A novel hypoxia-associated gene signature for prognosis prediction in head and neck squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37964257", "kind": "science-record", "revision": 4, "content_hash": "sha256:58a1ec450463c55f4115a816a45716594ace0aa8e0cf5e7e8f72750ac50d8747", "created_at": "2026-11-01T19:02:52Z", "updated_at": "2026-11-01T22:10:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A novel hypoxia-associated gene signature for prognosis prediction in head and neck squamous cell carcinoma.", "doi": "10.1186/s12903-023-03489-8", "pmid": "37964257", "authors": ["Jingyi Luo", "Yuejiao Huang", "Jiahe Wu", "Lin Dai", "Mingyou Dong", "Bo Cheng"], "journal": "BMC oral health", "year": 2023, "abstract": "BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the most common malignant tumor of head and neck, which seriously threatens human life and health. However, the mechanism of hypoxia-associated genes (HAGs) in HNSCC remains unelucidated. This study aims to establish a hypoxia-associated gene signature and the nomogram for predicting the prognosis of patients with HNSCC.\nMETHODS: Previous literature reports provided a list of HAGs. The TCGA database provided genetic and clinical information on HNSCC patients. First, a hypoxia-associated gene risk model was constructed for predicting overall survival (OS) in HNSCC patients and externally validated in four GEO datasets (GSE27020, GSE41613, GSE42743, and GSE117973). Then, immune status and metabolic pathways were analyzed. A nomogram was constructed and assessed the predictive value. Finally, experimental validation of the core genes was performed by qRT-PCR.\nRESULTS: A HNSCC prognostic model was constructed based on 8 HAGs. This risk model was validated in four external datasets and exhibited high predictive value in various clinical subgroups. Significant differences in immune cell infiltration levels and metabolic pathways were found between high and low risk subgroups. The nomogram was highly accurate for predicting OS in HNSCC patients.\nCONCLUSIONS: The 8 hypoxia-associated gene signature can serve as novel independent prognostic indicators in HNSCC patients. The nomogram combining the risk score and clinical stage enhanced predictive performance in predicting OS compared to the risk model and clinical characteristics alone.", "claims": [{"id": "claim-method", "statement": "To establish a prognostic model, the R package \"glmnet\" was used to perform the univariate Cox regression and LASSO analyses on the differentially expressed genes screened previously.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37964257", "locator": "sections[5] \"Development and validation of prognostic features\" paragraph 2", "quote": "To establish a prognostic model, the R package \"glmnet\" was used to perform the univariate Cox regression and LASSO analyses on the differentially expressed genes screened previously."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in GEO (https://www.ncbi.nlm.nih.gov/) and TCGA (https://www.genome.gov/Funded-Programs-Projects/Cancer-Genome-Atlas) databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37964257", "locator": "sections[28] \"Availability of data and materials\" paragraph 2", "quote": "The datasets presented in this study can be found in GEO (https://www.ncbi.nlm.nih.gov/) and TCGA (https://www.genome.gov/Funded-Programs-Projects/Cancer-Genome-Atlas) databases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The risk model predicted 1-year, 3-year, and 5-year survival with AUC values of 0.660, 0.714, and 0.672, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37964257", "locator": "sections[14] \"Development of prognostic biomarkers for hypoxia-associated genes\" paragraph 2", "quote": "The risk model predicted 1-year, 3-year, and 5-year survival with AUC values of 0.660, 0.714, and 0.672, respectively (Fig. 2F)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The risk model predicted 1-year, 3-year, and 5-year survival with AUC values of 0.660, 0.714, and 0.672, respectively.", "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:37964257"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:37964257", "data:geo:GSE117973"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE117973"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:59:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16214, "completion_tokens": 1890, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37964257", "type": "paper", "label": "pmid:37964257"}, {"id": "source:pmid:37964257", "type": "manuscript", "label": "PMID 37964257 full text"}, {"id": "data:geo:GSE117973", "type": "dataset", "label": "GEO GSE117973"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37964257", "type": "paper", "label": "pmid:37964257"}, {"id": "source:pmid:37964257", "type": "manuscript", "label": "PMID 37964257 full text"}, {"id": "data:geo:GSE117973", "type": "dataset", "label": "GEO GSE117973"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37964257", "type": "extraction", "used": ["source:pmid:37964257"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE117973", "type": "accession_resolution", "used": ["data:geo:GSE117973"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37964257", "parent_hash": "sha256:ecac7609e10348169da4a647586bc47b3bd19eaef97c439bc0006af0e8769c86", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE117973 licence not read", "asset:data:geo:GSE117973 not downloaded", "asset:data:geo:GSE27020 licence not read", "asset:data:geo:GSE27020 not downloaded", "asset:data:geo:GSE41613 licence not read", "asset:data:geo:GSE41613 not downloaded", "asset:data:geo:GSE42743 licence not read", "asset:data:geo:GSE42743 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Table S3. The primer sequence information of qPCR experiment. Additional file 2. Details of pa"], "order_basis": "paper_text_order:3929", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To establish a prognostic model, the R package \"glmnet\" was used to perform the univariate Cox regression and LASSO analyses on the differentially expressed genes screened previously."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}