Differentially expressed extracellular matrix genes functionally separate ameloblastoma from odontogenic keratocyst.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39272104", "kind": "science-record", "revision": 3, "content_hash": "sha256:99408af39935cdca0827c1c0ba42964aa5a2ebf16b0eda26153b560376967dd7", "created_at": "2026-11-01T20:29:26Z", "updated_at": "2026-11-01T22:12:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differentially expressed extracellular matrix genes functionally separate ameloblastoma from odontogenic keratocyst.", "doi": "10.1186/s12903-024-04866-7", "pmid": "39272104", "authors": ["Prasath Jeyaraman", "Arularasan Anbinselvam", "Sunday O Akintoye"], "journal": "BMC oral health", "year": 2024, "abstract": "BACKGROUND: Ameloblastoma and odontogenic keratocyst (OKC) are odontogenic tumors that develop from remnants of odontogenic epithelium. Both display locally invasive growth characteristics and high predilection for recurrence after surgical removal. Most ameloblastomas harbor BRAFV600E mutation while OKCs are associated with PATCH1 gene mutation but distinctive indicators of ameloblastoma growth characteristics relative to OKC are still unclear. The aim of this study was to assess hub genes that underlie ameloblastoma growth characteristics using bioinformatic analysis, ameloblastoma samples and mouse xenografts of human epithelial-derived ameloblastoma cells.\nMETHODS: RNA expression profiles were extracted from GSE186489 gene expression dataset acquired from Gene Expression Ominibus (GEO) database. Galaxy and iDEP online analysis tools were used to identify differentially expressed genes that were further characterized by gene ontology (GO) and pathway analysis using ShineyGO. The protein-protein interaction (PPI) network was constructed for significantly upregulated differentially expressed genes using online database STRING. The PPI network visualization was performed using Cytoscape and hub gene identification with cytoHubba. Top ten nodes were selected using maximum neighborhood component, degree and closeness algorithms and analysis of overlap was performed to confirm the hub genes. Epithelial-derived ameloblastoma cells from conventional ameloblastoma were transplanted into immunocompromised mice to recreate ameloblastoma in vivo based on the mouse xenograft model. The top 3 hub genes FN1, COL I and IGF-1 were validated by immunostaining and quantitative analysis of staining intensities to ameloblastoma, OKC samples and mouse ameloblastoma xenografts tissues.\nRESULTS: Seven hub genes were identified among which FN1, COL1A1/COL1A2 and IGF-1 are associated with extracellular matrix organization, collagen binding, cell adhesion and cell surface interaction. These were further validated by positive immunoreactivity within the stroma of ameloblastoma samples but both ameloblastoma xenograft and OKC displayed only FN1 and IGF-1 immunoreactivity while COL 1 was unreactive. The expression levels of both FN1 and IGF-1 were much lower in OKC relative to ameloblastoma.\nCONCLUSION: This study further validates a differentially upregulated expression of matrix proteins FN1, COL I and IGF-1 in ameloblastoma relative to OKC. It suggests that differential stromal architecture and growth characteristics of ameloblastoma relative to OKC could be an interplay of differentially upregulated genes in ameloblastoma.", "claims": [{"id": "claim-method", "statement": "Gene counts were obtained using featureCounts and inputted into the iDEP platform for the differential gene expression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39272104", "locator": "sections[4] \"Identification of differentially expressed genes\" paragraph 2", "quote": "Gene counts were obtained using featureCounts and inputted into the iDEP platform for the differential gene expression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE186489 datasets analyzed during the current study are available in the Gene Expression Omnibus repository [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186489] Supplementary table of differentially expressed genes is provided.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39272104", "locator": "sections[20] \"Data availability\" paragraph 2", "quote": "The GSE186489 datasets analyzed during the current study are available in the Gene Expression Omnibus repository [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186489] Supplementary table of differentially expressed genes is provided."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven hub genes were identified among which FN1, COL1A1/COL1A2 and IGF-1 are associated with extracellular matrix organization, collagen binding, cell adhesion and cell surface interaction.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39272104", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Seven hub genes were identified among which FN1, COL1A1/COL1A2 and IGF-1 are associated with extracellular matrix organization, collagen binding, cell adhesion and cell surface interaction."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seven hub genes were identified among which FN1, COL1A1/COL1A2 and IGF-1 are associated with extracellular matrix organization, collagen binding, cell adhesion and cell surface interaction.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39272104"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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