The ontogeny of myeloid-stromal synovial tissue niches in rheumatoid arthritis

The ontogeny of myeloid-stromal synovial tissue niches in rheumatoid arthritis | 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 The ontogeny of myeloid-stromal synovial tissue niches in rheumatoid arthritis Mariola Kurowska-Stolarska, Aziza Elmesmari, Domenico Somma, Lucy MacDonald, and 28 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8079358/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 Recent single-cell multi-omic and spatial analyses of synovial biopsies have transformed our understanding of myeloid cell–driven mechanisms underlying human joint pathology and tissue homeostasis in Rheumatoid arthritis (RA). However, the developmental trajectories of synovial tissue macrophage (STM) subsets in humans remain poorly understood, due in part to the lack of models that faithfully replicate synovial tissue niches. This hinders the exploration of the therapeutic potential of targeting specific synovial myeloid cell clusters. Using multi-omics analyses of synovial tissue from an allogeneic bone marrow transplant recipient, we show that joint-specific tissue-resident STM subsets, including both health- and disease-associated clusters, can derive from peripheral blood monocytes. Analysis of embryonic synovial joints revealed that macrophage localization and maturation in the joints are preceded by local stromal niche specialisation, indicating that synovial fibroblasts (FLS) provide tissue-specific instructive cues to STM precursors. To elucidate human STM developmental trajectories, we established a SNP-based fate-tracking human synovial organoid system by embedding distinct blood-derived myeloid precursors, together with FLS clusters from RA synovial biopsies and endothelial cells, into 3D structures. These organoids reproduced key synovial tissue features, including lining and sublining architecture and stromal–myeloid cell cluster composition. Importantly, they supported differentiation of all resident STM subsets: homeostatic lining TREM2pos macrophages, their pathogenic TREM2lowSPP1pos counterparts that characterize the RA hyperplastic lining, and both homeostatic and RA-associated perivascular LYVE1pos STM clusters, all traced to monocytic precursors. In summary, we show that development of STM subsets is driven by fibroblast-conditioned spatial niches. We have established a novel, tractable ex vivo platform to dissect the niche-specific cues driving homeostatic versus pathogenic phenotypic clusters. Biological sciences/Immunology/Applied immunology Biological sciences/Immunology/Innate immunity Full Text Additional Declarations There is NO Competing Interest. 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-8079358","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":547753208,"identity":"ef556842-24ac-4429-ba84-d417709ae308","order_by":0,"name":"Mariola Kurowska-Stolarska","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABhElEQVRIie2SMWvCQBTHXzjIlJL1RLBf4SQQKrXmq7xwEBeFQhehYjOli9hVcei3cG3kQBeLq1AoBiF06BAoiFArvcREShHasZT8hrv/wf3u3vEOICfnD8J8AB8u90GCALpMSxkpED8Jh737qZIoclF2M4XyZJKKikn4plh+ujDgoJBM0dgxxZw+Bn7EamDSZrDSts4pUH28xPazVbidvb1gu1O7o6hEGxDpqeaszsZ9xqFK64Zx4jXKri4Iw8mVPdSaozOcCD7oIyl0QZip4jsgNEak4qjFpttSHnyuUlQRS9AcMVR9zp4QigCimtY3D2PlRhYmlca2ZbkQKzu0SvpryHDXiRXy/kVZJLcIMBJFbdiJYnuoDGmDLG2P1KSixreYmRKCfMtUK3dDYnx4DncpN5jdQ3vQD02wewIL94FX6bK6kRXmkChqXZfY1FGC/pZfuPo4WEZrtOicr6Jo3bF0TYjFpnWeti5DO/o3VCoHWariHrryEySKu/27vTk5OTn/l08gB5BWm0SBeQAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-2124-7777","institution":"University of Glasgow","correspondingAuthor":true,"prefix":"","firstName":"Mariola","middleName":"","lastName":"Kurowska-Stolarska","suffix":""},{"id":547753209,"identity":"32967e61-3262-49a4-928c-a7962f4aa552","order_by":1,"name":"Aziza Elmesmari","email":"","orcid":"","institution":"University of Glasgow","correspondingAuthor":false,"prefix":"","firstName":"Aziza","middleName":"","lastName":"Elmesmari","suffix":""},{"id":547753210,"identity":"106c71be-46b0-40b6-ac8e-28f187166d7d","order_by":2,"name":"Domenico Somma","email":"","orcid":"","institution":"University of Glasgow","correspondingAuthor":false,"prefix":"","firstName":"Domenico","middleName":"","lastName":"Somma","suffix":""},{"id":547753211,"identity":"ebfee128-9f57-4dcf-8d46-bd7a79b5a412","order_by":3,"name":"Lucy MacDonald","email":"","orcid":"https://orcid.org/0000-0001-7727-3873","institution":"Glasgow University","correspondingAuthor":false,"prefix":"","firstName":"Lucy","middleName":"","lastName":"MacDonald","suffix":""},{"id":547753212,"identity":"0622b6db-10ae-4858-a06c-a720f1233d2c","order_by":4,"name":"Jack Frew","email":"","orcid":"","institution":"University of Glasgow","correspondingAuthor":false,"prefix":"","firstName":"Jack","middleName":"","lastName":"Frew","suffix":""},{"id":547753213,"identity":"660897d2-90db-464e-8880-9f6f7ab2babc","order_by":5,"name":"Zuzanna Kuczynska","email":"","orcid":"","institution":"University of Glasgow","correspondingAuthor":false,"prefix":"","firstName":"Zuzanna","middleName":"","lastName":"Kuczynska","suffix":""},{"id":547753214,"identity":"75c82c5c-0930-4495-a378-6f96a05051a0","order_by":6,"name":"Clara Di Mario","email":"","orcid":"","institution":"Fondazione Policlinico Universitario A. 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However, the developmental trajectories of synovial tissue macrophage (STM) subsets in humans remain poorly understood, due in part to the lack of models that faithfully replicate synovial tissue niches. This hinders the exploration of the therapeutic potential of targeting specific synovial myeloid cell clusters. Using multi-omics analyses of synovial tissue from an allogeneic bone marrow transplant recipient, we show that joint-specific tissue-resident STM subsets, including both health- and disease-associated clusters, can derive from peripheral blood monocytes. Analysis of embryonic synovial joints revealed that macrophage localization and maturation in the joints are preceded by local stromal niche specialisation, indicating that synovial fibroblasts (FLS) provide tissue-specific instructive cues to STM precursors. To elucidate human STM developmental trajectories, we established a SNP-based fate-tracking human synovial organoid system by embedding distinct blood-derived myeloid precursors, together with FLS clusters from RA synovial biopsies and endothelial cells, into 3D structures. These organoids reproduced key synovial tissue features, including lining and sublining architecture and stromal–myeloid cell cluster composition. Importantly, they supported differentiation of all resident STM subsets: homeostatic lining TREM2pos macrophages, their pathogenic TREM2lowSPP1pos counterparts that characterize the RA hyperplastic lining, and both homeostatic and RA-associated perivascular LYVE1pos STM clusters, all traced to monocytic precursors. In summary, we show that development of STM subsets is driven by fibroblast-conditioned spatial niches. 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