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Prakash P, Erdjument-Bromage H, O'Dea MR, Munson CN, Labib D, Fossati V, Neubert TA, Liddelow SA. Proteomic profiling of interferon-responsive reactive astrocytes in rodent and human. Glia 2024; 72:625-642. [PMID: 38031883 PMCID: PMC10843807 DOI: 10.1002/glia.24494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023]
Abstract
Astrocytes are a heterogeneous population of central nervous system glial cells that respond to pathological insults and injury by undergoing a transformation called "reactivity." Reactive astrocytes exhibit distinct and context-dependent cellular, molecular, and functional state changes that can either support or disturb tissue homeostasis. We recently identified a reactive astrocyte sub-state defined by interferon-responsive genes like Igtp, Ifit3, Mx1, and others, called interferon-responsive reactive astrocytes (IRRAs). To further this transcriptomic definition of IRRAs, we wanted to define the proteomic changes that occur in this reactive sub-state. We induced IRRAs in immunopanned rodent astrocytes and human iPSC-differentiated astrocytes using TNF, IL1α, C1Q, and IFNβ and characterized their proteomic profile (both cellular and secreted) using unbiased quantitative proteomics. We identified 2335 unique cellular proteins, including IFIT2/3, IFITM3, OASL1/2, MX1/2/3, and STAT1. We also report that rodent and human IRRAs secrete PAI1, a serine protease inhibitor which may influence reactive states and functions of nearby cells. Finally, we evaluated how IRRAs are distinct from neurotoxic reactive astrocytes (NRAs). While NRAs are described by expression of the complement protein C3, it was not upregulated in IRRAs. Instead, we found ~90 proteins unique to IRRAs not identified in NRAs, including OAS1A, IFIT3, and MX1. Interferon signaling in astrocytes is critical for the antiviral immune response and for regulating synaptic plasticity and glutamate transport mechanisms. How IRRAs contribute to these functions is unknown. This study provides the basis for future experiments to define the functional roles of IRRAs in the context of neurodegenerative disorders.
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Affiliation(s)
- Priya Prakash
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
| | - Hediye Erdjument-Bromage
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Michael R O'Dea
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
| | - Christy N Munson
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
| | - David Labib
- The New York Stem Cell Foundation Research Institute, New York, New York, USA
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, New York, USA
| | - Thomas A Neubert
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, New York, USA
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, New York, USA
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Frazel PW, Fricano-Kugler K, May-Zhang AA, O'Dea MR, Prakash P, Desmet NM, Lee H, Meltzer RH, Fontanez KM, Hettige P, Agam Y, Lithwick-Yanai G, Lipson D, Luikart BW, Dasen JD, Liddelow SA. Single-cell analysis of the nervous system at small and large scales with instant partitions. bioRxiv 2023:2023.07.14.549051. [PMID: 37503160 PMCID: PMC10370061 DOI: 10.1101/2023.07.14.549051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Single-cell RNA sequencing is a new frontier across all biology, particularly in neuroscience. While powerful for answering numerous neuroscience questions, limitations in sample input size, and initial capital outlay can exclude some researchers from its application. Here, we tested a recently introduced method for scRNAseq across diverse scales and neuroscience experiments. We benchmarked against a major current scRNAseq technology and found that PIPseq performed similarly, in line with earlier benchmarking data. Across dozens of samples, PIPseq recovered many brain cell types at small and large scales (1,000-100,000 cells/sample) and was able to detect differentially expressed genes in an inflammation paradigm. Similarly, PIPseq could detect expected and new differentially expressed genes in a brain single cell suspension from a knockout mouse model; it could also detect rare, virally-la-belled cells following lentiviral targeting and gene knockdown. Finally, we used PIPseq to investigate gene expression in a nontraditional model species, the little skate (Leucoraja erinacea). In total, PIPSeq was able to detect single-cell gene expression changes across models and species, with an added benefit of large scale capture and sequencing of each sample.
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Fernández-Castañeda A, Lu P, Geraghty AC, Song E, Lee MH, Wood J, O'Dea MR, Dutton S, Shamardani K, Nwangwu K, Mancusi R, Yalçın B, Taylor KR, Acosta-Alvarez L, Malacon K, Keough MB, Ni L, Woo PJ, Contreras-Esquivel D, Toland AMS, Gehlhausen JR, Klein J, Takahashi T, Silva J, Israelow B, Lucas C, Mao T, Peña-Hernández MA, Tabachnikova A, Homer RJ, Tabacof L, Tosto-Mancuso J, Breyman E, Kontorovich A, McCarthy D, Quezado M, Vogel H, Hefti MM, Perl DP, Liddelow S, Folkerth R, Putrino D, Nath A, Iwasaki A, Monje M. Mild respiratory COVID can cause multi-lineage neural cell and myelin dysregulation. Cell 2022; 185:2452-2468.e16. [PMID: 35768006 PMCID: PMC9189143 DOI: 10.1016/j.cell.2022.06.008] [Citation(s) in RCA: 184] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/04/2022] [Accepted: 06/07/2022] [Indexed: 12/13/2022]
Abstract
COVID survivors frequently experience lingering neurological symptoms that resemble cancer-therapy-related cognitive impairment, a syndrome for which white matter microglial reactivity and consequent neural dysregulation is central. Here, we explored the neurobiological effects of respiratory SARS-CoV-2 infection and found white-matter-selective microglial reactivity in mice and humans. Following mild respiratory COVID in mice, persistently impaired hippocampal neurogenesis, decreased oligodendrocytes, and myelin loss were evident together with elevated CSF cytokines/chemokines including CCL11. Systemic CCL11 administration specifically caused hippocampal microglial reactivity and impaired neurogenesis. Concordantly, humans with lasting cognitive symptoms post-COVID exhibit elevated CCL11 levels. Compared with SARS-CoV-2, mild respiratory influenza in mice caused similar patterns of white-matter-selective microglial reactivity, oligodendrocyte loss, impaired neurogenesis, and elevated CCL11 at early time points, but after influenza, only elevated CCL11 and hippocampal pathology persisted. These findings illustrate similar neuropathophysiology after cancer therapy and respiratory SARS-CoV-2 infection which may contribute to cognitive impairment following even mild COVID.
