 J cm-2 1070-nm light at a 10-Hz frequency prompts microglia with an M1 inflammatory type to switch to an M2 anti-inflammatory type. This induces secretion of M2 microglial-derived exosomes containing miR-7670-3p, which targets activating transcription factor 6 (ATF6) during endoplasmic reticulum (ER) stress. Moreover, it is found that miR-7670-3p reduces ATF6 expression to further ameliorate ER stress, thus attenuating the inflammatory response and protecting dendritic spine integrity of neurons in the cortex and hippocampus of 5xFAD mice, ultimately leading to improvements in cognitive function. This study highlights the critical role of exosomes derive from 1070-nm light-modulated microglia in treating AD mice, which may provide a theoretical basis for the treatment of AD with the use of near-infrared photobiomodulation.
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Affiliation(s)
- Chengwei Chen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghai200040China
- National Center for Neurological DisordersShanghai200040China
- Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghai200040China
- Neurosurgical Institute of Fudan UniversityShanghai200040China
- Shanghai Clinical Medical Center of NeurosurgeryShanghai200040China
| | - Yuting Bao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghai200040China
- National Center for Neurological DisordersShanghai200040China
- Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghai200040China
- Neurosurgical Institute of Fudan UniversityShanghai200040China
- Shanghai Clinical Medical Center of NeurosurgeryShanghai200040China
| | - Lu Xing
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghai200040China
- National Center for Neurological DisordersShanghai200040China
- Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghai200040China
- Neurosurgical Institute of Fudan UniversityShanghai200040China
- Shanghai Clinical Medical Center of NeurosurgeryShanghai200040China
| | - Chengyong Jiang
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain ScienceFudan UniversityShanghai200032China
| | - Yu Guo
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghai200040China
- National Center for Neurological DisordersShanghai200040China
- Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghai200040China
- Neurosurgical Institute of Fudan UniversityShanghai200040China
- Shanghai Clinical Medical Center of NeurosurgeryShanghai200040China
| | - Shuangmei Tong
- Department of Pharmacy, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghai200040China
| | - Jiayi Zhang
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain ScienceFudan UniversityShanghai200032China
| | - Liang Chen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghai200040China
- National Center for Neurological DisordersShanghai200040China
- Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghai200040China
- Neurosurgical Institute of Fudan UniversityShanghai200040China
- Shanghai Clinical Medical Center of NeurosurgeryShanghai200040China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghai200040China
- National Center for Neurological DisordersShanghai200040China
- Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghai200040China
- Neurosurgical Institute of Fudan UniversityShanghai200040China
- Shanghai Clinical Medical Center of NeurosurgeryShanghai200040China
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7
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Patir A, Raper A, Fleming R, Henderson BEP, Murphy L, Henderson NC, Clark EL, Freeman TC, Barnett MW. Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis. G3 (BETHESDA, MD.) 2023; 13:jkad178. [PMID: 37548242 PMCID: PMC10542211 DOI: 10.1093/g3journal/jkad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 06/30/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well-established insect models for studying learning and memory, behavior, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination, and eusociality. Despite their importance to agriculture, knowledge of honey bee biology lags behind many other livestock species. In this study, we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15) and sought to determine their gene expression signatures. To identify cell-type populations, we examined the cell-to-cell network based on the similarity of the single-cells transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 17 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene coexpression analysis. We combined this analysis with literature mining, the honey bee protein atlas, and gene ontology analysis to determine cell cluster identity. Of the cell clusters identified, 17 were related to the nervous system and sensory organs, 7 to the fat body, 19 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes, and 1 to malpighian tubule/pericardial nephrocyte. To our knowledge, this is the first whole single-cell atlas of honey bees at any stage of development and demonstrates the potential for further work to investigate their biology at the cellular level.
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Affiliation(s)
- Anirudh Patir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Anna Raper
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Robert Fleming
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Beth E P Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neil C Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
- Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh,Edinburgh EH4 2XU, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tom C Freeman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Mark W Barnett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
- Beebytes Analytics CIC, The Roslin Innovation Centre, University of Edinburgh, The Charnock Bradley Building, Easter Bush, Midlothian EH25 9RG, UK
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8
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Kübler R, Ormel PR, Sommer IEC, Kahn RS, de Witte LD. Gene expression profiling of monocytes in recent-onset schizophrenia. Brain Behav Immun 2023; 111:334-342. [PMID: 37149105 DOI: 10.1016/j.bbi.2023.04.019] [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: 08/04/2022] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023] Open
Abstract
Immune-related mechanisms have been suggested to be involved in schizophrenia. Various studies have shown changes in monocytes isolated from the blood of schizophrenia patients, including changes in monocyte numbers, as well as altered protein and transcript levels of important markers. However, validation of these findings and understanding how these results are related to immune-related changes in the brain and schizophrenia genetic risk factors, is limited. The goal of this study was to better understand changes observed in monocytes of patients with early-onset schizophrenia. Using RNA sequencing, we analyzed gene expression profiles of monocytes isolated from twenty patients with early-onset schizophrenia and seventeen healthy controls. We validated expression changes of 7 out of 29 genes that were differentially expressed in previous studies including TNFAIP3, DUSP2, and IL6. At a transcriptome-wide level, we found 99 differentially expressed genes. Effect sizes of differentially expressed genes were moderately correlated with differential expression in brain tissue (Pearson's r = 0.49). Upregulated genes were enriched for genes in NF-κB and LPS signaling pathways. Downregulated genes were enriched for glucocorticoid response pathways. These pathways have been implicated in schizophrenia before and play a role in regulating the activation of myeloid cells. Interestingly, they are also involved in several non-inflammatory processes in the central nervous system, such as neurogenesis and neurotransmission. Future studies are needed to better understand how dysregulation of the NF-κB and glucocorticoid pathways affects inflammatory and non-inflammatory processes in schizophrenia. The fact that dysregulation of these pathways is also seen in brain tissue, provides potential possibilities for biomarker development.
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Affiliation(s)
- Raphael Kübler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul R Ormel
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Iris E C Sommer
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; Department of Neuroscience, University Medical Center Groningen, Groningen, the Netherlands
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands.
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9
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Dorion MF, Yaqubi M, Murdoch HJ, Hall JA, Dudley R, Antel JP, Durcan TM, Healy LM. Systematic comparison of culture media uncovers phenotypic shift of primary human microglia defined by reduced reliance to CSF1R signaling. Glia 2023; 71:1278-1293. [PMID: 36680780 DOI: 10.1002/glia.24338] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/17/2022] [Accepted: 01/02/2023] [Indexed: 01/22/2023]
Abstract
Efforts to understand microglia function in health and diseases have been hindered by the lack of culture models that recapitulate in situ cellular properties. In recent years, the use of serum-free media with brain-derived growth factors (colony stimulating factor 1 receptor [CSF1R] ligands and TGF-β1/2) have been favored for the maintenance of rodent microglia as they promote morphological features observed in situ. Here we study the functional and transcriptomic impacts of such media on human microglia (hMGL). Media formulation had little impact on microglia transcriptome assessed by RNA sequencing which was sufficient to significantly alter microglia capacity to phagocytose myelin debris and to elicit an inflammatory response to lipopolysaccharide. When compared to immediately ex vivo microglia from the same donors, the addition of fetal bovine serum to culture media, but not growth factors, was found to aid in the maintenance of key signature genes including those involved in phagocytic processes. A phenotypic shift characterized by CSF1R downregulation in culture correlated with a lack of reliance on CSF1R signaling for survival. Consequently, no improvement in cell survival was observed following culture supplementation with CSF1R ligands. Our study provides better understanding of hMGL in culture, with observations that diverge from those previously made in rodent microglia.
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Affiliation(s)
- Marie-France Dorion
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Moein Yaqubi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Hunter J Murdoch
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Jeffery A Hall
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Roy Dudley
- Department of Pediatric Neurosurgery, Montreal Children's Hospital, Montreal, Canada
| | - Jack P Antel
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Thomas Martin Durcan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Luke Michael Healy
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
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10
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Saura CA, Deprada A, Capilla-López MD, Parra-Damas A. Revealing cell vulnerability in Alzheimer's disease by single-cell transcriptomics. Semin Cell Dev Biol 2023; 139:73-83. [PMID: 35623983 DOI: 10.1016/j.semcdb.2022.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that by affecting specific brain cell types and regions cause severe pathological and functional changes in memory neural circuits. A comprehensive knowledge of the pathogenic mechanisms underlying AD requires a deeper understanding of the cell-specific pathological responses through integrative molecular analyses. Recent application of high-throughput single-cell transcriptomics to postmortem tissue has proved powerful to unravel cell susceptibility and biological networks responding to amyloid and tau pathologies. Here, we review single-cell transcriptomic studies successfully applied to decipher cell-specific gene expression programs and pathways in the brain of AD patients. Transcriptional information reveals both specific and common gene signatures affecting the major cerebral cell types, including astrocytes, endothelial cells, microglia, neurons, and oligodendrocytes. Cell type-specific transcriptomes associated with AD pathology and clinical symptoms are related to common biological networks affecting, among others pathways, synaptic function, inflammation, proteostasis, cell death, oxidative stress, and myelination. The general picture that emerges from systems-level single-cell transcriptomics is a spatiotemporal pattern of cell diversity and biological pathways, and novel cell subpopulations affected in AD brain. We argue that broader implementation of cell transcriptomics in larger AD human cohorts using standardized protocols is fundamental for reliable assessment of temporal and regional cell-type gene profiling. The possibility of applying this methodology for personalized medicine in clinics is still challenging but opens new roads for future diagnosis and treatment in dementia.
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Affiliation(s)
- Carlos A Saura
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain.
| | - Angel Deprada
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Maria Dolores Capilla-López
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Arnaldo Parra-Damas
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain
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11
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Anderson AG, Rogers BB, Loupe JM, Rodriguez-Nunez I, Roberts SC, White LM, Brazell JN, Bunney WE, Bunney BG, Watson SJ, Cochran JN, Myers RM, Rizzardi LF. Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer's disease-specific cis-regulatory elements. CELL GENOMICS 2023; 3:100263. [PMID: 36950385 PMCID: PMC10025452 DOI: 10.1016/j.xgen.2023.100263] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/06/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer's disease (AD) and unaffected controls have been well documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq plus snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell type-specific transposase accessible regions enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as candidate transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglia links were globally enriched for heritability of AD risk and previously identified active regulatory regions.
