{"paper_id":"452ffef9-29b7-4a3a-b01f-e8e8ceb0facb","body_text":"Integrated In silico and 3D Spheroid Models Reveal Key Genes and MiRNAs Driving Cisplatin/5-FU Resistance and Metastatic Potential in Gastric Cancer | 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 Integrated In silico and 3D Spheroid Models Reveal Key Genes and MiRNAs Driving Cisplatin/5-FU Resistance and Metastatic Potential in Gastric Cancer Zahra Iranmehr, Hamed Yasavoli-Sharahi, Fatemeh Ghaemi, Massoud Baghai Wadji, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8821810/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 10 You are reading this latest preprint version Abstract Background : Gastric cancer is a leading cause of cancer mortality worldwide, driven largely by chemotherapy resistance and metastasis. Cisplatin and 5-fluorouracil are common first-line agents, but tumor adaptation limits long-term efficacy; the combined role of microRNAs in resistance and metastasis remains unclear. Methods : We integrated bioinformatics analysis of GEO dataset GSE14210 with STRING network and miRNA prediction, and validated findings in MKN-45 and patient-derived 3D spheroid models exposed to cisplatin and 5-FU. Gene and miRNA expressions were assessed in metastatic versus non-metastatic tumor tissues and treated versus untreated spheroids. Results : We identified 414 upregulated DEGs, including 56 hubs (degree ≥10) and 21 hubs upregulated in tumors. Patterns of co-expression among CXCL8, CCL5, MMP9, STAT1 and miR-17-5p/miR-24-3p/miR-124-3p/miR-145-5p were consistently associated with resistance and metastatic features (p<0.05). MKN-45 spheroids showed post-treatment regrowth, whereas patient-derived spheroids did not recover ≥80% baseline under identical exposure. Conclusion : These findings highlight coordinated gene–miRNA expression patterns linked to chemotherapy resistance and metastasis in gastric cancer and support their further evaluation as candidate biomarkers and therapeutic targets. Health sciences/Biomarkers Biological sciences/Cancer Biological sciences/Computational biology and bioinformatics Health sciences/Oncology Gastric Cancer Drug Resistance Metastasis Integrated Analysis 3D Culture MicroRNAs Full Text Additional Declarations No competing interests reported. Supplementary Files Sup.TableS2DEGswithHubs.xlsx Sup.TableS3KEGGGO.xlsx Sup.TableS1MasterTableAllGenes.txt SubFig2.jpg SubFig3.jpg SupFig1.jpg Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 14 Apr, 2026 Reviews received at journal 09 Apr, 2026 Reviews received at journal 31 Mar, 2026 Reviewers agreed at journal 19 Mar, 2026 Reviewers agreed at journal 09 Mar, 2026 Reviewers invited by journal 01 Mar, 2026 Editor invited by journal 13 Feb, 2026 Editor assigned by journal 10 Feb, 2026 Submission checks completed at journal 10 Feb, 2026 First submitted to journal 08 Feb, 2026 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-8821810\",\"acceptedTermsAndConditions\":true,\"allowDirectSubmit\":false,\"archivedVersions\":[],\"articleType\":\"Article\",\"associatedPublications\":[],\"authors\":[{\"id\":600761998,\"identity\":\"c6347b48-df9e-454b-b863-d248758637e3\",\"order_by\":0,\"name\":\"Zahra Iranmehr\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Zahra\",\"middleName\":\"\",\"lastName\":\"Iranmehr\",\"suffix\":\"\"},{\"id\":600761999,\"identity\":\"07d3119a-8d99-4c25-9d21-8f4e7dad9dc8\",\"order_by\":1,\"name\":\"Hamed Yasavoli-Sharahi\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Hamed\",\"middleName\":\"\",\"lastName\":\"Yasavoli-Sharahi\",\"suffix\":\"\"},{\"id\":600762000,\"identity\":\"4b24f9df-0d29-4827-a4a5-556164a96de1\",\"order_by\":2,\"name\":\"Fatemeh