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      Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders

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          Abstract

          The meninges contain adaptive immune cells that provide immunosurveillance of the CNS. These cells are thought to derive from the systemic circulation. Through single-cell analyses, confocal imaging, bone marrow chimeras, and parabiosis experiments, we show that meningeal B cells derive locally from the calvaria, which harbors a bone marrow niche for hematopoiesis. B cells reach the meninges from the calvaria through specialized vascular connections. This calvarial–meningeal path of B cell development may provide the CNS with a constant supply of B cells educated by CNS antigens. Conversely, we show that a subset of antigen-experienced B cells that populate the meninges in aging mice are blood-borne. These results identify a private source for meningeal B cells. which may help maintain immune privilege within the CNS.

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          Comprehensive Integration of Single-Cell Data

          Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
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            Is Open Access

            Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

            A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
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              A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.

              Alzheimer's disease (AD) is a detrimental neurodegenerative disease with no effective treatments. Due to cellular heterogeneity, defining the roles of immune cell subsets in AD onset and progression has been challenging. Using transcriptional single-cell sorting, we comprehensively map all immune populations in wild-type and AD-transgenic (Tg-AD) mouse brains. We describe a novel microglia type associated with neurodegenerative diseases (DAM) and identify markers, spatial localization, and pathways associated with these cells. Immunohistochemical staining of mice and human brain slices shows DAM with intracellular/phagocytic Aβ particles. Single-cell analysis of DAM in Tg-AD and triggering receptor expressed on myeloid cells 2 (Trem2)(-/-) Tg-AD reveals that the DAM program is activated in a two-step process. Activation is initiated in a Trem2-independent manner that involves downregulation of microglia checkpoints, followed by activation of a Trem2-dependent program. This unique microglia-type has the potential to restrict neurodegeneration, which may have important implications for future treatment of AD and other neurodegenerative diseases. VIDEO ABSTRACT.
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                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                June 03 2021
                : eabf9277
                Affiliations
                [1 ]Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
                [2 ]Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.
                [3 ]Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
                [4 ]Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
                [5 ]Department of Molecular Microbiology, Center for Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO 63110, USA.
                [6 ]Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO 63110, USA.
                [7 ]Departments of Cell Biology and Physiology and Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA.
                [8 ]Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, MO 63130, USA.
                [9 ]McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63110, USA.
                [10 ]Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.
                [11 ]Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA.
                [12 ]Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
                Article
                10.1126/science.abf9277
                34083450
                af2dedfc-c3bb-42eb-8cbe-2aaebe88ac29
                © 2021
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