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Affiliation(s)
| | - Brianne B. Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jacob M. Loupe
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Lauren M. White
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - William E. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Blynn G. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stanley J. Watson
- Mental Health Research Institute, University of Michigan, Ann Arbor, MI, USA
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12
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Chadarevian JP, Lombroso SI, Peet GC, Hasselmann J, Tu C, Marzan DE, Capocchi J, Purnell FS, Nemec KM, Lahian A, Escobar A, England W, Chaluvadi S, O'Brien CA, Yaqoob F, Aisenberg WH, Porras-Paniagua M, Bennett ML, Davtyan H, Spitale RC, Blurton-Jones M, Bennett FC. Engineering an inhibitor-resistant human CSF1R variant for microglia replacement. J Exp Med 2023; 220:e20220857. [PMID: 36584406 DOI: 10.1084/jem.20220857] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 11/11/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) can replace endogenous microglia with circulation-derived macrophages but has high mortality. To mitigate the risks of HSCT and expand the potential for microglia replacement, we engineered an inhibitor-resistant CSF1R that enables robust microglia replacement. A glycine to alanine substitution at position 795 of human CSF1R (G795A) confers resistance to multiple CSF1R inhibitors, including PLX3397 and PLX5622. Biochemical and cell-based assays show no discernable gain or loss of function. G795A- but not wildtype-CSF1R expressing macrophages efficiently engraft the brain of PLX3397-treated mice and persist after cessation of inhibitor treatment. To gauge translational potential, we CRISPR engineered human-induced pluripotent stem cell-derived microglia (iMG) to express G795A. Xenotransplantation studies demonstrate that G795A-iMG exhibit nearly identical gene expression to wildtype iMG, respond to inflammatory stimuli, and progressively expand in the presence of PLX3397, replacing endogenous microglia to fully occupy the brain. In sum, we engineered a human CSF1R variant that enables nontoxic, cell type, and tissue-specific replacement of microglia.
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Affiliation(s)
- Jean Paul Chadarevian
- Department of Neurobiology & Behavior, University of California, Irvine , Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine , Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine , Irvine, CA, USA
| | - Sonia I Lombroso
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
- Pharmacology Graduate Group, Biomedical Graduate Studies Program, University of Pennsylvania , Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania , Philadelphia, PA, USA
| | - Graham C Peet
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
- Neuroscience Graduate Program and Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus , Aurora, CO, USA
| | - Jonathan Hasselmann
- Department of Neurobiology & Behavior, University of California, Irvine , Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine , Irvine, CA, USA
| | - Christina Tu
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine , Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine , Irvine, CA, USA
| | - Dave E Marzan
- Department of Biology, The College of New Jersey , Ewing, NJ, USA
| | - Joia Capocchi
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine , Irvine, CA, USA
| | - Freddy S Purnell
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
| | - Kelsey M Nemec
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
- Department of Neuroscience, Perelman School of Medicine , Philadelphia, PA, USA
| | - Alina Lahian
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine , Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine , Irvine, CA, USA
| | - Adrian Escobar
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine , Irvine, CA, USA
| | - Whitney England
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, CA, USA
| | - Sai Chaluvadi
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
- Department of Neuroscience, Perelman School of Medicine , Philadelphia, PA, USA
| | - Carleigh A O'Brien
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
| | - Fazeela Yaqoob
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
| | - William H Aisenberg
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
| | | | - Mariko L Bennett
- Department of Neuroscience, Perelman School of Medicine , Philadelphia, PA, USA
- Division of Neurology, Children's Hospital of Philadelphia , Philadelphia, PA, USA
| | - Hayk Davtyan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine , Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine , Irvine, CA, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, CA, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, University of California, Irvine , Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine , Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine , Irvine, CA, USA
| | - F Chris Bennett
- Department of Psychiatry, Perelman School of Medicine , University of Pennsylvania, Philadelphia, PA, USA
- Division of Neurology, Children's Hospital of Philadelphia , Philadelphia, PA, USA
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13
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Shih BB, Brown SM, Barrington J, Lefevre L, Mabbott NA, Priller J, Thompson G, Lawrence AB, McColl BW. Defining the pig microglial transcriptome reveals its core signature, regional heterogeneity, and similarity with human and rodent microglia. Glia 2023; 71:334-349. [PMID: 36120803 PMCID: PMC10087207 DOI: 10.1002/glia.24274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022]
Abstract
Microglia play key roles in brain homeostasis as well as responses to neurodegeneration and neuroinflammatory processes caused by physical disease and psychosocial stress. The pig is a physiologically relevant model species for studying human neurological disorders, many of which are associated with microglial dysfunction. Furthermore, pigs are an important agricultural species, and there is a need to understand how microglial function affects their welfare. As a basis for improved understanding to enhance biomedical and agricultural research, we sought to characterize pig microglial identity at genome-wide scale and conduct inter-species comparisons. We isolated pig hippocampal tissue and microglia from frontal cortex, hippocampus, and cerebellum, as well as alveolar macrophages from the lungs and conducted RNA-sequencing (RNAseq). By comparing the transcriptomic profiles between microglia, macrophages, and hippocampal tissue, we derived a set of 239 highly enriched genes defining the porcine core microglial signature. We found brain regional heterogeneity based on 150 genes showing significant (adjusted p < 0.01) regional variations and that cerebellar microglia were most distinct. We compared normalized gene expression for microglia from human, mice and pigs using microglia signature gene lists derived from each species and demonstrated that a core microglial marker gene signature is conserved across species, but that species-specific expression subsets also exist. Our data provide a valuable resource defining the pig microglial transcriptome signature that validates and highlights pigs as a useful large animal species bridging between rodents and humans in which to study the role of microglia during homeostasis and disease.
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Affiliation(s)
- Barbara B Shih
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Sarah M Brown
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Jack Barrington
- UK Dementia Research Institute, The University of Edinburgh, Edinburgh Medical School, The Chancellor's Building, Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Lucas Lefevre
- UK Dementia Research Institute, The University of Edinburgh, Edinburgh Medical School, The Chancellor's Building, Edinburgh, UK.,Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Neil A Mabbott
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Josef Priller
- UK Dementia Research Institute, The University of Edinburgh, Edinburgh Medical School, The Chancellor's Building, Edinburgh, UK.,Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.,DZNE, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gerard Thompson
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Alistair B Lawrence
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.,Scotland's Rural College (SRUC), Edinburgh, UK
| | - Barry W McColl
- UK Dementia Research Institute, The University of Edinburgh, Edinburgh Medical School, The Chancellor's Building, Edinburgh, UK.,Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
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14
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Huang KC, Gomes C, Meyer JS. Retinal Ganglion Cells in a Dish: Current Strategies and Recommended Best Practices for Effective In Vitro Modeling of Development and Disease. Handb Exp Pharmacol 2023; 281:83-102. [PMID: 36907969 PMCID: PMC10497719 DOI: 10.1007/164_2023_642] [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] [Indexed: 03/14/2023]
Abstract
The ability to derive retinal ganglion cells (RGCs) from human pluripotent stem cells (hPSCs) provides an extraordinary opportunity to study the development of RGCs as well as cellular mechanisms underlying their degeneration in optic neuropathies. In the past several years, multiple approaches have been established that allow for the generation of RGCs from hPSCs, with these methods greatly improved in more recent studies to yield mature RGCs that more faithfully recapitulate phenotypes within the eye. Nevertheless, numerous differences still remain between hPSC-RGCs and those found within the human eye, with these differences likely explained at least in part due to the environment in which hPSC-RGCs are grown. With the ultimate goal of generating hPSC-RGCs that most closely resemble those within the retina for proper studies of retinal development, disease modeling, as well as cellular replacement, we review within this manuscript the current effective approaches for the differentiation of hPSC-RGCs, as well as how they have been applied for the investigation of RGC neurodegenerative diseases such as glaucoma. Furthermore, we provide our opinions on the characteristics of RGCs necessary for their use as effective in vitro disease models and importantly, how these current systems should be improved to more accurately reflect disease states. The establishment of characteristics in differentiated hPSC-RGCs that more effectively mimic RGCs within the retina will not only enable their use as effective models of RGC development, but will also create a better disease model for the identification of mechanisms underlying the neurodegeneration of RGCs in disease states such as glaucoma, further facilitating the development of therapeutic approaches to rescue RGCs from degeneration in disease states.
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Affiliation(s)
- Kang-Chieh Huang
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cátia Gomes
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jason S Meyer
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA.
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15
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Antidepressants as a potential candidate to reduce microglia activation in neurodegenerative diseases. A systematic review and meta-analysis of preclinical studies. JOURNAL OF AFFECTIVE DISORDERS REPORTS 2023. [DOI: 10.1016/j.jadr.2023.100465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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16
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Tang YM, Pulimood NS, Stifani S. Comparing the Characteristics of Microglia Preparations Generated Using Different Human iPSC-Based Differentiation Methods to Model Neurodegenerative Diseases. ASN Neuro 2022; 14:17590914221145105. [PMID: 36524236 PMCID: PMC9761225 DOI: 10.1177/17590914221145105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
As the resident immune cells of the healthy nervous system, homeostatic microglia can rapidly become activated in response to injury/disease. Dysregulated microglia activation is a hallmark of nervous system disorders including neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer's disease. The elucidation of the biological and pathological roles of microglia has recently benefitted from the development of microglia-like cells using human induced pluripotent stem cell (iPSC)-based approaches. The success of iPSC-derived microglia preparations as a disease-relevant model system depends on their representation of the in vivo spatial and temporal heterogeneity of microglia under pathological conditions. Little is currently known about the potential of human iPSC-derived microglia generated using different methods for the study of neurodegenerative diseases. We compared the transcriptomes of human iPSC-derived microglia generated using two frequently used in vitro differentiation methods to determine whether separate strategies can generate microglia with distinct transcriptional signatures in vitro. We show that microglia derived using different differentiation methods display distinct maturation characteristics after equivalent times in culture. We also reveal that iPSC-derived microglia preparations generated using these two methods are composed of different subpopulations with transcriptomic signatures resembling those of in vivo regionally distinct microglia subtypes, specifically white-matter and gray-matter microglia. These findings highlight the need to better characterize the subtype composition of each microglia preparation prior to its use to model neurodegenerative diseases.
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Affiliation(s)
- Ye Man Tang
- Department of Neurology and Neurosurgery, Montreal Neurological
Institute-Hospital, McGill
University, Montreal, Quebec, Canada
| | - Nisha S. Pulimood
- Department of Neurology and Neurosurgery, Montreal Neurological
Institute-Hospital, McGill
University, Montreal, Quebec, Canada
| | - Stefano Stifani
- Department of Neurology and Neurosurgery, Montreal Neurological
Institute-Hospital, McGill
University, Montreal, Quebec, Canada,Stefano Stifani, Department of Neurology
and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University,
Montreal, Quebec, Canada H3A 2B4.