Ghaemi\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Fatemeh\",\"middleName\":\"\",\"lastName\":\"Ghaemi\",\"suffix\":\"\"},{\"id\":600762001,\"identity\":\"f51fc17e-1ef3-4477-9087-82e29dc4ef7f\",\"order_by\":3,\"name\":\"Massoud Baghai Wadji\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Department of Surgery, Firoozgar Hospital,Iran University of Medical Sciences,\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Massoud\",\"middleName\":\"Baghai\",\"lastName\":\"Wadji\",\"suffix\":\"\"},{\"id\":600762002,\"identity\":\"5d84605a-081e-429d-b99b-ae037e59dc94\",\"order_by\":4,\"name\":\"Seyed Rouhollah Miri\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences,\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Seyed\",\"middleName\":\"Rouhollah\",\"lastName\":\"Miri\",\"suffix\":\"\"},{\"id\":600762003,\"identity\":\"7847b5d0-8c53-4d03-a6fa-37f19dbd2e82\",\"order_by\":5,\"name\":\"Marzieh Ebrahimi\",\"email\":\"data:image/png;base64,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\",\"orcid\":\"\",\"institution\":\"Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR\",\"correspondingAuthor\":true,\"prefix\":\"\",\"firstName\":\"Marzieh\",\"middleName\":\"\",\"lastName\":\"Ebrahimi\",\"suffix\":\"\"}],\"badges\":[],\"createdAt\":\"2026-02-08 13:23:32\",\"currentVersionCode\":1,\"declarations\":\"\",\"doi\":\"10.21203/rs.3.rs-8821810/v1\",\"doiUrl\":\"https://doi.org/10.21203/rs.3.rs-8821810/v1\",\"draftVersion\":[],\"editorialEvents\":[],\"editorialNote\":\"\",\"failedWorkflow\":false,\"files\":[{\"id\":104408489,\"identity\":\"745bbc6c-092d-4c7f-8ae0-31a727b14cfb\",\"added_by\":\"auto\",\"created_at\":\"2026-03-11 12:42:39\",\"extension\":\"pdf\",\"order_by\":1,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"manuscript-pdf\",\"size\":2601809,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"FinalManuscript10.Feb.2026.pdf\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8821810/v1_covered_56533607-462b-40a4-bd4f-ea1896067b41.pdf\"},{\"id\":104402198,\"identity\":\"04d1d2fe-e8ad-4686-a1bd-32d74ca6d9e3\",\"added_by\":\"auto\",\"created_at\":\"2026-03-11 12:14:38\",\"extension\":\"xlsx\",\"order_by\":1,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":27327,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"Sup.TableS2DEGswithHubs.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8821810/v1/52ac938394562bef1f612ef1.xlsx\"},{\"id\":104040299,\"identity\":\"35ecf6fc-282c-47b3-86fb-7c8110858d39\",\"added_by\":\"auto\",\"created_at\":\"2026-03-06 04:22:42\",\"extension\":\"xlsx\",\"order_by\":2,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":20396,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"Sup.TableS3KEGGGO.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8821810/v1/966cc5c16295952a92474c34.xlsx\"},{\"id\":104402845,\"identity\":\"20732a74-a41c-4610-96c9-a057f5876232\",\"added_by\":\"auto\",\"created_at\":\"2026-03-11 12:16:37\",\"extension\":\"txt\",\"order_by\":3,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":821709,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"Sup.TableS1MasterTableAllGenes.txt\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8821810/v1/933af783233f799d6ea026d4.txt\"},{\"id\":104040301,\"identity\":\"6ca88c1c-e8a8-4093-87da-de0d95716314\",\"added_by\":\"auto\",\"created_at\":\"2026-03-06 04:22:42\",\"extension\":\"jpg\",\"order_by\":4,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":201630,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SubFig2.