Exploring the effects of matrix metalloproteinase-13 on the malignant biological behavior of tongue squamous cell carcinoma via the TNF signaling pathway based on bioinformatics methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39145072", "kind": "science-record", "revision": 3, "content_hash": "sha256:eb6178a9349884fab84e82bf744690d18b35d2bd82589387ade6fd07ec84311e", "created_at": "2026-11-01T20:29:15Z", "updated_at": "2026-11-01T22:12:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the effects of matrix metalloproteinase-13 on the malignant biological behavior of tongue squamous cell carcinoma via the TNF signaling pathway based on bioinformatics methods.", "doi": "10.21037/tcr-24-1016", "pmid": "39145072", "authors": ["Junqin Lu", "Yeqian Zhu", "Jie Zhang", "Ningning Cao"], "journal": "Translational cancer research", "year": 2024, "abstract": "Background: Identification of the etiology, molecular mechanisms, and carcinogenic pathways of tongue squamous cell carcinoma (TSCC) is crucial for developing new diagnostic and therapeutic strategies. This study used bioinformatics methods to identify key genes in TSCC and explored the potential functions and pathway mechanisms related to the malignant biological behavior of TSCC.\nMethods: Gene chip data sets (i.e., GSE13601 and GSE34106) containing the data of both TSCC patients and normal control subjects were selected from the Gene Expression Omnibus (GEO) database. Using a gene expression analysis tool (GEO2R) of the GEO database, the differentially expressed genes (DEGs) were identified using the following criteria: |log fold change| >1, and P<0.05. The GEO2R tool was also used to select the upregulated DEGs in the chip candidates based on a P value <0.05. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Ontology (GO) function analysis, and a protein-protein interaction (PPI) network analysis were then conducted. The results were displayed using R language packages, including volcano plots, Venn diagrams, heatmaps, and enriched pathway bubble charts. Genes from the MalaCards database were compared with the candidate genes, and a thorough review of the literature was conducted to determine the clinical significance of these genes. Finally, feature gene-directed chemical drugs or targeted drugs were predicted using the Comparative Toxicogenomics Database (CTD).\nResults: In total, 767 upregulated DEGs were identified from GSE13601 and 695 from GSE34106. By intersecting the upregulated DEGs from both data sets using a Venn diagram, 100 DEGs related to TSCC were identified. The enrichment analysis of the KEGG signaling pathways identified the majority of the pathways associated with the upregulated DEGs, including the Toll-like receptor signaling pathway, the extracellular matrix-receptor interaction, the tumor necrosis factor (TNF) signaling pathway, cytokine-cytokine receptor interaction, the chemokine signaling pathway, the interlukin-17 signaling pathway, and natural killer cell-mediated cytotoxicity. The PPI network and module analyses of the shared DEGs ultimately resulted in five clusters and 55 candidate genes. A further intersection analysis of the TSCC-related genes in the MalaCards database via a Venn diagram identified three important shared DEGs; that is, matrix metalloproteinase-1 (MMP1), MMP9, and MMP13. In the CTD, seven drugs related to MMP13 were identified for treating tongue tumors.\nConclusions: This study identified key genes and signaling pathways involved in TSCC and thus extended understandings of the molecular mechanisms that underlie the development and progression of TSCC. Additionally, this study showed that MMP13 may influence the malignant biological behavior of TSCC through the TNF signaling pathway. This finding could provide a theoretical basis for research into early differential diagnosis and targeted treatment.", "claims": [{"id": "claim-method", "statement": "For the DEG analysis, a t-test was used to calculate the P values and adjusted P values. The P values were adjusted using the false discovery rate method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39145072", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "For the DEG analysis, a t-test was used to calculate the P values and adjusted P values. The P values were adjusted using the false discovery rate method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE13601 and GSE34106 data sets of gene chips were acquired from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The data sets comprised data for both TSCC tumor patients and normal control subjects.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39145072", "locator": "sections[4] \"Data source\" paragraph 2", "quote": "The GSE13601 and GSE34106 data sets of gene chips were acquired from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The data sets comprised data for both TSCC tumor patients and normal control subjects."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study showed that MMP13 may influence the malignant biological behavior of TSCC through the TNF signaling pathway.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39145072", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Additionally, this study showed that MMP13 may influence the malignant biological behavior of TSCC through the TNF signaling pathway."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study showed that MMP13 may influence the malignant biological behavior of TSCC through the TNF signaling pathway.", "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:39145072"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13601"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13601"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39145072", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-24-1016", "sha256": "sha256:bf1d15174a5edd502da24fb1097bab4f267a06f5405a83a5095bf50bdf5befc7", "bytes": 31398, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-24-1016", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11319986", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13601", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13601", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13601", "version": null, "note": "The GSE13601 and GSE34106 data sets of gene chips were acquired from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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