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17
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Trease AJ, Niu M, Morsey B, Guda C, Byrareddy SN, Buch S, Fox HS. Antiretroviral therapy restores the homeostatic state of microglia in SIV-infected rhesus macaques. J Leukoc Biol 2022; 112:969-981. [PMID: 35686500 PMCID: PMC9796061 DOI: 10.1002/jlb.3hi0422-635r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/11/2022] [Indexed: 12/31/2022] Open
Abstract
Microglia and macrophages are essential for homeostatic maintenance and innate immune response in the brain. They are the first line of defense against infections such as HIV/SIV in the brain. However, they are susceptible to infection and function as viral reservoirs even under effective viral suppression. While current antiretroviral regimens successfully suppress viremia and improve quality of life and lifespan, neurologic complications persist and are in part attributed to activated microglia. We sought to test the hypothesis that brain microglia return to a more homeostatic-like state when viremia is suppressed by combination antiretroviral therapy. Using the SIV-rhesus macaque model, we combined single-cell RNA sequencing, bioinformatics, and pathway analysis to compare gene expression profiles of brain myeloid cells under 4 conditions: uninfected, SIV infected, SIV infected with cART suppression, and SIV encephalitis (SIVE). Our study reveals greater myeloid diversity and an elevated proinflammatory state are associated with untreated SIV infection compared with uninfected animals. The development of encephalitis and suppression of viremia both reduced myeloid diversity. However, they had converse effects on the activation state of microglia and inflammation. Notably, suggestive of a restoration of a homeostatic state in microglia, gene expression and activation of pathways related to inflammation and immune response in cART-suppressed monkeys were most similar to that in uninfected monkeys. Untreated SIV infection shared characteristics, especially in brain macrophages to SIVE, with SIVE showing dramatic inflammation. In support of our hypothesis, our study demonstrates that cART indeed restores this key component of the brain's homeostatic state. Summary: ScRNA-seq of rhesus monkey microglia reveals clusters of cells in activated states in the setting of SIV infection, which is primarily reversed by suppressing viremia with combination antiretroviral therapy.
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Affiliation(s)
- Andrew J. Trease
- Department of Neurological SciencesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Meng Niu
- Department of Genetics, Cell Biology and AnatomyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Brenda Morsey
- Department of Neurological SciencesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and AnatomyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Shilpa Buch
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Howard S. Fox
- Department of Neurological SciencesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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18
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Monzón-Sandoval J, Burlacu E, Agarwal D, Handel AE, Wei L, Davis J, Cowley SA, Cader MZ, Webber C. Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models. Dis Model Mech 2022; 15:277958. [PMID: 36254682 PMCID: PMC9612871 DOI: 10.1242/dmm.049349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/30/2022] [Indexed: 01/15/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, and risk-influencing genetics implicates microglia and neuroimmunity in the pathogenesis of AD. Induced pluripotent stem cell (iPSC)-derived microglia (iPSC-microglia) are increasingly used as a model of AD, but the relevance of historical immune stimuli to model AD is unclear. We performed a detailed cross-comparison over time on the effects of combinatory stimulation of iPSC-microglia, and in particular their relevance to AD. We used single-cell RNA sequencing to measure the transcriptional response of iPSC-microglia after 24 h and 48 h of stimulation with prostaglandin E2 (PGE2) or lipopolysaccharide (LPS)+interferon gamma (IFN-γ), either alone or in combination with ATPγS. We observed a shared core transcriptional response of iPSC-microglia to ATPγS and to LPS+IFN-γ, suggestive of a convergent mechanism of action. Across all conditions, we observed a significant overlap, although directional inconsistency to genes that change their expression levels in human microglia from AD patients. Using a data-led approach, we identify a common axis of transcriptomic change across AD genetic mouse models of microglia and show that only LPS provokes a transcriptional response along this axis in mouse microglia and LPS+IFN-γ in human iPSC-microglia. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Elena Burlacu
- John Radcliffe Hospital, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DS, UK
| | - Devika Agarwal
- Nuffield Department of Medicine Research Building, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.,Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam E Handel
- John Radcliffe Hospital, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DS, UK
| | - Liting Wei
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - John Davis
- Nuffield Department of Medicine Research Building, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Sally A Cowley
- Translational Molecular Neuroscience Group, New Biochemistry Building, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX1 3QU, UK
| | - M Zameel Cader
- John Radcliffe Hospital, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DS, UK.,James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Caleb Webber
- UK Dementia Research Institute, Cardiff University, Cardiff CF24 4HQ, UK
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19
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Leibrand CR, Paris JJ, Jones AM, Ohene-Nyako M, Rademeyer KM, Nass SR, Kim WK, Knapp PE, Hauser KF, McRae M. Independent actions by HIV-1 Tat and morphine to increase recruitment of monocyte-derived macrophages into the brain in a region-specific manner. Neurosci Lett 2022; 788:136852. [PMID: 36028004 PMCID: PMC9845733 DOI: 10.1016/j.neulet.2022.136852] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/07/2022] [Accepted: 08/18/2022] [Indexed: 01/21/2023]
Abstract
Despite advances in the treatment of human immunodeficiency virus (HIV), approximately one-half of people infected with HIV (PWH) experience neurocognitive impairment. Opioid use disorder (OUD) can exacerbate the cognitive and pathological changes seen in PWH. HIV increases inflammation and immune cell trafficking into the brain; however, less is known about how opioid use disorder affects the recruitment of immune cells. Accordingly, we examined the temporal consequences of HIV-1 Tat and/or morphine on the recruitment of endocytic cells (predominantly perivascular macrophages and microglia) in the dorsal striatum and hippocampus by infusing multi-colored, fluorescently labeled dextrans before and after exposure. To address this question, transgenic mice that conditionally expressed HIV-1 Tat (Tat+), or their control counterparts (Tat-), received three sequential intracerebroventricular (i.c.v.) infusions of Cascade Blue-, Alexa Fluor 488-, and Alexa Fluor 594-labeled dextrans, respectively infused 1 day before, 1-day after, or 13-days after morphine and/or Tat exposure. At the end of the study, the number of cells labeled with each fluorescent dextran were counted. The data demonstrated a significantly higher influx of newly-labeled cells into the perivascular space than into the parenchyma. In the striatum, Tat or morphine exposure increased the number of endocytic cells in the perivascular space, while only morphine increased the recruitment of endocytic cells into the parenchyma. In the hippocampus, morphine (but not Tat) increased the influx of dextran-labeled cells into the perivascular space, but there were too few labeled cells within the hippocampal parenchyma to analyze. Collectively, these data suggest that HIV-1 Tat and morphine act independently to increase the recruitment of endocytic cells into the brain in a region-specific manner.
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Affiliation(s)
- Crystal R Leibrand
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Jason J Paris
- Department of BioMolecular Sciences, School of Pharmacy, The University of Mississippi, University, MS 38677, United States
| | - Austin M Jones
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Michael Ohene-Nyako
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Kara M Rademeyer
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Sara R Nass
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Woong-Ki Kim
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, United States
| | - Pamela E Knapp
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Kurt F Hauser
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - MaryPeace McRae
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States.
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20
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Ibanez KR, McFarland KN, Phillips J, Allen M, Lessard CB, Zobel L, De La Cruz EG, Shah S, Vo Q, Wang X, Quicksall Z, Ryu D, Funk C, Ertekin-Taner N, Prokop S, Golde TE, Chakrabarty P. Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways. Alzheimers Res Ther 2022; 14:104. [PMID: 35897046 PMCID: PMC9327202 DOI: 10.1186/s13195-022-01044-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND The S209F variant of Abelson Interactor Protein 3 (ABI3) increases risk for Alzheimer's disease (AD), but little is known about its function in relation to AD pathogenesis. METHODS Here, we use a mouse model that is deficient in Abi3 locus to study how the loss of function of Abi3 impacts two cardinal neuropathological hallmarks of AD-amyloid β plaques and tau pathology. Our study employs extensive neuropathological and transcriptomic characterization using transgenic mouse models and adeno-associated virus-mediated gene targeting strategies. RESULTS Analysis of bulk RNAseq data confirmed age-progressive increase in Abi3 levels in rodent models of AD-type amyloidosis and upregulation in AD patients relative to healthy controls. Using RNAscope in situ hybridization, we localized the cellular distribution of Abi3 in mouse and human brains, finding that Abi3 is expressed in both microglial and non-microglial cells. Next, we evaluated Abi3-/- mice and document that both Abi3 and its overlapping gene, Gngt2, are disrupted in these mice. Using multiple transcriptomic datasets, we show that expression of Abi3 and Gngt2 are tightly correlated in rodent models of AD and human brains, suggesting a tight co-expression relationship. RNAseq of the Abi3-Gngt2-/- mice revealed upregulation of Trem2, Plcg2, and Tyrobp, concomitant with induction of an AD-associated neurodegenerative signature, even in the absence of AD-typical neuropathology. In APP mice, loss of Abi3-Gngt2 resulted in a gene dose- and age-dependent reduction in Aβ deposition. Additionally, in Abi3-Gngt2-/- mice, expression of a pro-aggregant form of human tau exacerbated tauopathy and astrocytosis. Further, using in vitro culture assays, we show that the AD-associated S209F mutation alters the extent of ABI3 phosphorylation. CONCLUSIONS These data provide an important experimental framework for understanding the role of Abi3-Gngt2 function and early inflammatory gliosis in AD. Our studies also demonstrate that inflammatory gliosis could have opposing effects on amyloid and tau pathology, highlighting the unpredictability of targeting immune pathways in AD.
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Affiliation(s)
- Kristen R Ibanez
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Karen N McFarland
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Department of Neurology, University of Florida, Gainesville, FL, 32610, USA
| | - Jennifer Phillips
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Christian B Lessard
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Lillian Zobel
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Elsa Gonzalez De La Cruz
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Shivani Shah
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Quan Vo
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Daniel Ryu
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Stefan Prokop
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Department of Pathology, University of Florida, Gainesville, FL, 32610, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Todd E Golde
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
- Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA
| | - Paramita Chakrabarty
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA.
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
- Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA.
