The lysosomal LAMTOR-Rag axis functions as a checkpoint for antiviral interferon production

The lysosomal LAMTOR-Rag axis functions as a checkpoint for antiviral interferon production | 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 lysosomal LAMTOR-Rag axis functions as a checkpoint for antiviral interferon production Chun-Yan Lim, Zeming Feng, Lulu Wang, Shujun Chen, Miao Lei, Xiuzhen Yang, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5376814/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 21 Jan, 2026 Read the published version in The EMBO Journal → Version 1 posted You are reading this latest preprint version Abstract Lysosomes, best known for their nutrient-sensing and degradative roles, have emerged as essential hubs for antiviral defense. While higher organisms depend on type I interferon (IFN) induction for antiviral responses, the mechanism by which lysosomal signaling enables IFN-β production remains unclear. Here, we identify an evolutionarily repurposed lysosomal pathway—centered on the LAMTOR-Rag GTPase complex—that governs IFN-β production through dual transcriptional and post-transcriptional regulation. Genetic ablation of LAMTOR or Rag GTPases in macrophages abolishes IFN-β responses despite intact pattern recognition receptor (PRR) signaling, uncovering a lysosome-specific checkpoint essential for antiviral immunity. Mechanistically, Rag GTPase activity controls IRF expression to prime IFN transcription, while upon PRR stimulation, the tumor suppressor FLCN recruits p38 MAPK to lysosomes, where Rag-dependent p38 phosphorylation stabilizes Ifnb1 mRNA. Nutrient availability dynamically modulates Rag nucleotide states, linking IFN production to metabolic capacity. Notably, this checkpoint operates independently of mTORC1, illustrating how an ancient nutrient-sensing module was co-opted for immune regulation. Disruption of the LAMTOR-Rag–FLCN–p38 axis impairs IFN induction in vitro and antiviral responses in vivo, underscoring its physiological significance. Our findings redefine the lysosome as a central signaling hub integrating metabolic and immune cues, providing evolutionary and mechanistic insights into antiviral defense and potential therapeutic strategies for viral infections and inflammatory diseases. Biological sciences/Cell biology/Cell signalling Biological sciences/Chemical biology/Mechanism of action Biological sciences/Immunology/Infectious diseases Biological sciences/Biochemistry/Kinases Full Text Additional Declarations There is NO Competing Interest. Cite Share Download PDF Status: Published Journal Publication published 21 Jan, 2026 Read the published version in The EMBO Journal → 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-5376814","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":504607639,"identity":"991ec7f3-ad90-44f3-bf35-89a4bde92b6a","order_by":0,"name":"Chun-Yan Lim","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA8klEQVRIiWNgGAWjYBACPmYgIQFmMh9gYChgSCCohQ2hhQ2o2oAYLQgmjwGRWth5DzBYtt1J7J/d8/nlDwO7PAb2ww8Yfu7A5zC+BAbJtmeJM+6c3WYhYZBczMCTZsDYewafFqB7JNsOJzbcyN1mYGDAnNjAkMPAzNhGhJb5N3KeGSQY1Cc28L8hUsuGGznMDw4YAK2TIMYWiXOHjTfeSDNjbDA4Xswm8czgYC8eLfz8ZwyYJcoOy867kfz444+K6jx+/uSHD37i0QIE7L+BUenYALQRHKWgmDqAVwMQMH5gYLAH0swfCKkcBaNgFIyCkQkAipBKNCa2WjEAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0003-0403-3232","institution":"Guangzhou National Laboratory","correspondingAuthor":true,"prefix":"","firstName":"Chun-Yan","middleName":"","lastName":"Lim","suffix":""},{"id":504607640,"identity":"166804f0-4963-4eda-8c49-b02eaabcaf8e","order_by":1,"name":"Zeming Feng","email":"","orcid":"https://orcid.org/0000-0002-8564-896X","institution":"Huazhong University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Zeming","middleName":"","lastName":"Feng","suffix":""},{"id":504607641,"identity":"7d3437bf-7a9f-43ab-816d-6b353631966f","order_by":2,"name":"Lulu Wang","email":"","orcid":"","institution":"Sun Yat-sen University","correspondingAuthor":false,"prefix":"","firstName":"Lulu","middleName":"","lastName":"Wang","suffix":""},{"id":504607642,"identity":"7ffbcd44-904e-4987-8f1f-c163346406ab","order_by":3,"name":"Shujun Chen","email":"","orcid":"","institution":"Guangzhou National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Shujun","middleName":"","lastName":"Chen","suffix":""},{"id":504607643,"identity":"d9d69183-a7aa-4523-864c-8bd42033cb07","order_by":4,"name":"Miao Lei","email":"","orcid":"","institution":"Guangzhou Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Miao","middleName":"","lastName":"Lei","suffix":""},{"id":504607644,"identity":"29648525-c1f1-406e-b74c-807a7b7a305b","order_by":5,"name":"Xiuzhen Yang","email":"","orcid":"","institution":"Guangzhou National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Xiuzhen","middleName":"","lastName":"Yang","suffix":""},{"id":504607645,"identity":"f64a9a19-4539-4944-91dc-2bd2929d33ae","order_by":6,"name":"Kaixiong Ma","email":"","orcid":"","institution":"Guangzhou Medical University","correspondingAuthor":false,"prefix":"","firstName":"Kaixiong","middleName":"","lastName":"Ma","suffix":""},{"id":504607646,"identity":"348072e8-4313-49c3-9909-1302d16bdc52","order_by":7,"name":"Shi Yu","email":"","orcid":"https://orcid.org/0000-0003-0651-4769","institution":"Guangzhou National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Shi","middleName":"","lastName":"Yu","suffix":""},{"id":504607647,"identity":"5710a350-7576-4e61-9902-f00e7f366d49","order_by":8,"name":"Huina Hu","email":"","orcid":"","institution":"Guangzhou National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Huina","middleName":"","lastName":"Hu","suffix":""},{"id":504607648,"identity":"792e99c2-0488-40d6-8332-9e220611b524","order_by":9,"name":"Xin