Exploring the co-diagnostic genes of gastric cancer and chemotherapy brain damage and the prediction of active ingredients in traditional Chinese medicine based on network pharmacology and bioinformatics

Exploring the co-diagnostic genes of gastric cancer and chemotherapy brain damage and the prediction of active ingredients in traditional Chinese medicine based on network pharmacology and bioinformatics | 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 Research Article Exploring the co-diagnostic genes of gastric cancer and chemotherapy brain damage and the prediction of active ingredients in traditional Chinese medicine based on network pharmacology and bioinformatics Zhenyu He, Yueling Pang, Ruirong Peng, Huanhuan Ma, Yu Zhang, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6828967/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 Background Natural products have favorable clinical effects on gastric cancer (GC)-chemotherapy-induced cognitive impairment (CICI), but their specific mechanisms are unknown. Our study used network pharmacology and bioinformatics to explore traditional natural small molecules acting on GC and CICI and their mechanisms of action. Methods GC- and CICI-related target proteins were collected from databases. Protein-protein interaction (PPI) networks were constructed. Core submodules of the networks were screened. Differential genes (DGEs) and module genes were obtained by differential analysis of GSE118916 and weighted network analysis. The core targets were obtained. The effects of the small molecules on the expression of the key targets were investigated by constructing an in vitro cell model. Results 369 “GC and CICI” targets were screened. 1216 differential genes (DGEs) and 2721 modular genes (DGEs) were obtained by differential analysis and weighted network analysis respectively. KEGG enrichment was used to analyze the pathways related to “GC and CICI”. Seven core genes were identified. Finally, two key targets, PTGS2 and VCAM1 were identified through ROC and survival analysis. The molecular docking results showed that Kaempferol binds well to the key targets. In in vitro experiments, the results showed that Kaempferol could down-regulate the levels of PTGS2 and VCAM1. Conclusion The present study suggests that natural products are a promising option for the treatment of GC and CICI, and our demonstration of a specific molecular mechanism of Kaempferol's anti-GC and CICI provides a theoretical basis for a better clinical application of this compound. Network pharmacology Molecular docking Gastric cancer Chemotherapy-induced cognitive impairment Natural small molecules Molecular dynamics simulation Bioinformatics Full Text Additional Declarations No competing interests reported. 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-6828967","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":467000652,"identity":"05b0e06e-3505-4007-a575-60ad89fd967d","order_by":0,"name":"Zhenyu 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ingredients in traditional Chinese medicine based on network pharmacology and bioinformatics","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":"Network pharmacology, Molecular docking, Gastric cancer, Chemotherapy-induced cognitive impairment, Natural small molecules, Molecular dynamics simulation, Bioinformatics","lastPublishedDoi":"10.21203/rs.3.rs-6828967/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6828967/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eNatural products have favorable clinical effects on gastric cancer (GC)-chemotherapy-induced cognitive impairment (CICI), but their specific mechanisms are unknown. Our study used network pharmacology and bioinformatics to explore traditional natural small molecules acting on GC and CICI and their mechanisms of action.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eGC- and CICI-related target proteins were collected from databases. Protein-protein interaction (PPI) networks were constructed. Core submodules of the networks were screened. Differential genes (DGEs) and module genes were obtained by differential analysis of GSE118916 and weighted network analysis. The core targets were obtained. The effects of the small molecules on the expression of the key targets were investigated by constructing an in vitro cell model.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003e369 \u0026ldquo;GC and CICI\u0026rdquo; targets were screened. 1216 differential genes (DGEs) and 2721 modular genes (DGEs) were obtained by differential analysis and weighted network analysis respectively. KEGG enrichment was used to analyze the pathways related to \u0026ldquo;GC and CICI\u0026rdquo;. Seven core genes were identified. Finally, two key targets, PTGS2 and VCAM1 were identified through ROC and survival analysis. The molecular docking results showed that Kaempferol binds well to the key targets. In in vitro experiments, the results showed that Kaempferol could down-regulate the levels of PTGS2 and VCAM1.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eThe present study suggests that natural products are a promising option for the treatment of GC and CICI, and our demonstration of a specific molecular mechanism of Kaempferol's anti-GC and CICI provides a theoretical basis for a better clinical application of this compound.\u003c/p\u003e","manuscriptTitle":"Exploring the co-diagnostic genes of gastric cancer and chemotherapy brain damage and the prediction of active ingredients in traditional Chinese medicine based on network pharmacology and bioinformatics","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-06-06 07:43:17","doi":"10.21203/rs.3.rs-6828967/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":"8437cb20-6573-45ae-8c65-b25b36a34fdb","owner":[],"postedDate":"June 6th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-06-16T09:08:54+00:00","versionOfRecord":[],"versionCreatedAt":"2025-06-06 07:43:17","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6828967","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6828967","identity":"rs-6828967","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}