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21
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Exposure to the Amino Acids Histidine, Lysine, and Threonine Reduces mTOR Activity and Affects Neurodevelopment in a Human Cerebral Organoid Model. Nutrients 2022; 14:nu14102175. [PMID: 35631316 PMCID: PMC9145399 DOI: 10.3390/nu14102175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 02/05/2023] Open
Abstract
Evidence of the impact of nutrition on human brain development is compelling. Previous in vitro and in vivo results show that three specific amino acids, histidine, lysine, and threonine, synergistically inhibit mTOR activity and behavior. Therefore, the prenatal availability of these amino acids could be important for human neurodevelopment. However, methods to study the underlying mechanisms in a human model of neurodevelopment are limited. Here, we pioneer the use of human cerebral organoids to investigate the impact of amino acid supplementation on neurodevelopment. In this study, cerebral organoids were exposed to 10 mM and 50 mM of the amino acids threonine, histidine, and lysine. The impact was determined by measuring mTOR activity using Western blots, general cerebral organoid size, and gene expression by RNA sequencing. Exposure to threonine, histidine, and lysine led to decreased mTOR activity and markedly reduced organoid size, supporting findings in rodent studies. RNA sequencing identified comprehensive changes in gene expression, with enrichment in genes related to specific biological processes (among which are mTOR signaling and immune function) and to specific cell types, including proliferative precursor cells, microglia, and astrocytes. Altogether, cerebral organoids are responsive to nutritional exposure by increasing specific amino acid concentrations and reflect findings from previous rodent studies. Threonine, histidine, and lysine exposure impacts the early development of human cerebral organoids, illustrated by the inhibition of mTOR activity, reduced size, and altered gene expression.
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22
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Gumbs SBH, Berdenis van Berlekom A, Kübler R, Schipper PJ, Gharu L, Boks MP, Ormel PR, Wensing AMJ, de Witte LD, Nijhuis M. Characterization of HIV-1 Infection in Microglia-Containing Human Cerebral Organoids. Viruses 2022; 14:v14040829. [PMID: 35458559 PMCID: PMC9032670 DOI: 10.3390/v14040829] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 12/21/2022] Open
Abstract
The achievement of an HIV cure is dependent on the eradication or permanent silencing of HIV-latent viral reservoirs, including the understudied central nervous system (CNS) reservoir. This requires a deep understanding of the molecular mechanisms of HIV’s entry into the CNS, latency establishment, persistence, and reversal. Therefore, representative CNS culture models that reflect the intercellular dynamics and pathophysiology of the human brain are urgently needed in order to study the CNS viral reservoir and HIV-induced neuropathogenesis. In this study, we characterized a human cerebral organoid model in which microglia grow intrinsically as a CNS culture model to study HIV infection in the CNS. We demonstrated that both cerebral organoids and isolated organoid-derived microglia (oMG), infected with replication-competent HIVbal reporter viruses, support productive HIV infection via the CCR5 co-receptor. Productive HIV infection was only observed in microglial cells. Fluorescence analysis revealed microglia as the only HIV target cell. Susceptibility to HIV infection was dependent on the co-expression of microglia-specific markers and the CD4 and CCR5 HIV receptors. Altogether, this model will be a valuable tool within the HIV research community to study HIV–CNS interactions, the underlying mechanisms of HIV-associated neurological disorders (HAND), and the efficacy of new therapeutic and curative strategies on the CNS viral reservoir.
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Affiliation(s)
- Stephanie B. H. Gumbs
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (S.B.H.G.); (R.K.); (P.J.S.); (L.G.); (A.M.J.W.)
| | - Amber Berdenis van Berlekom
- Department of Psychiatry, University Medical Center Utrect Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands; (A.B.v.B.); (M.P.B.); (P.R.O.); (L.D.d.W.)
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Raphael Kübler
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (S.B.H.G.); (R.K.); (P.J.S.); (L.G.); (A.M.J.W.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pauline J. Schipper
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (S.B.H.G.); (R.K.); (P.J.S.); (L.G.); (A.M.J.W.)
| | - Lavina Gharu
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (S.B.H.G.); (R.K.); (P.J.S.); (L.G.); (A.M.J.W.)
| | - Marco P. Boks
- Department of Psychiatry, University Medical Center Utrect Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands; (A.B.v.B.); (M.P.B.); (P.R.O.); (L.D.d.W.)
| | - Paul R. Ormel
- Department of Psychiatry, University Medical Center Utrect Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands; (A.B.v.B.); (M.P.B.); (P.R.O.); (L.D.d.W.)
| | - Annemarie M. J. Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (S.B.H.G.); (R.K.); (P.J.S.); (L.G.); (A.M.J.W.)
| | - Lot D. de Witte
- Department of Psychiatry, University Medical Center Utrect Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands; (A.B.v.B.); (M.P.B.); (P.R.O.); (L.D.d.W.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Monique Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (S.B.H.G.); (R.K.); (P.J.S.); (L.G.); (A.M.J.W.)
- Correspondence:
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23
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Fixemer S, Ameli C, Hammer G, Salamanca L, Uriarte Huarte O, Schwartz C, Gérardy JJ, Mechawar N, Skupin A, Mittelbronn M, Bouvier DS. Microglia phenotypes are associated with subregional patterns of concomitant tau, amyloid-β and α-synuclein pathologies in the hippocampus of patients with Alzheimer's disease and dementia with Lewy bodies. Acta Neuropathol Commun 2022; 10:36. [PMID: 35296366 PMCID: PMC8925098 DOI: 10.1186/s40478-022-01342-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022] Open
Abstract
The cellular alterations of the hippocampus lead to memory decline, a shared symptom between Alzheimer’s disease (AD) and dementia with Lewy Bodies (DLB) patients. However, the subregional deterioration pattern of the hippocampus differs between AD and DLB with the CA1 subfield being more severely affected in AD. The activation of microglia, the brain immune cells, could play a role in its selective volume loss. How subregional microglia populations vary within AD or DLB and across these conditions remains poorly understood. Furthermore, how the nature of the hippocampal local pathological imprint is associated with microglia responses needs to be elucidated. To this purpose, we employed an automated pipeline for analysis of 3D confocal microscopy images to assess CA1, CA3 and DG/CA4 subfields microglia responses in post-mortem hippocampal samples from late-onset AD (n = 10), DLB (n = 8) and age-matched control (CTL) (n = 11) individuals. In parallel, we performed volumetric analyses of hyperphosphorylated tau (pTau), amyloid-β (Aβ) and phosphorylated α-synuclein (pSyn) loads. For each of the 32,447 extracted microglia, 16 morphological features were measured to classify them into seven distinct morphological clusters. Our results show similar alterations of microglial morphological features and clusters in AD and DLB, but with more prominent changes in AD. We identified two distinct microglia clusters enriched in disease conditions and particularly increased in CA1 and DG/CA4 of AD and CA3 of DLB. Our study confirms frequent concomitance of pTau, Aβ and pSyn loads across AD and DLB but reveals a specific subregional pattern for each type of pathology, along with a generally increased severity in AD. Furthermore, pTau and pSyn loads were highly correlated across subregions and conditions. We uncovered tight associations between microglial changes and the subfield pathological imprint. Our findings suggest that combinations and severity of subregional pTau, Aβ and pSyn pathologies transform local microglia phenotypic composition in the hippocampus. The high burdens of pTau and pSyn associated with increased microglial alterations could be a factor in CA1 vulnerability in AD.
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24
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de Witte LD, Wang Z, Snijders GLJL, Mendelev N, Liu Q, Sneeboer MAM, Boks MPM, Ge Y, Haghighi F. Contribution of Age, Brain Region, Mood Disorder Pathology, and Interindividual Factors on the Methylome of Human Microglia. Biol Psychiatry 2022; 91:572-581. [PMID: 35027166 PMCID: PMC11181298 DOI: 10.1016/j.biopsych.2021.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Transcriptome studies have revealed age-, disease-, and region-associated microglial phenotypes reflecting changes in microglial function during development, aging, central nervous system homeostasis, and pathology. The molecular mechanisms that contribute to these transcriptomic changes are largely unknown. The aim of this study was to characterize the DNA methylation landscape of human microglia and the factors that contribute to variations in the microglia methylome. We hypothesized that both age and brain region would have a large impact on DNA methylation in microglia. METHODS Microglia from postmortem brain tissue of four different brain regions of 22 donors, encompassing 1 patient with schizophrenia, 13 patients with mood disorder pathology, and 8 control subjects, were isolated and assayed using a genome-wide methylation array. RESULTS We found that human microglial cells have a methylation profile distinct from bulk brain tissue and neurons, and age explained a considerable part of the variation. Additionally, we showed that interindividual factors had a much larger effect on the methylation landscape of microglia than brain region, which was also seen at the transcriptome level. In our exploratory analysis, we found various differentially methylated regions that were related to disease status (mood disorder vs. control). This included differentially methylated regions that are linked to gene expression in microglia, as well as to myeloid cell function or neuropsychiatric disorders. CONCLUSIONS Although based on relatively small samples, these findings suggest that the methylation profile of microglia is responsive to interindividual variations and thereby plays an important role in the heterogeneity of microglia observed at the transcriptome level.
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Affiliation(s)
- Lot D de Witte
- Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zhaoyu Wang
- Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, New York; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gijsje L J L Snijders
- Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Natalia Mendelev
- Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, New York; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Qingkun Liu
- Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, New York; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marjolein A M Sneeboer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, University Medical Center Utrecht, UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; Department of Translational Neuroscience, University Medical Center Utrecht, UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Marco P M Boks
- Department of Psychiatry, University Medical Center Utrecht, UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Fatemeh Haghighi
- Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
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25
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Gumbs SBH, Kübler R, Gharu L, Schipper PJ, Borst AL, Snijders GJLJ, Ormel PR, van Berlekom AB, Wensing AMJ, de Witte LD, Nijhuis M. Human microglial models to study HIV infection and neuropathogenesis: a literature overview and comparative analyses. J Neurovirol 2022; 28:64-91. [PMID: 35138593 PMCID: PMC9076745 DOI: 10.1007/s13365-021-01049-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/03/2021] [Accepted: 12/18/2021] [Indexed: 02/08/2023]
Abstract
HIV persistence in the CNS despite antiretroviral therapy may cause neurological disorders and poses a critical challenge for HIV cure. Understanding the pathobiology of HIV-infected microglia, the main viral CNS reservoir, is imperative. Here, we provide a comprehensive comparison of human microglial culture models: cultured primary microglia (pMG), microglial cell lines, monocyte-derived microglia (MDMi), stem cell-derived microglia (iPSC-MG), and microglia grown in 3D cerebral organoids (oMG) as potential model systems to advance HIV research on microglia. Functional characterization revealed phagocytic capabilities and responsiveness to LPS across all models. Microglial transcriptome profiles of uncultured pMG showed the highest similarity to cultured pMG and oMG, followed by iPSC-MG and then MDMi. Direct comparison of HIV infection showed a striking difference, with high levels of viral replication in cultured pMG and MDMi and relatively low levels in oMG resembling HIV infection observed in post-mortem biopsies, while the SV40 and HMC3 cell lines did not support HIV infection. Altogether, based on transcriptional similarities to uncultured pMG and susceptibility to HIV infection, MDMi may serve as a first screening tool, whereas oMG, cultured pMG, and iPSC-MG provide more representative microglial culture models for HIV research. The use of current human microglial cell lines (SV40, HMC3) is not recommended.