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8821810/v1/517a67c42603c2040c958446.jpg\"},{\"id\":104040304,\"identity\":\"5f7a0502-86a5-4bd8-8081-076c90a4ac8e\",\"added_by\":\"auto\",\"created_at\":\"2026-03-06 04:22:42\",\"extension\":\"jpg\",\"order_by\":5,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":216839,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SubFig3.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8821810/v1/8037ed96994f3f06e06195f6.jpg\"},{\"id\":104403005,\"identity\":\"45221e49-aba5-48bc-9df3-b8ec05a5bde0\",\"added_by\":\"auto\",\"created_at\":\"2026-03-11 12:17:09\",\"extension\":\"jpg\",\"order_by\":6,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":322555,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupFig1.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8821810/v1/6e0f0bec7621b3647be328c2.jpg\"}],\"financialInterests\":\"No competing interests reported.\",\"formattedTitle\":\"Integrated In silico and 3D Spheroid Models Reveal Key Genes and MiRNAs Driving Cisplatin/5-FU Resistance and Metastatic Potential in Gastric Cancer\",\"fulltext\":[],\"fulltextSource\":\"\",\"fullText\":\"\",\"funders\":[],\"hasAdminPriorityOnWorkflow\":false,\"hasManuscriptDocX\":false,\"hasOptedInToPreprint\":true,\"hasPassedJournalQc\":\"\",\"hasAnyPriority\":false,\"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\":\"info@researchsquare.com\",\"identity\":\"scientific-reports\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":false,\"externalIdentity\":\"scirep\",\"sideBox\":\"Learn more about [Scientific Reports](http://www.nature.com/srep/)\",\"snPcode\":\"\",\"submissionUrl\":\"\",\"title\":\"Scientific Reports\",\"twitterHandle\":\"\",\"acdcEnabled\":true,\"dfaEnabled\":true,\"editorialSystem\":\"stoa\",\"reportingPortfolio\":\"Scientific Reports\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":true},\"keywords\":\"Gastric Cancer, Drug Resistance, Metastasis, Integrated Analysis, 3D Culture, MicroRNAs\",\"lastPublishedDoi\":\"10.21203/rs.3.rs-8821810/v1\",\"lastPublishedDoiUrl\":\"https://doi.org/10.21203/rs.3.rs-8821810/v1\",\"license\":{\"name\":\"CC BY 4.0\",\"url\":\"https://creativecommons.org/licenses/by/4.0/\"},\"manuscriptAbstract\":\"\\u003cp\\u003e\\u003cstrong\\u003eBackground\\u003c/strong\\u003e: Gastric cancer is a leading cause of cancer mortality worldwide, driven largely by chemotherapy resistance and metastasis. Cisplatin and 5-fluorouracil are common first-line agents, but tumor adaptation limits long-term efficacy; the combined role of microRNAs in resistance and metastasis remains unclear.\\u0026nbsp;\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eMethods\\u003c/strong\\u003e: We integrated bioinformatics analysis of GEO dataset GSE14210 with STRING network and miRNA prediction, and validated findings in MKN-45 and patient-derived 3D spheroid models exposed to cisplatin and 5-FU. Gene and miRNA expressions were assessed in metastatic versus non-metastatic tumor tissues and treated versus untreated spheroids.\\u0026nbsp;\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eResults\\u003c/strong\\u003e: We identified 414 upregulated DEGs, including 56 hubs (degree ≥10) and 21 hubs upregulated in tumors. Patterns of co-expression among CXCL8, CCL5, MMP9, STAT1 and miR-17-5p/miR-24-3p/miR-124-3p/miR-145-5p were consistently associated with resistance and metastatic features (p\\u0026lt;0.05). MKN-45 spheroids showed post-treatment regrowth, whereas patient-derived spheroids did not recover ≥80% baseline under identical exposure.