Identification of senescence-related lncRNA prognostic index correlating with prognosis and radiosensitivity in prostate cancer patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37742230", "kind": "science-record", "revision": 3, "content_hash": "sha256:579b84e019d0d0fa36754950fc23fe3eb85397b03592de267b67fefd583ce187", "created_at": "2026-11-01T20:27:26Z", "updated_at": "2026-11-01T22:10:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of senescence-related lncRNA prognostic index correlating with prognosis and radiosensitivity in prostate cancer patients.", "doi": "10.18632/aging.204888", "pmid": "37742230", "authors": ["Dechao Feng", "Li Li", "Xu Shi", "Weizhen Zhu", "Jie Wang", "Ruicheng Wu", "Dengxiong Li", "Wuran Wei", "Ping Han"], "journal": "Aging", "year": 2023, "abstract": "BACKGROUND: An increasing number of studies are shown how crucial a role cellular senescence plays in tumor development. In this study, we developed a senescence-related lncRNA prognostic index (SRLPI) to forecast radiosensitivity and the probability of biochemical recurrence (BCR) in patients with prostate cancer (PCa).\nMETHODS: PCa cohorts in TCGA and GEO databases were downloaded. Senescence-and prognosis-related lncRNA with differential expression in tumor and normal samples were identified and used to establish the SRLPI score. Mutation landscape, function pathway, tumor stemness and heterogeneity and tumor immune microenvironment were also analyzed. We performed the analysis using R 3.6.3 and the appropriate tools.\nRESULTS: A SRLPI score was constructed based on SNHG1 and MIAT in the TCGA cohort. Our classification of PCa patients into high- and low-risk groups was based on the median SRLPI score. When compared to the low-SRLPI group, the high-SRLPI group was more vulnerable to BCR (HR: 3.33). In terms of BCR-free survival and metastasis-free survival, the GSE116918 showed similar findings. Surprisingly, the SRLPI score demonstrated a high level of radiosensitivity for diagnosis (AUC: 0.98). Age, Gleason score, T stage, N stage, positive lymph nodes, and residual tumor were all significantly greater in patients with high SRLPI scores. Furthermore, this score was significantly related to markers of senescence. Protein secretion and androgen response were found to be substantially enriched in the low-SRLPI group, whereas E2F targets were found to be strongly enriched in the high-SRLPI group for pathway analysis. For the tumor microenvironment assessment, B cells, CD8+ T cells, immune score and TIDE score were positively related to SRLPI score while endothelial level was negatively associated with SRLPI score with statistical significance.\nCONCLUSIONS: We developed a SRLPI score that was related to prognosis and radiosensitivity and might be helpful in clinical practice.", "claims": [{"id": "claim-method", "statement": "We then performed lasso and multivariate Cox regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37742230", "locator": "sections[3] \"Data preparation\" paragraph 2", "quote": "We then performed lasso and multivariate Cox regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37742230", "locator": "sections[8] \"Availability of supporting data\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The high-SRLPI group was more vulnerable to biochemical recurrence than the low-SRLPI group (HR: 3.33).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37742230", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "When compared to the low-SRLPI group, the high-SRLPI group was more vulnerable to BCR (HR: 3.33)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The high-SRLPI group was more vulnerable to biochemical recurrence than the low-SRLPI group (HR: 3.33).", "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:37742230"], "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:GSE116918"], "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:GSE116918"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37742230", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.204888", "sha256": "sha256:ca9e708d8786e3acfb9cac18244fe6f27fdf1248152ba152054fd4159db69314", "bytes": 29855, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.204888", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10564441", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116918", "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=GSE116918", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116918", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE116918", "GSE70768", "GSE53902"], "resolved_accessions": ["GSE116918", "GSE70768", "GSE53902"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."], "basis": "The paper names GSE116918, GSE70768, GSE53902 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:37742230", "data:geo:GSE116918"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116918"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:12:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8380, "completion_tokens": 1621, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37742230", "type": "paper", "label": "pmid:37742230"}, {"id": "source:pmid:37742230", "type": "manuscript", "label": "PMID 37742230 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37742230", "type": "paper", "label": "pmid:37742230"}, {"id": "source:pmid:37742230", "type": "manuscript", "label": "PMID 37742230 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37742230", "type": "extraction", "used": ["source:pmid:37742230"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116918", "type": "accession_resolution", "used": ["data:geo:GSE116918"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37742230", "parent_hash": "sha256:452310bd2ac19de4a3abef8bc5337872c1173cf31456e124de5552887e3c8746", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE116918 licence not read", "asset:data:geo:GSE116918 not downloaded", "asset:data:geo:GSE53902 licence not read", "asset:data:geo:GSE53902 not downloaded", "asset:data:geo:GSE70768 licence not read", "asset:data:geo:GSE70768 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ins information on PCa, was used to download RNA-sequencing profiles, genetic mutations, and related cli"], "order_basis": "paper_text_order:2237", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We then performed lasso and multivariate Cox regression analysis."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}