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Affiliation(s)
- Stephanie B H Gumbs
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Raphael Kübler
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine, New York, NY, USA
| | - Lavina Gharu
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pauline J Schipper
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anne L Borst
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gijsje J L J Snijders
- Department of Psychiatry, Icahn School of Medicine, New York, NY, USA
- Department of Psychiatry, University Medical Center Utrecht, Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Paul R Ormel
- Department of Psychiatry, University Medical Center Utrecht, Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Amber Berdenis van Berlekom
- Department of Psychiatry, University Medical Center Utrecht, Brain Center, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, University Medical Center Utrecht, Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Annemarie M J Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine, New York, NY, USA
- Department of Psychiatry, University Medical Center Utrecht, Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Monique Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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26
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Boche D, Gordon MN. Diversity of transcriptomic microglial phenotypes in aging and Alzheimer's disease. Alzheimers Dement 2022; 18:360-376. [PMID: 34223696 PMCID: PMC9059230 DOI: 10.1002/alz.12389] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 02/03/2023]
Abstract
The morphological plasticity of microglia has fascinated neuroscientists for 100 years. Attempts to classify functional phenotypes are hampered by similarities between endogenous brain microglia and peripheral myeloid cells that can enter the brain under pathological conditions. Recent advances in single-cell -omic methodologies have led to an explosion of data regarding gene expression in microglia. Herein, we review the diversity of microglial phenotypes in healthy brains, aging, and Alzheimer's disease (AD); identify knowledge gaps in the body of evidence; and suggest areas in which new knowledge would be useful. Data from human samples and mouse models are compared and contrasted. Understanding the molecular complexity of the microglial response repertoire will suggest new avenues for therapeutic treatments in AD.
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Affiliation(s)
- Delphine Boche
- Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Marcia N. Gordon
- Translational Neuroscience, Michigan State University College of Human Medicine, Grand Rapids, MI, USA,corresponding author: Marcia N. Gordon, PhD, Michigan State University GRRC, 400 Monroe Ave NW, Grand Rapids, MI, 49503 USA, , Telephone: (616) 234-2837
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27
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Jiang X, He H, Mo L, Liu Q, Yang F, Zhou Y, Li L, Su D, Yi S, Zhang J. Mapping the Plasticity of Morphology, Molecular Properties and Function in Mouse Primary Microglia. Front Cell Neurosci 2022; 15:811061. [PMID: 35153675 PMCID: PMC8825496 DOI: 10.3389/fncel.2021.811061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Microglia exert diverse functions by responding in diverse ways to different stimuli, yet little is known about the plasticity of various phenotypes that microglia display. We used interferon (IFN)-γ, interleukin (IL)-4 and IL-10 to induce different phenotypes in mouse primary microglia. RNA sequencing was used to identify genes differentially expressed in response to stimulation, and the different stimulated populations were compared in terms of morphology, proliferative capacity, phagocytic ability and neurotoxicity. IFN-γ induced an “immunodefensive” phenotype characterizing both induction of filopodia and upregulation of inducible nitric oxide synthase (iNOS) and tumor necrosis factor α. Microglia with this phenotype mediated an acute inflammatory response accompanied by excellent proliferative capacity and neurotoxicity, and remained susceptible to remodeling for up to 48 h after initial stimulation. IL-4 induced an enduring “neuroimmunoregulatory” phenotype involving induction of lamellipodium and persistent upregulation of arginase (Arg)-1 and YM-1 expression. Microglia with this phenotype remained susceptible to remodeling for up to 24 h after initial stimulation. IL-10 induced an “immunosuppressive” phenotype involving induction of ameba-like morphology and upregulation of transforming growth factor β and IL-10 as well as inhibition of inflammation. This phenotype was accompanied by inhibition of self-proliferation, while its morphology, molecular properties and function were the least susceptible to remodeling. IFN-γ, IL-4, or IL-10 appear to induce substantially different phenotypes in microglia. The immunodefensive microglia induced by IFN-γ showed remarkable plasticity, which may help repair CNS inflammation damage under pathological condition. Chronic activation with IL-10 decreases microglial plasticity, which may help protect the brain form the immune response. Our research justifies and guides further studies into the molecular pathways that operate in each phenotype to help multitasking microglia regulate homeostasis in the brain.
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Affiliation(s)
- Xue Jiang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Hui He
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Li Mo
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qin Liu
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Fan Yang
- Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Ying Zhou
- Guizhou Provincial People’s Hospital, Guiyang, China
| | - Liangyuan Li
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dapeng Su
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Saini Yi
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jinqiang Zhang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- *Correspondence: Jinqiang Zhang,
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28
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Lopes KDP, Snijders GJL, Humphrey J, Allan A, Sneeboer MAM, Navarro E, Schilder BM, Vialle RA, Parks M, Missall R, van Zuiden W, Gigase FAJ, Kübler R, van Berlekom AB, Hicks EM, Bӧttcher C, Priller J, Kahn RS, de Witte LD, Raj T. Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies. Nat Genet 2022; 54:4-17. [PMID: 34992268 PMCID: PMC9245609 DOI: 10.1038/s41588-021-00976-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 10/19/2021] [Indexed: 12/12/2022]
Abstract
Microglia have emerged as important players in brain aging and pathology. To understand how genetic risk for neurological and psychiatric disorders is related to microglial function, large transcriptome studies are essential. Here, we describe the transcriptome analysis of 255 primary human microglia samples isolated at autopsy from multiple brain regions of 100 human subjects. We performed systematic analyses to investigate various aspects of microglial heterogeneities, including brain region and aging. We mapped expression and splicing quantitative trait loci and showed that many neurological disease susceptibility loci are mediated through gene expression or splicing in microglia. Fine-mapping of these loci nominated candidate causal variants that are within microglia-specific enhancers, finding associations with microglia expression of USP6NL for Alzheimer’s disease and P2RY12 for Parkinson’s disease. We have built the most comprehensive catalog to date of genetic effects on the microglia transcriptome and propose candidate functional variants in neurological and psychiatric disorders.
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Affiliation(s)
- Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gijsje J L Snijders
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marjolein A M Sneeboer
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo A Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Welmoed van Zuiden
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Frederieke A J Gigase
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA
| | - Raphael Kübler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amber Berdenis van Berlekom
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Emily M Hicks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chotima Bӧttcher
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA.
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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29
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Smith AM, Davey K, Tsartsalis S, Khozoie C, Fancy N, Tang SS, Liaptsi E, Weinert M, McGarry A, Muirhead RCJ, Gentleman S, Owen DR, Matthews PM. Diverse human astrocyte and microglial transcriptional responses to Alzheimer's pathology. Acta Neuropathol 2022; 143:75-91. [PMID: 34767070 PMCID: PMC8732962 DOI: 10.1007/s00401-021-02372-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/26/2021] [Accepted: 09/13/2021] [Indexed: 02/12/2023]
Abstract
To better define roles that astrocytes and microglia play in Alzheimer’s disease (AD), we used single-nuclei RNA-sequencing to comprehensively characterise transcriptomes in astrocyte and microglia nuclei selectively enriched during isolation post-mortem from neuropathologically defined AD and control brains with a range of amyloid-beta and phospho-tau (pTau) pathology. Significant differences in glial gene expression (including AD risk genes expressed in both the astrocytes [CLU, MEF2C, IQCK] and microglia [APOE, MS4A6A, PILRA]) were correlated with tissue amyloid or pTau expression. The differentially expressed genes were distinct between with the two cell types and pathologies, although common (but cell-type specific) gene sets were enriched with both pathologies in each cell type. Astrocytes showed enrichment for proteostatic, inflammatory and metal ion homeostasis pathways. Pathways for phagocytosis, inflammation and proteostasis were enriched in microglia and perivascular macrophages with greater tissue amyloid, but IL1-related pathway enrichment was found specifically in association with pTau. We also found distinguishable sub-clusters in the astrocytes and microglia characterised by transcriptional signatures related to either homeostatic functions or disease pathology. Gene co-expression analyses revealed potential functional associations of soluble biomarkers of AD in astrocytes (CLU) and microglia (GPNMB). Our work highlights responses of both astrocytes and microglia for pathological protein clearance and inflammation, as well as glial transcriptional diversity in AD.
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30
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Timmerman R, Zuiderwijk-Sick EA, Oosterhof N, 't Jong AEJ, Veth J, Burm SM, van Ham TJ, Bajramovic JJ. Transcriptome analysis reveals the contribution of oligodendrocyte and radial glia-derived cues for maintenance of microglia identity. Glia 2021; 70:728-747. [PMID: 34961968 DOI: 10.1002/glia.24136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/26/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Microglia are increasingly being recognized as druggable targets in neurodegenerative disorders, and good in vitro models are crucial to address cell biological questions. Major challenges are to recapitulate the complex microglial morphology and their in vivo transcriptome. We have therefore exposed primary microglia from adult rhesus macaques to a variety of different culture conditions including exposure to soluble factors as M-CSF, IL-34, and TGF-β as well as serum replacement approaches, and compared their morphologies and transcriptomes to those of mature, homeostatic in vivo microglia. This enabled us to develop a new, partially serum-free, monoculture protocol, that yields high numbers of ramified cells. We also demonstrate that exposure of adult microglia to M-CSF or IL-34 induces similar transcriptomes, and that exposure to TGF-β has much less pronounced effects than it does on rodent microglia. However, regardless of culture conditions, the transcriptomes of in vitro and in vivo microglia remained substantially different. Analysis of differentially expressed genes inspired us to perform 3D-spherical coculture experiments of microglia with oligodendrocytes and radial glia. In such spheres, microglia signature genes were strongly induced, even in the absence of neurons and astrocytes. These data reveal a novel role for oligodendrocyte and radial glia-derived cues in the maintenance of microglial identity, providing new anchor points to study microglia in health and disease.
