Intron retention resolves microgravity and non-gravitational stress programs across immune organs in spaceflight

Intron retention resolves microgravity and non-gravitational stress programs across immune organs in spaceflight | 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 Intron retention resolves microgravity and non-gravitational stress programs across immune organs in spaceflight Norihiro Okada This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8535943/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Intron retention (IR) provides an early regulatory readout of stress, often preceding steady-state changes in mRNA expression. Here, we asked whether IR can resolve complex spaceflight stress into separable mechanistic components and map how stress information propagates across tissues. We integrated high-confidence IR profiles from mouse spaceflight experiments with datasets representing mechanical unloading (microgravity) and non-mechanical, non-gravitational (NG; radiation–oxidative) stress. IR-based analysis disentangled these stress axes and uncovered a conserved five-layer regulatory architecture—mechanical input, signaling-gate, nuclear/genome-integrity, RNA/splicing–proteostasis/trafficking, and immune–metabolic adaptive output layers—through which immune organs interpret spaceflight stress. Microgravity and NG stress entered this hierarchy through distinct routes yet converged at IR as a common mode of upstream control, preceding most downstream transcriptional changes. This IR-centered framework provides a general strategy for decomposing complex, multi-factorial stress into interpretable modules. Leveraging this resolution, we identified a subset of IRGs whose normalization tracked the recovery of interacting structural partners, revealing a network-coupled “drag” phenomenon detectable when stress programmes are partitioned at the IR level. Together, our results establish IR as a unifying regulatory code—a command tier—that organizes stress-response hierarchies and exposes emergent network behaviors across mechanical, radiative, and immune perturbations. Biological sciences/Biological techniques/Bioinformatics Biological sciences/Molecular biology/Transcriptomics Full Text Additional Declarations Yes there is potential Competing Interest. N.O., K.O., and A.M. were supported by a research grant from Tsumura & Co. The remaining author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest. Supplementary Files SupplementaryTablesCommnBio.xlsx SupplementaryFigs.final.pptx Cite Share Download PDF Status: Posted 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-8535943","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":574089561,"identity":"4aa1c63f-1dde-4d73-9f9f-9c115cefd212","order_by":0,"name":"Norihiro 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The remaining\r\nauthor declares that the research was conducted in the absence of any commercial or\r\nfinancial relationships that could be construed as potential conflicts of interest.","formattedTitle":"Intron retention resolves microgravity and non-gravitational\r\nstress programs across immune organs in spaceflight","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"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":"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-8535943/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8535943/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Intron retention (IR) provides an early regulatory readout of stress, often preceding steady-state changes in mRNA expression. Here, we asked whether IR can resolve complex spaceflight stress into separable mechanistic components and map how stress information propagates across tissues. We integrated high-confidence IR profiles from mouse spaceflight experiments with datasets representing mechanical unloading (microgravity) and non-mechanical, non-gravitational (NG; radiation–oxidative) stress. IR-based analysis disentangled these stress axes and uncovered a conserved five-layer regulatory architecture—mechanical input, signaling-gate, nuclear/genome-integrity, RNA/splicing–proteostasis/trafficking, and immune–metabolic adaptive output layers—through which immune organs interpret spaceflight stress. Microgravity and NG stress entered this hierarchy through distinct routes yet converged at IR as a common mode of upstream control, preceding most downstream transcriptional changes. This IR-centered framework provides a general strategy for decomposing complex, multi-factorial stress into interpretable modules. Leveraging this resolution, we identified a subset of IRGs whose normalization tracked the recovery of interacting structural partners, revealing a network-coupled “drag” phenomenon detectable when stress programmes are partitioned at the IR level. 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