Alternative Polyadenylation Regulatory Factors Signature for Survival Prediction in Kidney Renal Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38617569", "kind": "science-record", "revision": 3, "content_hash": "sha256:0a926965468f31f0b357246323f2ad6d65f5f3d864f2667305d1c83aeb30fbda", "created_at": "2026-11-01T19:20:35Z", "updated_at": "2026-11-01T21:32:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Alternative Polyadenylation Regulatory Factors Signature for Survival Prediction in Kidney Renal Cell Carcinoma.", "doi": "10.1177/11769351231180789", "pmid": "38617569", "authors": ["Xiaoyu Wang", "Yao Lin", "Zheng Li", "Yueqi Li", "Mingcong Chen"], "journal": "Cancer informatics", "year": 2024, "abstract": "Background: Alternative polyadenylation (APA) plays a vital regulatory role in various diseases. It is widely accepted that APA is regulated by APA regulatory factors.\nObjective: Whether APA regulatory factors affect the prognosis of renal cell carcinoma remains unclear, and this is the main topic of this study.\nMethods: We downloaded the transcriptome and clinical data from The Cancer Genome Atlas (TCGA) database. We used the Lasso regression system to construct an APA model for analyzing the relationship between common APA regulatory factors and renal cell carcinoma. We also validated our APA model using independent GEO datasets (GSE29609, GSE76207).\nResults: It was found that the expression levels of 5 APA regulatory factors (CPSF1, CPSF2, CSTF2, PABPC1, and PABPC4) were significantly associated with tumor gene mutation burden (TMB) score in renal clear cell carcinoma, and the risk score constructed using the expression level of 5 key APA regulatory factors could be used to predict the outcome of renal clear cell carcinoma. The TMB score is associated with the remodeling of the immune microenvironment.\nConclusions: By identifying key APA regulatory factors in renal cell carcinoma and constructing risk scores for key APA regulatory factors, we showed that key APA regulators affect prognosis of renal clear cell carcinoma patients. In addition, the risk score level is associated with TMB, indicating that APA may affect the efficacy of immunotherapy through immune microenvironment-related genes. This helps us better understand the mRNA processing mechanism of renal clear cell carcinoma.", "claims": [{"id": "claim-method", "statement": "Lasso Cox regression analysis was performed on the above significantly differently expressed APA regulators.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38617569", "locator": "sections[8] \"Construction of APA regulator signature-based risk assessment model in KIRC\" paragraph 2", "quote": "Lasso Cox regression analysis was performed on the above significantly differently expressed APA regulators."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability Statement: The datasets analyzed during the current study are available in TCGA database (https://cancergenome.nih.gov/), TIMER datebase (https://cistrome.shinyapps.io/timer/), GEPIA datebase (http://gepia.cancer-pku.cn/), and Cbioportal datebase (https://www.cbioportal.org/study/clinicalData?id=kirc_tcga).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38617569", "locator": "sections[14] \"Footnotes\" paragraph 2", "quote": "Data Availability Statement: The datasets analyzed during the current study are available in TCGA database (https://cancergenome.nih.gov/), TIMER datebase (https://cistrome.shinyapps.io/timer/), GEPIA datebase (http://gepia.cancer-pku.cn/), and Cbioportal datebase (https://www.cbioportal.org/study/clinicalData?id=kirc_tcga)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The risk score constructed using the expression levels of 5 key APA regulatory factors could be used to predict the outcome of renal clear cell carcinoma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38617569", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "It was found that the expression levels of 5 APA regulatory factors (CPSF1, CPSF2, CSTF2, PABPC1, and PABPC4) were significantly associated with tumor gene mutation burden (TMB) score in renal clear cell carcinoma, and the risk score constructed using the expression level of 5 key APA regulatory factors could be used to predict the outcome of renal clear cell carcinoma."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The risk score constructed using the expression levels of 5 key APA regulatory factors could be used to predict the outcome of renal clear cell carcinoma.", "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:38617569"], "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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