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Affiliation(s)
- Raissa Timmerman
- Alternatives Unit, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | - Nynke Oosterhof
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Anke E J 't Jong
- Alternatives Unit, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Jennifer Veth
- Alternatives Unit, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Saskia M Burm
- Alternatives Unit, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jeffrey J Bajramovic
- Alternatives Unit, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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31
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Edara VV, Manning KE, Ellis M, Lai L, Moore KM, Foster SL, Floyd K, Davis-Gardner ME, Mantus G, Nyhoff LE, Bechnak S, Alaaeddine G, Naji A, Samaha H, Lee M, Bristow L, Hussaini L, Ciric CR, Nguyen PV, Gagne M, Roberts-Torres J, Henry AR, Godbole S, Grakoui A, Sexton M, Piantadosi A, Waggoner JJ, Douek DC, Anderson EJ, Rouphael N, Wrammert J, Suthar MS. mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 Omicron variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34981056 DOI: 10.1101/2021.09.09.459619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines generate potent neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the global emergence of SARS-CoV-2 variants with mutations in the spike protein, the principal antigenic target of these vaccines, has raised concerns over the neutralizing activity of vaccine-induced antibody responses. The Omicron variant, which emerged in November 2021, consists of over 30 mutations within the spike protein. Here, we used an authentic live virus neutralization assay to examine the neutralizing activity of the SARS-CoV-2 Omicron variant against mRNA vaccine-induced antibody responses. Following the 2nd dose, we observed a 30-fold reduction in neutralizing activity against the omicron variant. Through six months after the 2nd dose, none of the sera from naïve vaccinated subjects showed neutralizing activity against the Omicron variant. In contrast, recovered vaccinated individuals showed a 22-fold reduction with more than half of the subjects retaining neutralizing antibody responses. Following a booster shot (3rd dose), we observed a 14-fold reduction in neutralizing activity against the omicron variant and over 90% of boosted subjects showed neutralizing activity against the omicron variant. These findings show that a 3rd dose is required to provide robust neutralizing antibody responses against the Omicron variant.
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32
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Moser VA, Workman MJ, Hurwitz SJ, Lipman RM, Pike CJ, Svendsen CN. Microglial transcription profiles in mouse and human are driven by APOE4 and sex. iScience 2021; 24:103238. [PMID: 34746703 PMCID: PMC8551075 DOI: 10.1016/j.isci.2021.103238] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/28/2021] [Accepted: 10/04/2021] [Indexed: 11/22/2022] Open
Abstract
Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). APOE4 is known to affect the function of microglia, but to what extent this gene drives microglial gene expression has thus far not been examined. Using a transgenic mouse model of AD that expresses human APOE, we identify a unique transcriptional profile associated with APOE4 expression. We also show a sex and APOE interaction, such that both female sex and APOE4 drive expression of this gene profile. We confirm these findings in human cells, using microglia derived from induced pluripotent stem cells (iMGL). Moreover, we find that these interactions are driven in part by genes related to metal processing, and we show that zinc treatment has APOE genotype-dependent effects on iMGL. These data identify a sex- and APOE4-associated microglial transcription profile and highlight the importance of considering interactive risk factors such as sex and environmental exposures.
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Affiliation(s)
- V. Alexandra Moser
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael J. Workman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Samantha J. Hurwitz
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rachel M. Lipman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Christian J. Pike
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Clive N. Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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33
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Lier J, Streit WJ, Bechmann I. Beyond Activation: Characterizing Microglial Functional Phenotypes. Cells 2021; 10:cells10092236. [PMID: 34571885 PMCID: PMC8464670 DOI: 10.3390/cells10092236] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/26/2021] [Indexed: 12/20/2022] Open
Abstract
Classically, the following three morphological states of microglia have been defined: ramified, amoeboid and phagocytic. While ramified cells were long regarded as “resting”, amoeboid and phagocytic microglia were viewed as “activated”. In aged human brains, a fourth, morphologically novel state has been described, i.e., dystrophic microglia, which are thought to be senescent cells. Since microglia are not replenished by blood-borne mononuclear cells under physiological circumstances, they seem to have an “expiration date” limiting their capacity to phagocytose and support neurons. Identifying factors that drive microglial aging may thus be helpful to delay the onset of neurodegenerative diseases, such as Alzheimer’s disease (AD). Recent progress in single-cell deep sequencing methods allowed for more refined differentiation and revealed regional-, age- and sex-dependent differences of the microglial population, and a growing number of studies demonstrate various expression profiles defining microglial subpopulations. Given the heterogeneity of pathologic states in the central nervous system, the need for accurately describing microglial morphology and expression patterns becomes increasingly important. Here, we review commonly used microglial markers and their fluctuations in expression in health and disease, with a focus on IBA1 low/negative microglia, which can be found in individuals with liver disease.
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Affiliation(s)
- Julia Lier
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany;
- Department of Neurology, University of Leipzig, 04109 Leipzig, Germany
- Correspondence:
| | - Wolfgang J. Streit
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, FL 32611, USA;
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany;
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34
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Snijders GJLJ, van Zuiden W, Sneeboer MAM, Berdenis van Berlekom A, van der Geest AT, Schnieder T, MacIntyre DJ, Hol EM, Kahn RS, de Witte LD. A loss of mature microglial markers without immune activation in schizophrenia. Glia 2021; 69:1251-1267. [PMID: 33410555 PMCID: PMC7986895 DOI: 10.1002/glia.23962] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023]
Abstract
Microglia, the immune cells of the brain, are important for neurodevelopment and have been hypothesized to play a role in the pathogenesis of schizophrenia (SCZ). Although previous postmortem studies pointed toward presence of microglial activation, this view has been challenged by more recent hypothesis-driven and hypothesis-free analyses. The aim of the present study is to further understand the observed microglial changes in SCZ. We first performed a detailed meta-analysis on studies that analyzed microglial cell density, microglial morphology, and expression of microglial-specific markers. We then further explored findings from the temporal cortex by performing immunostainings and qPCRs on an additional dataset. A random effect meta-analysis showed that the density of microglial cells was unaltered in SCZ (ES: 0.144 95% CI: 0.102 to 0.390, p = .250), and clear changes in microglial morphology were also absent. The expression of several microglial specific genes, such as CX3CR1, CSF1R, IRF8, OLR1, and TMEM119 was decreased in SCZ (ES: -0.417 95% CI: -0.417 to -0.546, p < .0001), consistent with genome-wide transcriptome meta-analysis results. These results indicate a change in microglial phenotype rather than density, which was validated with the use of TMEM119/Iba1 immunostainings on temporal cortex of a separate cohort. Changes in microglial gene expression were overlapping between SCZ and other psychiatric disorders, but largely opposite from changes reported in Alzheimer's disease. This distinct microglial phenotype provides a crucial molecular hallmark for future research into the role of microglia in SCZ and other psychiatric disorders.
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Affiliation(s)
- Gijsje J. L. J. Snijders
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht University, Brain Center Rudolf MagnusUniversity Medical Center Utrecht, Utrecht University (BCRM‐UMCU‐UU)UtrechtThe Netherlands
- Department of PsychiatryIcahn School of MedicineNew YorkNew YorkUSA
| | | | | | - Amber Berdenis van Berlekom
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht University, Brain Center Rudolf MagnusUniversity Medical Center Utrecht, Utrecht University (BCRM‐UMCU‐UU)UtrechtThe Netherlands
- Department of Translational Neuroscience (BCRM‐UMCU‐UU)UtrechtThe Netherlands
| | | | | | - Donald J. MacIntyre
- Division of Psychiatry, Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Elly M. Hol
- Department of Translational Neuroscience (BCRM‐UMCU‐UU)UtrechtThe Netherlands
- Neuroimmunology, Netherlands Institute for Neuroscience, An Institute of the Royal Academy of Arts and SciencesAmsterdamThe Netherlands
| | - René S. Kahn
- Department of PsychiatryIcahn School of MedicineNew YorkNew YorkUSA
- Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical CenterBronxNew YorkUSA
| | - Lot D. de Witte
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht University, Brain Center Rudolf MagnusUniversity Medical Center Utrecht, Utrecht University (BCRM‐UMCU‐UU)UtrechtThe Netherlands
- Department of PsychiatryIcahn School of MedicineNew YorkNew YorkUSA
- Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical CenterBronxNew YorkUSA
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Chang JW, Reyes SD, Faure-Kumar E, Lam SK, Lawlor MW, Leventer RJ, Lew SM, Lockhart PJ, Pope K, Weiner HL, Salamon N, Vinters HV, Mathern GW, Fallah A, Owens GC. Clonally Focused Public and Private T Cells in Resected Brain Tissue From Surgeries to Treat Children With Intractable Seizures. Front Immunol 2021; 12:664344. [PMID: 33889159 PMCID: PMC8056262 DOI: 10.3389/fimmu.2021.664344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
Using a targeted transcriptomics approach, we have analyzed resected brain tissue from a cohort of 53 pediatric epilepsy surgery cases, and have found that there is a spectrum of involvement of both the innate and adaptive immune systems as evidenced by the differential expression of immune-specific genes in the affected brain tissue. The specimens with the highest expression of immune-specific genes were from two Rasmussen encephalitis cases, which is known to be a neuro-immunological disease, but also from tuberous sclerosis complex (TSC), focal cortical dysplasia, and hemimegalencephaly surgery cases. We obtained T cell receptor (TCR) Vβ chain sequence data from brain tissue and blood from patients with the highest levels of T cell transcripts. The clonality indices and the frequency of the top 50 Vβ clonotypes indicated that T cells in the brain were clonally restricted. The top 50 Vβ clonotypes comprised both public and private (patient specific) clonotypes, and the TCR Vβ chain third complementarity region (CDR3) of the most abundant public Vβ clonotype in each brain sample was strikingly similar to a CDR3 that recognizes an immunodominant epitope in either human cytomegalovirus or Epstein Barr virus, or influenza virus A. We found that the frequency of 14 of the top 50 brain Vβ clonotypes from a TSC surgery case had significantly increased in brain tissue removed to control recurrent seizures 11 months after the first surgery. Conversely, we found that the frequency in the blood of 18 of the top 50 brain clonotypes from a second TSC patient, who was seizure free, had significantly decreased 5 months after surgery indicating that T cell clones found in the brain had contracted in the periphery after removal of the brain area associated with seizure activity and inflammation. However, the frequency of a public and a private clonotype significantly increased in the brain after seizures recurred and the patient underwent a second surgery. Combined single cell gene expression and TCR sequencing of brain-infiltrating leukocytes from the second surgery showed that the two clones were CD8 effector T cells, indicating that they are likely to be pathologically relevant.
