Prognosis and immunotherapy significances of a cancer-associated fibroblasts-related gene signature in bladder urothelial carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39503984", "kind": "science-record", "revision": 2, "content_hash": "sha256:1cfc9c9f2b3256bd63b5c141b884e53e3aa692f7a015c58148488ac3ec835c1b", "created_at": "2026-11-01T20:29:45Z", "updated_at": "2026-11-01T21:34:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognosis and immunotherapy significances of a cancer-associated fibroblasts-related gene signature in bladder urothelial carcinoma.", "doi": "10.1007/s12672-024-01505-z", "pmid": "39503984", "authors": ["Xiaobin Chen", "Yugen Li", "Jing Huang", "Qiang Zhang", "Chunlin Tan", "Yang Liu", "Zhongbo Du"], "journal": "Discover oncology", "year": 2024, "abstract": "BACKGROUND: The biological significance of cancer-associated fibroblasts (CAFs) in bladder urothelial carcinoma (BUC) warrants further investigation. There is an urgent need to explore the predictive utility of CAF-related genes for prognosis in BUC.\nMETHODS: The transcriptome and clinical data of 407 BUC patients in The Cancer Genome Atlas (TCGA) database were analyzed and a prognostic model was established. A total of 476 BUC cases from the E-MTAB-4321 database were used for validation. A risk model was constructed utilizing CAF-related genes through LASSO Cox regression, investigating its association with prognosis, gene mutations, immune cell infiltration, and drug sensitivity in BUC.\nRESULTS: We identified five CAF-related genes (EGFL6, NRSN2, SEMA3D, TM4SF1 and TPST1) in both the TCGA and E-MTAB-4321 datasets, and established a prognostic model using LASSO Cox regression. The high-risk group showed a significant correlation with poor survival. Furthermore, the low-risk group exhibited higher tumor mutational burden and lower levels of immune cell infiltration, and this model holds promise for guiding drug selection in BUC patients.\nCONCLUSIONS: These findings underscore the pivotal role of CAF-related genes in prognostic prediction for BUC patients. Clinical decision-making and tailored therapeutics stand to benefit from these results, providing a valuable reference for future research endeavors.", "claims": [{"id": "claim-method", "statement": "Using the \"survival\", \"surviminer\" and \"Glmnet\" packages [21, 22], the LASSO Cox regression was conducted in the TCGA database to establish a prognostic model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39503984", "locator": "sections[5] \"Construction and validation of a multi-gene signature\" paragraph 2", "quote": "Using the \"survival\", \"surviminer\" and \"Glmnet\" packages [21, 22], the LASSO Cox regression was conducted in the TCGA database to establish a prognostic model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data supporting the findings of this study are all available in public databases or on other demand and from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39503984", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The raw data supporting the findings of this study are all available in public databases or on other demand and from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The risk score is an independent prognostic factor for BUC patients (Fig. 4A, B, p < 0.001).", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Univariate and multivariate Cox regression analyses were conducted on clinical characteristics and risk scores within the TCGA cohort, revealing that the risk score is an independent prognostic factor for BUC patients (Fig. 4A, B, p < 0.001)."}, "evidence": [{"asset": "source:pmid:39503984", "locator": "sections[14] \"Independent prognostic analysis.\" paragraph 2", "quote": "Univariate and multivariate Cox regression analyses were conducted on clinical characteristics and risk scores within the TCGA cohort, revealing that the risk score is an independent prognostic factor for BUC patients (Fig. 4A, B, p < 0.001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The risk score is an independent prognostic factor for BUC patients (Fig. 4A, B, p < 0.001).", "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:39503984"], "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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