Chimeric organotypic brain slice cultures support the maturation and functional analysis of human iPSC-derived microglia

Chimeric organotypic brain slice cultures support the maturation and functional analysis of human iPSC-derived microglia | 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 Article Chimeric organotypic brain slice cultures support the maturation and functional analysis of human iPSC-derived microglia Deborah Kronenberg-Versteeg, Lena Erlebach, Marc Welzer, Teresa Bartling, and 20 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8176878/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 Microglia, the primary myeloid cells of the brain, are crucial for maintaining brain homeostasis and are implicated in various neuropathological processes. Microglial identity and function are determined by their ontogeny and the brain microenvironment. Therefore, model systems that faithfully reproduce mature human microglial molecular and functional phenotypes are crucial for understanding their role in brain health and disease. Here, we demonstrate that microglial precursors derived from induced pluripotent stem cells (iPSCs) can integrate and mature in murine organotypic brain slices. Importantly, we achieve a near-complete replacement of murine with human microglia and demonstrate that their maturation is driven solely by the tissue environment through previously underappreciated cross-species human colony stimulating factor 1 receptor (hCSF1R) binding of murine interleukin 34 (IL34). The iPSC-derived microglia in the chimeric brain slice cultures (cBSCs) exhibit functional responses and develop transcriptional states reminiscent of adult human microglia while responding to developing -synuclein proteopathy with heightened inflammatory state. Thus, our findings establish cBSCs as a tool for examining human microglia in a physiologically relevant environment, while maintaining the experimental flexibility of an in vitro system for mechanistically investigating neuropathological microglial responses. Biological sciences/Neuroscience/Glial biology/Microglia Biological sciences/Neuroscience/Diseases of the nervous system/Neurodegeneration Biological sciences/Biological techniques/Biological models/Neurological models Biological sciences/Cell biology/Mechanisms of disease Full Text Additional Declarations There is NO Competing Interest. Supplementary Files ChimericSliceCulturesExtendedData.pdf Extended Data 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-8176878","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":550534503,"identity":"23447f76-1038-4718-aeb9-988b8fa32ece","order_by":0,"name":"Deborah 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iPSC-derived microglia","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 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Microglial identity and function are determined by their ontogeny and the brain microenvironment. Therefore, model systems that faithfully reproduce mature human microglial molecular and functional phenotypes are crucial for understanding their role in brain health and disease. \r\nHere, we demonstrate that microglial precursors derived from induced pluripotent stem cells (iPSCs) can integrate and mature in murine organotypic brain slices. Importantly, we achieve a near-complete replacement of murine with human microglia and demonstrate that their maturation is driven solely by the tissue environment through previously underappreciated cross-species human colony stimulating factor 1 receptor (hCSF1R) binding of murine interleukin 34 (IL34). The iPSC-derived microglia in the chimeric brain slice cultures (cBSCs) exhibit functional responses and develop transcriptional states reminiscent of adult human microglia while responding to developing -synuclein proteopathy with heightened inflammatory state.\r\nThus, our findings establish cBSCs as a tool for examining human microglia in a physiologically relevant environment, while maintaining the experimental flexibility of an in vitro system for mechanistically investigating neuropathological microglial responses.","manuscriptTitle":"Chimeric organotypic brain slice cultures support the maturation and functional analysis of human iPSC-derived microglia","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-08 10:47:10","doi":"10.21203/rs.3.rs-8176878/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"0f1e0b5a-aefc-487c-b238-6eb52fe28596","owner":[],"postedDate":"December 8th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":58577060,"name":"Biological sciences/Neuroscience/Glial biology/Microglia"},{"id":58577061,"name":"Biological sciences/Neuroscience/Diseases of the nervous system/Neurodegeneration"},{"id":58577062,"name":"Biological sciences/Biological techniques/Biological models/Neurological models"},{"id":58577063,"name":"Biological sciences/Cell biology/Mechanisms of disease"}],"tags":[],"updatedAt":"2025-12-11T10:22:13+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-08 10:47:10","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8176878","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8176878","identity":"rs-8176878","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}