Dysregulated genes in HIGK-treated F. nucleatum and their possible association with HNSCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39744516", "kind": "science-record", "revision": 4, "content_hash": "sha256:730b08bf0436893396e6b087f4133c433167cf0a9ee01814d03ae43fea449930", "created_at": "2026-11-01T20:30:04Z", "updated_at": "2026-11-01T22:55:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dysregulated genes in HIGK-treated F. nucleatum and their possible association with HNSCC.", "doi": "10.22099/mbrc.2024.50171.1982", "pmid": "39744516", "authors": ["S B Shanmugam", "J Vijayashree Priyadharsini", "P Anitha", "A S Smiline Girija", "A Paramasivam"], "journal": "Molecular biology research communications", "year": 2025, "abstract": "The present study aims to identify the differentially expressed genes in HIGK treated with Fusobacterium nucleatum (Fn) and their possible role in establishing head and neck squamous cell carcinoma. The study design follows a computational approach wherein multiple databases and tools are used to derive the possible association between Fn exposure and the development of HNSCC. The GEOmnibus dataset GSE6927 provided data on the differentially expressed genes in the HIGK treated with Fn. The GEO2R analysis revealed 22 differentially expressed genes in HIGK cells treated with Fn. The expression profile of these genes was then analyzed in the HNSCC (TCGA, Firehose Legacy) dataset employing the UALCAN database. The present study revealed 5 genes viz., GSDMD, NUP214, ZNF426, FUT2, and SERPINB2 exhibiting similar expression patterns in Fn-treated HIGK and HNSCC datasets. The GSDMD and NUP214 were found to be upregulated, and the genes ZNF426, FUT2, and SERPINB2 were downregulated. Among the five genes, the ZNF426 demonstrated a significant association with the survival of HNSCC patients. The low expression of ZNF426 presented a poor prognosis compared to the high expression. The study's results identified ZNF426 as a candidate gene involved in Fusobacterium nucleatum infection and HNSCC. Validating this result is necessary to gain insights into the role of the ZNF426 gene in developing HNSCC. Furthermore, probing the epigenetic factors targeting ZNF426 can be a potential therapeutic lead.", "claims": [{"id": "claim-method", "statement": "The study also demonstrated the overall survival of patients with HNSCC using Kaplan-Meier analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39744516", "locator": "sections[2] \"MATERIALS AND METHODS\" paragraph 6", "quote": "The study also demonstrated the overall survival of patients with HNSCC using Kaplan-Meier analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GEOmnibus dataset GSE6927 was used for the study. This series comprised four samples of HIGK (Human Immortalized Gingival Keratinocytes) infected with Fusobacterium nucleatum (GSM159481, GSM159482, GSM159483, GSM159484), 4 Sham-infected HIGK cells (GSM159485, GSM159486, GSM159487, GSM159488).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39744516", "locator": "sections[2] \"MATERIALS AND METHODS\" paragraph 2", "quote": "The GEOmnibus dataset GSE6927 was used for the study. This series comprised four samples of HIGK (Human Immortalized Gingival Keratinocytes) infected with Fusobacterium nucleatum (GSM159481, GSM159482, GSM159483, GSM159484), 4 Sham-infected HIGK cells (GSM159485, GSM159486, GSM159487, GSM159488)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Low ZNF426 expression was associated with poor prognosis in HNSCC patients, with a significant survival difference (p=0.011).", "kind": "quantitative", "target": {"value": 0.011, "unit": "p-value", "tolerance": null, "source": "The Kaplan-Meier survival analysis demonstrated a significant change in the survival status of the HNSCC patients presenting with decreased expression of Zinc finger protein 426 (p=0.011) (Fig. 4)."}, "evidence": [{"asset": "source:pmid:39744516", "locator": "sections[3] \"RESULTS\" paragraph 9", "quote": "The Kaplan-Meier survival analysis demonstrated a significant change in the survival status of the HNSCC patients presenting with decreased expression of Zinc finger protein 426 (p=0.011) (Fig. 4)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Low ZNF426 expression was associated with poor prognosis in HNSCC patients, with a significant survival difference (p=0.011).", "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:39744516"], "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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