Identification of endothelial-related molecular subtypes for bladder cancer patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37025597", "kind": "science-record", "revision": 3, "content_hash": "sha256:db4f47a99fc42287965250a44344f3e10121cab9c25b47fe472037b071543237", "created_at": "2026-11-01T19:01:40Z", "updated_at": "2026-11-01T22:09:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of endothelial-related molecular subtypes for bladder cancer patients.", "doi": "10.3389/fonc.2023.1101055", "pmid": "37025597", "authors": ["Deng-Xiong Li", "De-Chao Feng", "Xu Shi", "Rui-Cheng Wu", "Kai Chen", "Ping Han"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "Background: Bladder cancer (BC) is a disease with significant heterogeneity and poor prognosis. The prognosis and therapeutic response of BC patients are significantly influenced by endothelial cells in the tumor microenvironment. In order to understand BC from the perspective of endothelial cells, we orchestrated molecular subtypes and identified key genes.\nMethods: Single-cell and bulk RNA sequencing data were extracted from online databases. R and its relative packages were used to analyze these data. Cluster analysis, prognostic value analysis, function analysis, immune checkpoints, tumor immune environment and immune prediction were conducted.\nResults: Five endothelial-related genes (CYTL1, FAM43A, HSPG2, RBP7, and TCF4) divided BC patients in the TCGA, GSE13507, and GSE32894 datasets into two clusters, respectively. In prognostic value analysis, patients in the cluster 2 were substantially associated with worse overall survival than those in the cluster 1 according to the results of TCGA, GSE13507 and GSE32894 datasets. In the results of functional analysis, the endothelial-related clusters was enriched in immune-related, endothelial-related and metabolism-related pathways. Samples in the cluster 1 had a statistically significant increase in CD4+ T cells and NK-cell infiltration. Cluster 1 was positively correlated with the cancer stem score and tumor mutational burden score. The results of immune prediction analysis indicated that 50.6% (119/235) of patients in the cluster 1 responded to immunotherapy, while the response rate in the cluster 2 decreased to 16.7% (26/155).\nConclusion: In this study, we categorized and discovered distinctive prognosis-related molecular subtypes and key genes from the perspective of endothelial cells at the genetic level by integrating single-cell and bulk RNA sequencing data, primarily to provide a roadmap for precision medicine.", "claims": [{"id": "claim-method", "statement": "After establishing the cluster, Kaplan−Meier curves were utilized to estimate the prognostic value of ERC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37025597", "locator": "sections[5] \"Evaluation of the cluster and function analysis\" paragraph 2", "quote": "After establishing the cluster, Kaplan−Meier curves were utilized to estimate the prognostic value of ERC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data from this study were downloaded from an online database. Therefore, everyone can get the data online. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37025597", "locator": "sections[15] \"Data availability statement\" paragraph 2", "quote": "All data from this study were downloaded from an online database. Therefore, everyone can get the data online. Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Patients in cluster 1 had an immunotherapy response rate of 50.6% (119/235), whereas the response rate in cluster 2 was 16.7% (26/155).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37025597", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The results of immune prediction analysis indicated that 50.6% (119/235) of patients in the cluster 1 responded to immunotherapy, while the response rate in the cluster 2 decreased to 16.7% (26/155)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Patients in cluster 1 had an immunotherapy response rate of 50.6% (119/235), whereas the response rate in cluster 2 was 16.7% (26/155).", "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:37025597"], "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:37025597", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2023.1101055", "sha256": "sha256:5c9c5a345b79c99cf26135a2a46cc7f0419c2718ee9c65bab6b6c57889f1077a", "bytes": 34166, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2023.1101055", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10070733", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13507", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13507", "version": null, "note": "All data from this study were downloaded from an online database. Therefore, everyone can get the data online. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data from this study were downloaded from an online database. Therefore, everyone can get the data online. 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