Xu","email":"","orcid":"","institution":"Sun Yat-sen University","correspondingAuthor":false,"prefix":"","firstName":"Xin","middleName":"","lastName":"Xu","suffix":""},{"id":504607649,"identity":"e83120a6-3fd1-43f9-968c-ba470afae6d7","order_by":10,"name":"Sihan Cao","email":"","orcid":"","institution":"Guangzhou Medical University","correspondingAuthor":false,"prefix":"","firstName":"Sihan","middleName":"","lastName":"Cao","suffix":""},{"id":504607650,"identity":"8b2a0c6c-e999-4e57-a48f-9ee5acd6e421","order_by":11,"name":"Qi Zheng","email":"","orcid":"","institution":"Guangzhou National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Qi","middleName":"","lastName":"Zheng","suffix":""},{"id":504607651,"identity":"0bd73816-b445-4389-b1bf-135f892bc265","order_by":12,"name":"Shaobo Wang","email":"","orcid":"https://orcid.org/0000-0003-0481-707X","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Shaobo","middleName":"","lastName":"Wang","suffix":""},{"id":504607652,"identity":"d0e3cbeb-9a82-42bb-b5ef-6f4455836b31","order_by":13,"name":"Wenxiang Hu","email":"","orcid":"https://orcid.org/0000-0002-6754-5625","institution":"Guangzhou National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Wenxiang","middleName":"","lastName":"Hu","suffix":""},{"id":504607653,"identity":"90cff222-5b14-4f8e-9caa-c84d818f6d95","order_by":14,"name":"Kaixuan Zheng","email":"","orcid":"","institution":"Sun Yat-sen University","correspondingAuthor":false,"prefix":"","firstName":"Kaixuan","middleName":"","lastName":"Zheng","suffix":""}],"badges":[],"createdAt":"2024-11-02 07:05:05","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5376814/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5376814/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s44318-026-00695-2","type":"published","date":"2026-01-22T00:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":101017947,"identity":"169bc263-8807-4401-a5be-5ab3696ceaae","added_by":"auto","created_at":"2026-01-23 23:55:04","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":34280324,"visible":true,"origin":"","legend":"Article File","description":"","filename":"RevisedManucriptallinone.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5376814/v1_covered_edeb9c26-5998-4351-a710-37554d606f8d.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"The lysosomal LAMTOR-Rag axis functions as a checkpoint for antiviral interferon production","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-5376814/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5376814/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Lysosomes, best known for their nutrient-sensing and degradative roles, have emerged as essential hubs for antiviral defense. While higher organisms depend on type I interferon (IFN) induction for antiviral responses, the mechanism by which lysosomal signaling enables IFN-β production remains unclear. Here, we identify an evolutionarily repurposed lysosomal pathway—centered on the LAMTOR-Rag GTPase complex—that governs IFN-β production through dual transcriptional and post-transcriptional regulation. Genetic ablation of LAMTOR or Rag GTPases in macrophages abolishes IFN-β responses despite intact pattern recognition receptor (PRR) signaling, uncovering a lysosome-specific checkpoint essential for antiviral immunity. Mechanistically, Rag GTPase activity controls IRF expression to prime IFN transcription, while upon PRR stimulation, the tumor suppressor FLCN recruits p38 MAPK to lysosomes, where Rag-dependent p38 phosphorylation stabilizes Ifnb1 mRNA. Nutrient availability dynamically modulates Rag nucleotide states, linking IFN production to metabolic capacity. Notably, this checkpoint operates independently of mTORC1, illustrating how an ancient nutrient-sensing module was co-opted for immune regulation. Disruption of the LAMTOR-Rag–FLCN–p38 axis impairs IFN induction in vitro and antiviral responses in vivo, underscoring its physiological significance. Our findings redefine the lysosome as a central signaling hub integrating metabolic and immune cues, providing evolutionary and mechanistic insights into antiviral defense and potential therapeutic strategies for viral infections and inflammatory diseases.","manuscriptTitle":"The lysosomal LAMTOR-Rag axis functions as a checkpoint for antiviral interferon production","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-26 04:49:05","doi":"10.21203/rs.3.rs-5376814/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"67dfc75a-a4e9-4fa6-b2b4-8cd78628c5f2","owner":[],"postedDate":"August 26th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":53609291,"name":"Biological sciences/Cell biology/Cell signalling"},{"id":53609292,"name":"Biological sciences/Chemical biology/Mechanism of action"},{"id":53609293,"name":"Biological sciences/Immunology/Infectious diseases"},{"id":53609294,"name":"Biological sciences/Biochemistry/Kinases"}],"tags":[],"updatedAt":"2026-01-23T23:54:32+00:00","versionOfRecord":{"articleIdentity":"rs-5376814","link":"https://doi.org/10.1038/s44318-026-00695-2","journal":{"identity":"the-embo-journal","isVorOnly":true,"title":"The EMBO Journal"},"publishedOn":"2026-01-22 00:00:00","publishedOnDateReadable":"January 22nd, 2026"},"versionCreatedAt":"2025-08-26 04:49:05","video":"","vorDoi":"10.1038/s44318-026-00695-2","vorDoiUrl":"https://doi.org/10.1038/s44318-026-00695-2","workflowStages":[]},"version":"v1","identity":"rs-5376814","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5376814","identity":"rs-5376814","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}