Tumor hypoxia in immune infiltration and prognosis of bladder cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39145090", "kind": "science-record", "revision": 2, "content_hash": "sha256:0f1f71afa92dc0482648d63f6f18862a9f5ce789387dba205b3ee791226911a6", "created_at": "2026-11-01T20:29:16Z", "updated_at": "2026-11-01T21:33:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Tumor hypoxia in immune infiltration and prognosis of bladder cancer.", "doi": "10.21037/tcr-23-2375", "pmid": "39145090", "authors": ["Fanghong Xu", "Xinyue Yao", "Nanjing Zhou", "Zuohuai Hu", "Chenrui Guo", "Hang Zhou", "Xiaokai Yan"], "journal": "Translational cancer research", "year": 2024, "abstract": "Background: Bladder cancer (BC) is the sixth most common cancer and the ninth leading cause of cancer death among men in the world. Previous studies have shown that tumor hypoxia plays an important role in the occurrence and development of BC, but the role of tumor hypoxia in the prognosis and immune infiltration of BC remains unclear. Our aim was to perform a bioinformatics analysis combined with a clinical analysis to explore the roles of hypoxia in BC.\nMethods: We acquired datasets (GSE13507, GSE5287, and GSE1827) containing mRNA expression information from BC cohorts from the Gene Expression Omnibus (GEO) and measured the Hypoxia score using the Gene Set Variation Analysis (GSVA). Then we used X-tile method and log-rank test and Pearson's correlation test to analyze the relation among the Hypoxia score and the clinicopathological and immunological characteristics of BC and used stepwise Cox regression analysis to establish a Prognostic model.\nResults: Hypoxia was found to be closely associated with tumor grade, pathological type, invasion, and prognosis of BC in our study. Moreover, we determined that hypoxia was closely related to the infiltration abundance of multiple immune cells through a correlation analysis, and the tumor immune cell infiltration was further found to be significantly associated with the tumor grade and tumor type of BC. Furthermore, we constructed several models based on the Hypoxia score and tumor immune infiltration with C-indexes ranging from 0.703 and 0.888, which showed good performance in predicting the prognosis of BC.\nConclusions: Our study showed that hypoxia plays an important role in the progression, prognosis, and tumor immune infiltration of BC. Our models based on hypoxia and tumor immune infiltration play a guiding role in the prognosis and treatment of BC patients.", "claims": [{"id": "claim-method", "statement": "We measured the Hypoxia score using the Gene Set Variation Analysis (GSVA) (22,23).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39145090", "locator": "sections[5] \"Score of hypoxia and immune cell infiltration in BC\" paragraph 2", "quote": "We measured the Hypoxia score using the Gene Set Variation Analysis (GSVA) (22,23)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Datasets (GSE13507, GSE5287, and GSE1827) containing mRNA expression information from BC cohorts were acquired from the Gene Expression Omnibus (GEO).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39145090", "locator": "sections[4] \"BC data acquisition and processing\" paragraph 2", "quote": "Datasets (GSE13507, GSE5287, and GSE1827) containing mRNA expression information from BC cohorts were acquired from the Gene Expression Omnibus (GEO)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Furthermore, we constructed several models based on the Hypoxia score and tumor immune infiltration with C-indexes ranging from 0.703 and 0.888, which showed good performance in predicting the prognosis of BC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39145090", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Furthermore, we constructed several models based on the Hypoxia score and tumor immune infiltration with C-indexes ranging from 0.703 and 0.888, which showed good performance in predicting the prognosis of BC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Furthermore, we constructed several models based on the Hypoxia score and tumor immune infiltration with C-indexes ranging from 0.703 and 0.888, which showed good performance in predicting the prognosis of BC.", "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:39145090"], "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:GSE13507"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE13507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39145090", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-23-2375", "sha256": 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