Comprehensive analysis of T cell exhaustion related signature for predicting prognosis and immunotherapy response in HNSCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38430429", "kind": "science-record", "revision": 3, "content_hash": "sha256:be17551fa65bcff6f81539e7a3b7f33c24da26a791d7f8e8a20cc89e93522313", "created_at": "2026-11-01T19:20:22Z", "updated_at": "2026-11-01T22:11:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of T cell exhaustion related signature for predicting prognosis and immunotherapy response in HNSCC.", "doi": "10.1007/s12672-024-00921-5", "pmid": "38430429", "authors": ["Wei Zhang", "Mei Qu", "Chun Yin", "Zhiliang Jin", "Ya Hu"], "journal": "Discover oncology", "year": 2024, "abstract": "BACKGROUND: T cell exhaustion (TEX) signifies a condition of T cell disorder which implicate the therapeutic benefits and prognostic significance in patients with cancer. However, its role in the Head and Neck Squamous Carcinoma (HNSCC) remains incompletely understood.\nMETHODS: The detailed data of HNSCC samples were obtained from The Cancer Genome Atlas (TCGA) database and two Gene Expression Omnibus (GEO) datasets. We computed the expression scores of four TEX-related pathways and detected gene modules closely linked to these pathways, indicating prognostic significance. Following this, regression analyses were performed to select eight genes for the development of a predictive signature. The predictive capacity of this signature was evaluated. Additionally, we examined the relationships between TEX-related signature risk scores and the effectiveness of immunotherapy as well as drug sensitivity.\nRESULTS: A novel prognostic model, comprising eight TEX-related genes, was established for patients with HNSCC. The prognostic value was further confirmed using additional GEO datasets: GSE65858 and GSE27020. This signature enables the stratification of patients into high- and low- risk groups, each showing distinct survival outcomes and responsiveness to immunotherapy. The low-risk group demonstrated improved prognosis and enhanced efficacy of immunotherapy. In addition, AZD6482, TAF1, Ribociclib, LGK974, PF4708671 and other drugs showed increased sensitivity in the high-risk group based on drug sensitivity values, offering tailored therapeutic recommendations for individuals with various risks profiles.\nCONCLUSION: In conclusion, we developed a novel T cell exhaustion-associated signature, which holds considerable predictive value for both the prognosis of patients with HNSCC and the effectiveness of tumor immunotherapy.", "claims": [{"id": "claim-method", "statement": "We utilized single-sample gene set enrichment analysis (ssGSEA), implemented through the ‘GSVA’ R package [20], to estimate the enrichment score of TEX-related pathways for each patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38430429", "locator": "sections[4] \"Activity analysis of TEX-related pathways\" paragraph 2", "quote": "We utilized single-sample gene set enrichment analysis (ssGSEA), implemented through the ‘GSVA’ R package [20], to estimate the enrichment score of TEX-related pathways for each patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets are available in the TCGA database (https://portal.gdc.cancer.gov/) and GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38430429", "locator": "sections[25] \"Data availability\" paragraph 2", "quote": "The datasets are available in the TCGA database (https://portal.gdc.cancer.gov/) and GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A novel prognostic model, comprising eight TEX-related genes, was established for patients with HNSCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38430429", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A novel prognostic model, comprising eight TEX-related genes, was established for patients with HNSCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A novel prognostic model, comprising eight TEX-related genes, was established for patients with HNSCC.", "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:38430429"], "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:GSE27020"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE27020"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38430429", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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