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Affiliation(s)
- Julia W Chang
- Department of Neurosurgery, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Samuel D Reyes
- Department of Neurosurgery, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Emmanuelle Faure-Kumar
- Department of Medicine: Division of Digestive Diseases, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Sandi K Lam
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Ann & Robert H. Lurie Children's Hospital, Chicago, IL, United States
| | - Michael W Lawlor
- Department of Pathology, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, United States
| | - Richard J Leventer
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Sean M Lew
- Department of Neurosurgery, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, United States
| | - Paul J Lockhart
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Kathryn Pope
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Howard L Weiner
- Department of Pediatric Neurosurgery, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Noriko Salamon
- Department of Radiological Sciences, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Harry V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Gary W Mathern
- Department of Neurosurgery, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Aria Fallah
- Department of Neurosurgery, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States.,Mattel Children's Hospital, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Geoffrey C Owens
- Department of Neurosurgery, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
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Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A. Machine learning identifies candidates for drug repurposing in Alzheimer's disease. Nat Commun 2021; 12:1033. [PMID: 33589615 PMCID: PMC7884393 DOI: 10.1038/s41467-021-21330-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/21/2021] [Indexed: 01/31/2023] Open
Abstract
Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a large amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA) for another indication is a more rapid and less expensive option. We present DRIAD (Drug Repurposing In AD), a machine learning framework that quantifies potential associations between the pathology of AD severity (the Braak stage) and molecular mechanisms as encoded in lists of gene names. DRIAD is applied to lists of genes arising from perturbations in differentiated human neural cell cultures by 80 FDA-approved and clinically tested drugs, producing a ranked list of possible repurposing candidates. Top-scoring drugs are inspected for common trends among their targets. We propose that the DRIAD method can be used to nominate drugs that, after additional validation and identification of relevant pharmacodynamic biomarker(s), could be readily evaluated in a clinical trial.
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Affiliation(s)
- Steve Rodriguez
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Clemens Hug
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Petar Todorov
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Nienke Moret
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Kyle Evans
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - George Zhou
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nathan T Johnson
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Mark W Albers
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA.
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
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37
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Johnson TS, Xiang S, Dong T, Huang Z, Cheng M, Wang T, Yang K, Ni D, Huang K, Zhang J. Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer's Disease. Sci Rep 2021; 11:353. [PMID: 33432017 PMCID: PMC7801680 DOI: 10.1038/s41598-020-79740-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/09/2020] [Indexed: 11/09/2022] Open
Abstract
Alzheimer's disease (AD) brains are characterized by progressive neuron loss and gliosis. Previous studies of gene expression using bulk tissue samples often fail to consider changes in cell-type composition when comparing AD versus control, which can lead to differences in expression levels that are not due to transcriptional regulation. We mined five large transcriptomic AD datasets for conserved gene co-expression module, then analyzed differential expression and differential co-expression within the modules between AD samples and controls. We performed cell-type deconvolution analysis to determine whether the observed differential expression was due to changes in cell-type proportions in the samples or to transcriptional regulation. Our findings were validated using four additional datasets. We discovered that the increased expression of microglia modules in the AD samples can be explained by increased microglia proportions in the AD samples. In contrast, decreased expression and perturbed co-expression within neuron modules in the AD samples was likely due in part to altered regulation of neuronal pathways. Several transcription factors that are differentially expressed in AD might account for such altered gene regulation. Similarly, changes in gene expression and co-expression within astrocyte modules could be attributed to combined effects of astrogliosis and astrocyte gene activation. Gene expression in the astrocyte modules was also strongly correlated with clinicopathological biomarkers. Through this work, we demonstrated that combinatorial analysis can delineate the origins of transcriptomic changes in bulk tissue data and shed light on key genes and pathways involved in AD.
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Affiliation(s)
- Travis S Johnson
- Department of Biostatistics, Indiana University, School of Medicine, Indianapolis, IN, 46202, USA
| | - Shunian Xiang
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN, 46202, USA
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Tianhan Dong
- Department of Pharmacology, Indiana University, School of Medicine, Indianapolis, IN, 46202, USA
| | - Zhi Huang
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Michael Cheng
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN, 46202, USA
| | - Tianfu Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Kai Yang
- Department of Pediatrics, Indiana University, School of Medicine, Indianapolis, IN, 46202, USA
| | - Dong Ni
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Kun Huang
- Department of Medicine, Indiana University, School of Medicine, Indianapolis, IN, 46202, USA.
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN, 46202, USA.
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Tsatsanis A, McCorkindale AN, Wong BX, Patrick E, Ryan TM, Evans RW, Bush AI, Sutherland GT, Sivaprasadarao A, Guennewig B, Duce JA. The acute phase protein lactoferrin is a key feature of Alzheimer's disease and predictor of Aβ burden through induction of APP amyloidogenic processing. Mol Psychiatry 2021; 26:5516-5531. [PMID: 34400772 PMCID: PMC8758478 DOI: 10.1038/s41380-021-01248-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/17/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023]
Abstract
Amyloidogenic processing of the amyloid precursor protein (APP) forms the amyloid-β peptide (Aβ) component of pathognomonic extracellular plaques of AD. Additional early cortical changes in AD include neuroinflammation and elevated iron levels. Activation of the innate immune system in the brain is a neuroprotective response to infection; however, persistent neuroinflammation is linked to AD neuropathology by uncertain mechanisms. Non-parametric machine learning analysis on transcriptomic data from a large neuropathologically characterised patient cohort revealed the acute phase protein lactoferrin (Lf) as the key predictor of amyloid pathology. In vitro studies showed that an interaction between APP and the iron-bound form of Lf secreted from activated microglia diverted neuronal APP endocytosis from the canonical clathrin-dependent pathway to one requiring ADP ribosylation factor 6 trafficking. By rerouting APP recycling to the Rab11-positive compartment for amyloidogenic processing, Lf dramatically increased neuronal Aβ production. Lf emerges as a novel pharmacological target for AD that not only modulates APP processing but provides a link between Aβ production, neuroinflammation and iron dysregulation.
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Affiliation(s)
- Andrew Tsatsanis
- grid.5335.00000000121885934The ALBORADA Drug Discovery Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK ,grid.9909.90000 0004 1936 8403Faculty of Biological Sciences, School of Biomedical Sciences, University of Leeds, Leeds, West Yorkshire UK
| | - Andrew N. McCorkindale
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, Charles Perkins Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW Australia
| | - Bruce X. Wong
- grid.5335.00000000121885934The ALBORADA Drug Discovery Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK ,grid.9909.90000 0004 1936 8403Faculty of Biological Sciences, School of Biomedical Sciences, University of Leeds, Leeds, West Yorkshire UK ,grid.1008.90000 0001 2179 088XMelbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC Australia
| | - Ellis Patrick
- grid.1013.30000 0004 1936 834XFaculty of Science, School of Mathematics and Statistics, University of Sydney, Camperdown, NSW Australia
| | - Tim M. Ryan
- grid.1008.90000 0001 2179 088XMelbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC Australia
| | - Robert W. Evans
- grid.7728.a0000 0001 0724 6933School of Engineering and Design, Brunel University, London, UK
| | - Ashley I. Bush
- grid.1008.90000 0001 2179 088XMelbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC Australia
| | - Greg T. Sutherland
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, Charles Perkins Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW Australia
| | - Asipu Sivaprasadarao
- grid.9909.90000 0004 1936 8403Faculty of Biological Sciences, School of Biomedical Sciences, University of Leeds, Leeds, West Yorkshire UK
| | - Boris Guennewig
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, Brain and Mind Centre and School of Medical Sciences, The University of Sydney, Camperdown, NSW Australia
| | - James A. Duce
- grid.5335.00000000121885934The ALBORADA Drug Discovery Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK ,grid.9909.90000 0004 1936 8403Faculty of Biological Sciences, School of Biomedical Sciences, University of Leeds, Leeds, West Yorkshire UK ,grid.1008.90000 0001 2179 088XMelbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC Australia
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39
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Ormel PR, Böttcher C, Gigase FAJ, Missall RD, van Zuiden W, Fernández Zapata MC, Ilhan D, de Goeij M, Udine E, Sommer IEC, Priller J, Raj T, Kahn RS, Hol EM, de Witte LD. A characterization of the molecular phenotype and inflammatory response of schizophrenia patient-derived microglia-like cells. Brain Behav Immun 2020; 90:196-207. [PMID: 32798663 DOI: 10.1016/j.bbi.2020.08.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/28/2020] [Accepted: 08/12/2020] [Indexed: 01/02/2023] Open
Abstract
Different lines of evidence support a causal role for microglia in the pathogenesis of schizophrenia. However, how schizophrenia patient-derived microglia are affected at the phenotypic and functional level is still largely unknown. We used a recently described model to induce patient-derived microglia-like cells and used this to analyze changes in the molecular phenotype and function of myeloid cells in schizophrenia. We isolated monocytes from twenty recent-onset schizophrenia patients and twenty non-psychiatric controls. We cultured the cells towards an induced microglia-like phenotype (iMG), analyzed the phenotype of the cells by RNA sequencing and mass cytometry, and their response to LPS. Mass cytometry showed a high heterogeneity of iMG in cells derived from patients as well as controls. The prevalence of two iMG clusters was significantly higher in schizophrenia patients (adjusted p-value < 0.001). These subsets are characterized by expression of ApoE, Ccr2, CD18, CD44, and CD95, as well as IRF8, P2Y12, Cx3cr1 and HLA-DR. In addition, we found that patient-derived iMG show an enhanced response to LPS, with increased secretion of TNF-α. Further studies are needed to replicate these findings, to determine whether similar subclusters are present in schizophrenia patients in vivo, and to address how these subclusters are related to the increased response to LPS, as well as other microglial functions.
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Affiliation(s)
- Paul R Ormel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands; Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Chotima Böttcher
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Frederieke A J Gigase
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roy D Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Welmoed van Zuiden
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Camila Fernández Zapata
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dilara Ilhan
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Michelle de Goeij
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Evan Udine
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Iris E C Sommer
- Department of Neuroscience, University Medical Center Groningen, Groningen, The Netherlands
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute of Health, Berlin, Germany; Deutsches Zentrum Für Neurodegenartive Erkrankungen (DZNE), Bonn, Germany; Cluster of Excellence NeuroCure, Berlin, Germany; University of Edinburgh and UK Dementia Research Institute, Edinburgh, UK
| | - Towfique Raj
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elly M Hol
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands; Department of Neuroimmunology, Netherlands Institute for Neuroscience, An Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands; Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA.
