Whole-Brain Single-Neuron Atlas Reveals Microglial Security Hole Accelerating Neuronal Vulnerability

Whole-Brain Single-Neuron Atlas Reveals Microglial Security Hole Accelerating Neuronal Vulnerability | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Biological Sciences - Article Whole-Brain Single-Neuron Atlas Reveals Microglial Security Hole Accelerating Neuronal Vulnerability Hiroki Ueda, Tomoki Mitani, Kosei Yamaura, Rikuhiro Yamada, Katsuhiko Matsumoto, and 8 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5827312/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Neurodegenerative diseases are characterized by progressive neuronal loss, yet subtle degeneration remains difficult to detect, hindering advancements in early diagnosis and intervention strategies. Here, we present a 3D, whole-brain, single-neuron atlas that aligns and compares neurons at single-cell resolution, surpassing 2D spatial limitations to precisely detect heterogeneous neurodegenerative lesions. Using the AppNL-G-F model of Alzheimer’s disease, we found that neuronal loss begins concurrently with amyloid-β deposition, indicating a more acute timeline than proposed by the amyloid hypothesis. We also identified age-dependent microglial redistribution from gray-matter–rich to white-matter–rich regions in wild-type mice, accelerated in AppNL-G-F, potentially reducing neuroprotective function. Spatial single-cell-resolution risk analysis revealed microglial depletion, rather than proliferation, as an early risk indicator for neuronal loss, and microgliosis often coexists with microglial loss, suggesting heightened microglial vulnerability. Integration with spatial transcriptomics showed neurons near microglia with reduced homeostatic gene expression are especially vulnerable. Together, these findings demonstrated that amyloid pathology skews microglial distribution and promotes their exhaustion, leading to microglial spatial disorganization and neuronal vulnerability, resulting in “microglial security holes”. Our study underscores the transformative potential of 3D analysis in neurodegenerative research, offering a versatile platform for organ-level spatial multi-omics integration to advance detection and therapeutic strategies. Biological sciences/Biological techniques/Imaging/3-D reconstruction Biological sciences/Neuroscience/Neural ageing Full Text Additional Declarations Yes there is potential Competing Interest. CUBICStars Inc., which H.R.U. founded and where T.T.M., K.M., and E.A.S. are employed, has filed patents regarding CUBIC-HV and CUBIC-Cloud. The company also provides CUBIC-Cloud web services. H.R.U., E.A.S., T.T.M., and K.M. are co-inventors on patents and patent applications owned or filed by RIKEN covering the CUBIC reagents and/or MOVIE. E.A.S. receives collaboration funding from Kantum Ushikata Co., LTD., which is related to the development of devices for cellomics. Supplementary Files SupplementaryTable1.xlsx Supplementary Table 1 Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5827312","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":413804290,"identity":"3960f882-14fe-4d4f-8d9e-d46d42328d6e","order_by":0,"name":"Hiroki 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E.A.S. receives collaboration funding from Kantum Ushikata Co., LTD., which is related to the development of devices for cellomics.","formattedTitle":"Whole-Brain Single-Neuron Atlas Reveals Microglial Security Hole Accelerating Neuronal Vulnerability","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-5827312/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5827312/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Neurodegenerative diseases are characterized by progressive neuronal loss, yet subtle degeneration remains difficult to detect, hindering advancements in early diagnosis and intervention strategies. Here, we present a 3D, whole-brain, single-neuron atlas that aligns and compares neurons at single-cell resolution, surpassing 2D spatial limitations to precisely detect heterogeneous neurodegenerative lesions. Using the AppNL-G-F model of Alzheimer’s disease, we found that neuronal loss begins concurrently with amyloid-β deposition, indicating a more acute timeline than proposed by the amyloid hypothesis. We also identified age-dependent microglial redistribution from gray-matter–rich to white-matter–rich regions in wild-type mice, accelerated in AppNL-G-F, potentially reducing neuroprotective function. Spatial single-cell-resolution risk analysis revealed microglial depletion, rather than proliferation, as an early risk indicator for neuronal loss, and microgliosis often coexists with microglial loss, suggesting heightened microglial vulnerability. Integration with spatial transcriptomics showed neurons near microglia with reduced homeostatic gene expression are especially vulnerable. Together, these findings demonstrated that amyloid pathology skews microglial distribution and promotes their exhaustion, leading to microglial spatial disorganization and neuronal vulnerability, resulting in “microglial security holes”. 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