Bioinformatics analysis reveals that ANXA1 and SPINK5 are novel tumor suppressor genes in patients with oral squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35116500", "kind": "science-record", "revision": 6, "content_hash": "sha256:4fb5e9753e114600cc69fbb7a63a0c8389c507c5d2ec6b3f22c4bbd9ffe2bb48", "created_at": "2026-11-01T17:36:50Z", "updated_at": "2026-11-01T22:48:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis reveals that ANXA1 and SPINK5 are novel tumor suppressor genes in patients with oral squamous cell carcinoma.", "doi": "10.21037/tcr-20-3382", "pmid": "35116500", "authors": ["Hua-Tao Wu", "Wen-Tian Chen", "Wen-Jia Chen", "Chun-Lan Li", "Jing Liu"], "journal": "Translational cancer research", "year": 2021, "abstract": "BACKGROUND: Oral squamous cell carcinoma (OSCC) is a solid tumor of squamous epithelial origin. Currently, surgery is still the main treatment for OSCC, with radiotherapy and chemotherapy as important adjuvant treatments. However, the problem of poor prognosis of OSCC patients still exists in clinical practice. To explore further potential biomarkers or treatment targets in OSCC patients, this study used a high-throughput gene expression database to study the potential molecular mechanisms of OSCC carcinogenesis.\nMETHODS: The GEO database related to OSCC was searched and analyzed using GEO2R. Oncomine and the Human Protein Atlas were used to evaluate the expression level of differentially-expressed genes (DEGs). The cBioPortal dataset was used to analyze the mutations of the potential DEGs and patient survival.\nRESULTS: Three GEO datasets, GSE146483, GSE138206, and GSE148944, were downloaded and 7 DEGs were found in common in OSCC tissues. Using Oncomine and the Human Protein Atlas, ANXA1, IL1RN, and SPINK5 were decreased in cancer tissues, while protein levels of APOE and IFI35 were increased accordingly. Interestingly, low levels of ANXA1 and SPINKS were associated with the TNM stage of OSCC patients. No mutations in DEGs were found in OSCC patients, based on the cBioPortal dataset. Survival analysis indicated OSCC patients with high MSR1 had poor overall survival (OS), while low expression of CXCR4, ANXA1, IL1RN, and SPINK5 also predicted poor OS in OSCC patients.\nCONCLUSIONS: Our findings uncovered 7 potential biomarkers of OSCC patients, with ANXA1 and SPINK5 serving as potential tumor suppressor genes in OSCC.", "claims": [{"id": "claim-method", "statement": "For analyzing differential expression in the GEO datasets, the limma package of R software, GEO2R, was used to analyze the original datasets, with a cutoff value |log FC| >1 and P-value <0.01.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116500", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "For analyzing differential expression in the GEO datasets, the limma package of R software, GEO2R, was used to analyze the original datasets, with a cutoff value |log FC| >1 and P-value <0.01."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE146483 included 8 OSCC tissues and 3 normal oral mucosal epithelial keratinocytes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116500", "locator": "sections[3] \"Microarray datasets\" paragraph 3", "quote": "GSE146483 included 8 OSCC tissues and 3 normal oral mucosal epithelial keratinocytes."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Analysis of three GEO datasets using GEO2R identified seven differentially expressed genes common to OSCC tissues.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35116500", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Three GEO datasets, GSE146483, GSE138206, and GSE148944, were downloaded and 7 DEGs were found in common in OSCC tissues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Analysis of three GEO datasets using GEO2R identified seven differentially expressed genes common to OSCC tissues.", "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:35116500"], "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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