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40
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Pascua-Maestro R, Corraliza-Gomez M, Fadrique-Rojo C, Ledesma MD, Schuchman EH, Sanchez D, Ganfornina MD. Apolipoprotein D-mediated preservation of lysosomal function promotes cell survival and delays motor impairment in Niemann-Pick type A disease. Neurobiol Dis 2020; 144:105046. [PMID: 32798728 DOI: 10.1016/j.nbd.2020.105046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/20/2020] [Accepted: 08/08/2020] [Indexed: 12/31/2022] Open
Abstract
Lysosomal Storage Diseases (LSD) are genetic diseases causing systemic and nervous system dysfunction. The glia-derived lipid binding protein Apolipoprotein D (ApoD) is required for lysosomal functional integrity in glial and neuronal cells, ensuring cell survival upon oxidative stress or injury. Here we test whether ApoD counteracts the pathogenic consequences of a LSD, Niemann Pick-type-A disease (NPA), where mutations in the acid sphingomyelinase gene result in sphingomyelin accumulation, lysosomal permeabilization and early-onset neurodegeneration. We performed a multivariable analysis of behavioral, cellular and molecular outputs in 12 and 24 week-old male and female NPA model mice, combined with ApoD loss-of-function mutation. Lack of ApoD in NPA mice accelerates cerebellar-dependent motor deficits, enhancing loss of Purkinje neurons. We studied ApoD expression in brain sections from a NPA patient and age-matched control, and the functional consequences of ApoD supplementation in primary human fibroblasts from two independent NPA patients and two control subjects. Cell viability, lipid peroxidation, and lysosomal functional integrity (pH, Cathepsin B activity, Galectin-3 exclusion) were examined. ApoD is endogenously overexpressed in NPA patients and NPA mouse brains and targeted to lysosomes of NPA patient cells, including Purkinje neurons and cultured fibroblasts. The accelerated lysosomal targeting of ApoD by oxidative stress is hindered in NPA fibroblasts, contributing to NPA lysosomes vulnerability. Exogenously added ApoD reduces NPA-prompted lysosomal permeabilization and alkalinization, reverts lipid peroxides accumulation, and significantly increases NPA cell survival. ApoD administered simultaneously to sphingomyelin overload results in complete rescue of cell survival. Our results reveal that ApoD protection of lysosomal integrity counteracts NPA pathology. ApoD supplementation could significantly delay not only the progression of NPA disease, but also of other LSDs through its beneficial effects in lysosomal functional maintenance.
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Affiliation(s)
- Raquel Pascua-Maestro
- Instituto de Biología y Genética Molecular, Universidad de Valladolid-CSIC, 47003 Valladolid, Spain
| | - Miriam Corraliza-Gomez
- Instituto de Biología y Genética Molecular, Universidad de Valladolid-CSIC, 47003 Valladolid, Spain
| | - Cristian Fadrique-Rojo
- Instituto de Biología y Genética Molecular, Universidad de Valladolid-CSIC, 47003 Valladolid, Spain
| | - Maria D Ledesma
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain
| | | | - Diego Sanchez
- Instituto de Biología y Genética Molecular, Universidad de Valladolid-CSIC, 47003 Valladolid, Spain.
| | - Maria D Ganfornina
- Instituto de Biología y Genética Molecular, Universidad de Valladolid-CSIC, 47003 Valladolid, Spain.
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41
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Miron VE, Priller J. Investigating Microglia in Health and Disease: Challenges and Opportunities. Trends Immunol 2020; 41:785-793. [PMID: 32736967 DOI: 10.1016/j.it.2020.07.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022]
Abstract
Microglia are tissue-resident macrophages implicated in central nervous system (CNS) development, homeostasis, and response to injury. Recent advances in transcriptomics, multiplex protein expression analysis, and experimental depletion of microglia have cemented their importance. However, it is still unclear which models are best suited to investigate microglia and explore their function in human disease. Here, we discuss issues regarding off-targeting during experimental manipulation, and differences and similarities between human and rodent microglia. With new developments in transgenic lines and human-rodent chimeras, we anticipate that in coming years, a clearer picture of microglia function in health and disease will emerge.
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Affiliation(s)
- Veronique E Miron
- Medical Research Council Centre for Reproductive Health, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK.
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin Berlin and DZNE, Berlin, Germany; UK Dementia Research Institute, The University of Edinburgh, Edinburgh, UK
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42
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Patir A, Fraser AM, Barnett MW, McTeir L, Rainger J, Davey MG, Freeman TC. The transcriptional signature associated with human motile cilia. Sci Rep 2020; 10:10814. [PMID: 32616903 PMCID: PMC7331728 DOI: 10.1038/s41598-020-66453-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
Cilia are complex microtubule-based organelles essential to a range of processes associated with embryogenesis and tissue homeostasis. Mutations in components of these organelles or those involved in their assembly may result in a diverse set of diseases collectively known as ciliopathies. Accordingly, many cilia-associated proteins have been described, while those distinguishing cilia subtypes are poorly defined. Here we set out to define genes associated with motile cilia in humans based on their transcriptional signature. To define the signature, we performed network deconvolution of transcriptomics data derived from tissues possessing motile ciliated cell populations. For each tissue, genes coexpressed with the motile cilia-associated transcriptional factor, FOXJ1, were identified. The consensus across tissues provided a transcriptional signature of 248 genes. To validate these, we examined the literature, databases (CilDB, CentrosomeDB, CiliaCarta and SysCilia), single cell RNA-Seq data, and the localisation of mRNA and proteins in motile ciliated cells. In the case of six poorly characterised signature genes, we performed new localisation experiments on ARMC3, EFCAB6, FAM183A, MYCBPAP, RIBC2 and VWA3A. In summary, we report a set of motile cilia-associated genes that helps shape our understanding of these complex cellular organelles.
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Affiliation(s)
- Anirudh Patir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Amy M Fraser
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Mark W Barnett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Lynn McTeir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Joe Rainger
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Megan G Davey
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Tom C Freeman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK.
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43
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Summers KM, Bush SJ, Wu C, Su AI, Muriuki C, Clark EL, Finlayson HA, Eory L, Waddell LA, Talbot R, Archibald AL, Hume DA. Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas. Front Genet 2020; 10:1355. [PMID: 32117413 PMCID: PMC7034361 DOI: 10.3389/fgene.2019.01355] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
The domestic pig (Sus scrofa) is both an economically important livestock species and a model for biomedical research. Two highly contiguous pig reference genomes have recently been released. To support functional annotation of the pig genomes and comparative analysis with large human transcriptomic data sets, we aimed to create a pig gene expression atlas. To achieve this objective, we extended a previous approach developed for the chicken. We downloaded RNAseq data sets from public repositories, down-sampled to a common depth, and quantified expression against a reference transcriptome using the mRNA quantitation tool, Kallisto. We then used the network analysis tool Graphia to identify clusters of transcripts that were coexpressed across the merged data set. Consistent with the principle of guilt-by-association, we identified coexpression clusters that were highly tissue or cell-type restricted and contained transcription factors that have previously been implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes, such as the cell cycle and oxidative phosphorylation. The same approach was used to identify coexpression clusters within RNAseq data from multiple individual liver and brain samples, highlighting cell type, process, and region-specific gene expression. Evidence of conserved expression can add confidence to assignment of orthology between pig and human genes. Many transcripts currently identified as novel genes with ENSSSCG or LOC IDs were found to be coexpressed with annotated neighbouring transcripts in the same orientation, indicating they may be products of the same transcriptional unit. The meta-analytic approach to utilising public RNAseq data is extendable to include new data sets and new species and provides a framework to support the Functional Annotation of Animals Genomes (FAANG) initiative.
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Affiliation(s)
- Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Andrew I. Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Charity Muriuki
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Emily L. Clark
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | | | - Lel Eory
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Lindsey A. Waddell
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Richard Talbot
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Alan L. Archibald
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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Healy LM, Yaqubi M, Ludwin S, Antel JP. Species differences in immune-mediated CNS tissue injury and repair: A (neuro)inflammatory topic. Glia 2019; 68:811-829. [PMID: 31724770 DOI: 10.1002/glia.23746] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/04/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022]
Abstract
Cells of the adaptive and innate immune systems in the brain parenchyma and in the meningeal spaces contribute to physiologic functions and disease states in the central nervous system (CNS). Animal studies have demonstrated the involvement of immune constituents, along with major histocompatibility complex (MHC) molecules, in neural development and rare genetic disorders (e.g., colony stimulating factor 1 receptor [CSF1R] deficiency). Genome wide association studies suggest a comparable role of the immune system in humans. Although the CNS can be the target of primary autoimmune disorders, no current experimental model captures all of the features of the most common human disorder placed in this category, multiple sclerosis (MS). Such features include spontaneous onset, environmental contributions, and a recurrent/progressive disease course in a genetically predisposed host. Numerous therapeutic interventions related to antigen and cytokine specific therapies have demonstrated effectiveness in experimental autoimmune encephalomyelitis (EAE), the animal model used to define principles underlying immune-mediated mechanisms in MS. Despite the similarities in the two diseases, most treatments used to ameliorate EAE have failed to translate to the human disease. As directly demonstrated in animal models and implicated by correlative studies in humans, adaptive and innate immune constituents within the systemic compartment and resident in the CNS contribute to the disease course of neurodegenerative and neurobehavioral disorders. The expanding knowledge of the molecular properties of glial cells provides increasing insights into species related variables. These variables affect glial bidirectional interactions with the immune system as well as their own production of "immune molecules" that mediate tissue injury and repair.
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Affiliation(s)
- Luke M Healy
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Moein Yaqubi
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Samuel Ludwin
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
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Chew G, Petretto E. Transcriptional Networks of Microglia in Alzheimer's Disease and Insights into Pathogenesis. Genes (Basel) 2019; 10:E798. [PMID: 31614849 PMCID: PMC6826883 DOI: 10.3390/genes10100798] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Microglia, the main immune cells of the central nervous system, are increasingly implicated in Alzheimer's disease (AD). Manifold transcriptomic studies in the brain have not only highlighted microglia's role in AD pathogenesis, but also mapped crucial pathological processes and identified new therapeutic targets. An important component of many of these transcriptomic studies is the investigation of gene expression networks in AD brain, which has provided important new insights into how coordinated gene regulatory programs in microglia (and other cell types) underlie AD pathogenesis. Given the rapid technological advancements in transcriptional profiling, spanning from microarrays to single-cell RNA sequencing (scRNA-seq), tools used for mapping gene expression networks have evolved to keep pace with the unique features of each transcriptomic platform. In this article, we review the trajectory of transcriptomic network analyses in AD from brain to microglia, highlighting the corresponding methodological developments. Lastly, we discuss examples of how transcriptional network analysis provides new insights into AD mechanisms and pathogenesis.
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Affiliation(s)
- Gabriel Chew
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 69857 Singapore, Singapore.
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 69857 Singapore, Singapore.
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