Identification and validation of basement membrane-related genes predicting prognosis and immune infiltration associated with bladder cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39029072", "kind": "science-record", "revision": 2, "content_hash": "sha256:e46a0de447fa8c974f94721d22eba9c9d7456cf0c268df5c91e0baa733f28599", "created_at": "2026-11-01T20:29:06Z", "updated_at": "2026-11-01T21:33:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of basement membrane-related genes predicting prognosis and immune infiltration associated with bladder cancer.", "doi": "10.1097/MD.0000000000038858", "pmid": "39029072", "authors": ["Fie Lai", "Lin He", "Thongher Lia", "Zhen Yang", "Chaoyou Huang"], "journal": "Medicine", "year": 2024, "abstract": "Bladder cancer (BC) is fatal during muscle invasion and treatment progress is limited. In this study, we aimed to construct and validate basement membrane (BM)-associated gene prognosis to predict BC progression and tumor immune infiltration correlation. We choreographed BM-related genes in the Cancer Genome Atlas (TCGA) database using COX regression and least absolute shrinkage and selection operator (LASSO) analysis, and the predictive value of BM-related genes was further validated by the GSE32548, GSE129845, and immunohistochemistry staining. All analyses were performed with R-version 4.2.2, and its appropriate packages. Three genes were identified to construct a gene signature to predictive of BC prognosis. We divided the TCGA database into 2 groups, and patients in the high-risk group had worse overall survival (OS) than those in the low-risk group. In GSE32548, we confirmed that patients in the high-risk group had a poorer prognosis compared to those in the low-risk group in terms of OS. Immunohistochemical staining of EPEMP1, GPC2, and ITGA3 showed significantly higher expression at the protein level in BC tissues than in normal tissues. The Spearman analysis showed risk score was positively correlated with B cell naïve, Macrophages M2, and Mast cells resting. stromal score, immune score, and ESTIMATE scores were significantly higher in the high-risk group. drugs sensitivity analysis showed IC50 of Cisplatin, Gemcitabine, and Methotrexate in the high-risk group was significantly higher than that in the low-risk group. We identified 3 prognostic genes from a novel perspective of BM genes as effective risk stratification tools for BC patients.", "claims": [{"id": "claim-method", "statement": "We choreographed BM-related genes in the Cancer Genome Atlas (TCGA) database using COX regression and least absolute shrinkage and selection operator (LASSO) analysis, and the predictive value of BM-related genes was further validated by the GSE32548, GSE129845, and immunohistochemistry staining.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39029072", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We choreographed BM-related genes in the Cancer Genome Atlas (TCGA) database using COX regression and least absolute shrinkage and selection operator (LASSO) analysis, and the predictive value of BM-related genes was further validated by the GSE32548, GSE129845, and immunohistochemistry staining."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are publicly available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39029072", "locator": "sections[27] \"(untitled)\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are publicly available."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Three genes were identified to construct a gene signature to predictive of BC prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39029072", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Three genes were identified to construct a gene signature to predictive of BC prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Three genes were identified to construct a gene signature to predictive of BC prognosis.", "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:39029072"], "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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