\\u0026nbsp;\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eConclusion\\u003c/strong\\u003e: These findings highlight coordinated gene–miRNA expression patterns linked to chemotherapy resistance and metastasis in gastric cancer and support their further evaluation as candidate biomarkers and therapeutic targets.\\u003c/p\\u003e\",\"manuscriptTitle\":\"Integrated In silico and 3D Spheroid Models Reveal Key Genes and MiRNAs Driving Cisplatin/5-FU Resistance and Metastatic Potential in Gastric Cancer\",\"msid\":\"\",\"msnumber\":\"\",\"nonDraftVersions\":[{\"code\":1,\"date\":\"2026-03-06 04:22:37\",\"doi\":\"10.21203/rs.3.rs-8821810/v1\",\"editorialEvents\":[{\"type\":\"communityComments\",\"content\":0},{\"type\":\"decision\",\"content\":\"Revision requested\",\"date\":\"2026-04-14T09:54:11+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-04-09T15:26:35+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-03-31T11:43:42+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"78360556540231611607062848106019927592\",\"date\":\"2026-03-19T05:52:11+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"17873561244423225041813467461984816408\",\"date\":\"2026-03-09T07:08:58+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewersInvited\",\"content\":\"\",\"date\":\"2026-03-01T22:27:43+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorInvited\",\"content\":\"\",\"date\":\"2026-02-13T10:18:58+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorAssigned\",\"content\":\"\",\"date\":\"2026-02-10T08:39:24+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"checksComplete\",\"content\":\"\",\"date\":\"2026-02-10T08:37:42+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"submitted\",\"content\":\"Scientific Reports\",\"date\":\"2026-02-08T13:16:59+00:00\",\"index\":\"\",\"fulltext\":\"\"}],\"status\":\"published\",\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"scientific-reports\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":false,\"externalIdentity\":\"scirep\",\"sideBox\":\"Learn more about [Scientific Reports](http://www.nature.com/srep/)\",\"snPcode\":\"\",\"submissionUrl\":\"\",\"title\":\"Scientific Reports\",\"twitterHandle\":\"\",\"acdcEnabled\":true,\"dfaEnabled\":true,\"editorialSystem\":\"stoa\",\"reportingPortfolio\":\"Scientific Reports\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":true}}],\"origin\":\"\",\"ownerIdentity\":\"933cc7f3-180d-4904-9b1e-c3cac5ccbed0\",\"owner\":[],\"postedDate\":\"March 6th, 2026\",\"published\":true,\"recentEditorialEvents\":[],\"rejectedJournal\":[],\"revision\":\"\",\"amendment\":\"\",\"status\":\"in-revision\",\"subjectAreas\":[{\"id\":63932469,\"name\":\"Health sciences/Biomarkers\"},{\"id\":63932470,\"name\":\"Biological sciences/Cancer\"},{\"id\":63932471,\"name\":\"Biological sciences/Computational biology and bioinformatics\"},{\"id\":63932472,\"name\":\"Health sciences/Oncology\"}],\"tags\":[],\"updatedAt\":\"2026-04-14T10:15:48+00:00\",\"versionOfRecord\":[],\"versionCreatedAt\":\"2026-03-06 04:22:37\",\"video\":\"\",\"vorDoi\":\"\",\"vorDoiUrl\":\"\",\"workflowStages\":[]},\"version\":\"v1\",\"identity\":\"rs-8821810\",\"journalConfig\":\"researchsquare\"},\"__N_SSP\":true},\"page\":\"/article/[identity]/[[...version]]\",\"query\":{\"redirect\":\"/article/rs-8821810\",\"identity\":\"rs-8821810\",\"version\":[\"v1\"]},\"buildId\":\"XKTyCvWXoU3ODBz1xrDgd\",\"isFallback\":false,\"isExperimentalCompile\":false,\"dynamicIds\":[84888],\"gssp\":true,\"scriptLoader\":[]}","source_license":"CC-BY-4.0","license_restricted":false}