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Affiliation(s)
| | - Peiwen Lu
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Anna C Geraghty
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Eric Song
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Myoung-Hwa Lee
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Jamie Wood
- Abilities Research Center, Department of Rehabilitation and Human Performance, Mount Sinai School of Medicine, New York, NY, USA
| | - Michael R O'Dea
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA
| | - Selena Dutton
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kiarash Shamardani
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kamsi Nwangwu
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Rebecca Mancusi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Belgin Yalçın
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kathryn R Taylor
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Lehi Acosta-Alvarez
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Karen Malacon
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Michael B Keough
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Lijun Ni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Pamelyn J Woo
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | | | | | | | - Jon Klein
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | | | - Julio Silva
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | | | - Carolina Lucas
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | | | | | - Robert J Homer
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Laura Tabacof
- Abilities Research Center, Department of Rehabilitation and Human Performance, Mount Sinai School of Medicine, New York, NY, USA
| | - Jenna Tosto-Mancuso
- Abilities Research Center, Department of Rehabilitation and Human Performance, Mount Sinai School of Medicine, New York, NY, USA
| | - Erica Breyman
- Abilities Research Center, Department of Rehabilitation and Human Performance, Mount Sinai School of Medicine, New York, NY, USA
| | - Amy Kontorovich
- Cardiovascular Research Institute, Mount Sinai School of Medicine, New York, NY, USA
| | - Dayna McCarthy
- Abilities Research Center, Department of Rehabilitation and Human Performance, Mount Sinai School of Medicine, New York, NY, USA
| | | | - Hannes Vogel
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Marco M Hefti
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Daniel P Perl
- Department of Pathology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | - Shane Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA; Departments of Neuroscience & Physiology and of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA; Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - David Putrino
- Abilities Research Center, Department of Rehabilitation and Human Performance, Mount Sinai School of Medicine, New York, NY, USA
| | - Avindra Nath
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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Green LA, O'Dea MR, Hoover CA, DeSantis DF, Smith CJ. The embryonic zebrafish brain is seeded by a lymphatic-dependent population of mrc1 + microglia precursors. Nat Neurosci 2022; 25:849-864. [PMID: 35710983 PMCID: PMC10680068 DOI: 10.1038/s41593-022-01091-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/06/2022] [Indexed: 02/02/2023]
Abstract
Microglia are the resident macrophages of the CNS that serve critical roles in brain construction. Although human brains contain microglia by 4 weeks gestation, an understanding of the earliest microglia that seed the brain during its development remains unresolved. Using time-lapse imaging in zebrafish, we discovered a mrc1a+ microglia precursor population that seeds the brain before traditionally described microglia. These early microglia precursors are dependent on lymphatic vasculature that surrounds the brain and are independent of pu1+ yolk sac-derived microglia. Single-cell RNA-sequencing datasets reveal Mrc1+ microglia in the embryonic brains of mice and humans. We then show in zebrafish that these early mrc1a+ microglia precursors preferentially expand during pathophysiological states in development. Taken together, our results identify a critical role of lymphatics in the microglia precursors that seed the early embryonic brain.
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Affiliation(s)
- Lauren A Green
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- The Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, USA
| | - Michael R O'Dea
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Camden A Hoover
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- The Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, USA
| | - Dana F DeSantis
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- The Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, USA
| | - Cody J Smith
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
- The Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, USA.
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Sadick JS, O'Dea MR, Hasel P, Dykstra T, Faustin A, Liddelow SA. Astrocytes and oligodendrocytes undergo subtype-specific transcriptional changes in Alzheimer's disease. Neuron 2022; 110:1788-1805.e10. [PMID: 35381189 DOI: 10.1016/j.neuron.2022.03.008] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 01/24/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022]
Abstract
Resolving glial contributions to Alzheimer's disease (AD) is necessary because changes in neuronal function, such as reduced synaptic density, altered electrophysiological properties, and degeneration, are not entirely cell autonomous. To improve understanding of transcriptomic heterogeneity in glia during AD, we used single-nuclei RNA sequencing (snRNA-seq) to characterize astrocytes and oligodendrocytes from apolipoprotein (APOE) Ɛ2/3 human AD and age- and genotype-matched non-symptomatic (NS) brains. We enriched astrocytes before sequencing and characterized pathology from the same location as the sequenced material. We characterized baseline heterogeneity in both astrocytes and oligodendrocytes and identified global and subtype-specific transcriptomic changes between AD and NS astrocytes and oligodendrocytes. We also took advantage of recent human and mouse spatial transcriptomics resources to localize heterogeneous astrocyte subtypes to specific regions in the healthy and inflamed brain. Finally, we integrated our data with published AD snRNA-seq datasets, highlighting the power of combining datasets to resolve previously unidentifiable astrocyte subpopulations.
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Affiliation(s)
- Jessica S Sadick
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Michael R O'Dea
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Philip Hasel
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Taitea Dykstra
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Arline Faustin
- Center for Cognitive Neurology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA; Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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