M7G-related molecular subtypes can predict the prognosis and correlate with immunotherapy and chemotherapy responses in bladder cancer patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36732869", "kind": "science-record", "revision": 3, "content_hash": "sha256:55204b5bfe24ddf5991cd84e356635aac40772c17bc20afea73f67b7c66706cc", "created_at": "2026-11-01T19:01:17Z", "updated_at": "2026-11-01T22:08:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "M7G-related molecular subtypes can predict the prognosis and correlate with immunotherapy and chemotherapy responses in bladder cancer patients.", "doi": "10.1186/s40001-023-01012-x", "pmid": "36732869", "authors": ["Deng-Xiong Li", "De-Chao Feng", "Xiao-Ming Wang", "Rui-Cheng Wu", "Wei-Zhen Zhu", "Kai Chen", "Ping Han"], "journal": "European journal of medical research", "year": 2023, "abstract": "BACKGROUND: N7-methylguanosine (m7G) is closely associated with tumor prognosis and immune response in many cancer types. The correlation between m7G and bladder cancer (BC) needs further study. We aimed to orchestrate molecular subtypes and identify key genes for BC from the perspective of m7G.\nMETHODS: RNA-seq and clinical data of BC patients were extracted from TCGA and GSE13507 datasets. The patients were subtyped by \"ConsensusClusterPlus\" and \"limma.\" The clusters were validated by the Kaplan‒Meier curves, univariable and multivariate Cox regression models, the concordance index, and calibration curves. The immunotherapy response was evaluated by immune checkpoints, immune infiltration, TIDE score, and IMvigor210 cohort. Genomics of Drug Sensitivity in Cancer was utilized to predict the chemotherapy response between the clusters.\nRESULTS: The m7G-related cluster was ultimately established by EIF4G1, NUDT11, NUDT10, and CCNB1. The independent prognostic value of the m7G-related cluster was validated by the TCGA and GSE13507 datasets. The cluster was involved in immune-associated pathways, such as neutrophil degranulation, antigen processing cross-presentation, and signaling by interleukins pathways. Meanwhile, cluster 2 was positively correlated with many immune checkpoints, such as CD274, CTLA4, HAVCR2, LAG3, PDCD1, and PDCD1LG2. The cluster 2 was significantly correlated with a higher TIDE score than the cluster 1. Furthermore, in the IMvigor210 cohort, patients in the cluster 1 had a higher response rate than those in the cluster 2. Patients in the cluster 2 were sensitive to many chemotherapies.\nCONCLUSIONS: We successfully determined molecular subtypes and identified key genes for BC from the perspective of m7G, thereby providing a roadmap for the evolution of immunotherapy and precision medicine.", "claims": [{"id": "claim-method", "statement": "All 42 m7G-related genes were incorporated into the lasso regression model, which could apply penalties to these genes. The penalty parameter (λ) for the model was determined by tenfold cross-validation following the minimum criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36732869", "locator": "sections[3] \"Microarray data and molecular subtypes\" paragraph 3", "quote": "All 42 m7G-related genes were incorporated into the lasso regression model, which could apply penalties to these genes. The penalty parameter (λ) for the model was determined by tenfold cross-validation following the minimum criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data from this study were downloaded from online databases. Therefore, everyone can get the data online. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36732869", "locator": "sections[24] \"notes\" paragraph 1", "quote": "All data from this study were downloaded from online databases. Therefore, everyone can get the data online. Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper determined molecular subtypes and identified key genes for bladder cancer from the perspective of m7G.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36732869", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We successfully determined molecular subtypes and identified key genes for BC from the perspective of m7G, thereby providing a roadmap for the evolution of immunotherapy and precision medicine."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper determined molecular subtypes and identified key genes for bladder cancer from the perspective of m7G.", "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:36732869"], "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:36732869", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-023-01012-x", "sha256": "sha256:39abff62b453ecb11a2e1f13559344f06ab12ad82c970fa9e0032c0b70c6da6a", "bytes": 30350, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40001-023-01012-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9893617", "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 online databases. 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 online databases. Therefore, everyone can get the data online. 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