Development of a Novel Autophagy-Related Prognostic Signature and Nomogram for Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33392087", "kind": "science-record", "revision": 6, "content_hash": "sha256:70bc5fc72b46f909be37f01543c7d56179677024bf32fb9377289757c1620c1a", "created_at": "2026-11-01T15:41:21Z", "updated_at": "2026-11-01T21:24:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of a Novel Autophagy-Related Prognostic Signature and Nomogram for Hepatocellular Carcinoma.", "doi": "10.3389/fonc.2020.591356", "pmid": "33392087", "authors": ["Qiongxuan Fang", "Hongsong Chen"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "BACKGROUND: Hepatocellular carcinoma (HCC) is the seventh most common malignancy and the second most common cause of cancer-related deaths. Autophagy plays a crucial role in the development and progression of HCC.\nMETHODS: Univariate and Lasso Cox regression analyses were performed to determine a gene model that was optimal for overall survival (OS) prediction. Patients in the GSE14520 and GSE54236 datasets of the Cancer Genome Atlas (TCGA) were divided into the high-risk and low-risk groups according to established ATG models. Univariate and multivariate Cox regression analyses were used to identify risk factors for OS for the purpose of constructing nomograms. Calibration and receiver operating characteristic (ROC) curves were used to evaluate model performance. Real-time PCR was used to validate the effects of the presence or absence of an autophagy inhibitor on gene expression in HepG2 and Huh7 cell lines.\nRESULTS: OS in the high-risk group was significantly shorter than that in the low-risk group. Gene set enrichment analysis (GSEA) indicated that the association between the low-risk group and autophagy- as well as immune-related pathways was significant. ULK2, PPP3CC, and NAFTC1 may play vital roles in preventing HCC progression. Furthermore, tumor environment analysis via ESTIMATION indicated that the low-risk group was associated with high immune and stromal scores. Based on EPIC prediction, CD8+ T and B cell fractions in the TCGA and GSE54236 datasets were significantly higher in the low-risk group than those in the high-risk group. Finally, based on the results of univariate and multivariate analyses three variables were selected for nomogram development. The calibration plots showed good agreement between nomogram prediction and actual observations. Inhibition of autophagy resulted in the overexpression of genes constituting the gene model in HepG2 and Huh7 cells.\nCONCLUSIONS: The current study determined the role played by autophagy-related genes (ATGs) in the progression of HCC and constructed a novel nomogram that predicts OS in HCC patients, through a combined analysis of TCGA and gene expression omnibus (GEO) databases.", "claims": [{"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:33392087", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:33392087", "data:geo:GSE14520", "asset:table:pmid:33392087:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14520"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:20:44Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 35023, "completion_tokens": 2527, "cached_tokens": 11784}}, "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:33392087", "type": "paper", "label": "pmid:33392087"}, {"id": "source:pmid:33392087", "type": "manuscript", "label": "PMID 33392087 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33392087", "type": "paper", "label": "pmid:33392087"}, {"id": "source:pmid:33392087", "type": "manuscript", "label": "PMID 33392087 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33392087", "type": "extraction", "used": ["source:pmid:33392087"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14520", "type": "accession_resolution", "used": ["data:geo:GSE14520"], "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:33392087", "parent_hash": "sha256:1a6318cf970cb81730e36deb54bfe5c622df402876463e475156db551c0d3d6c", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE54236 licence not read", "asset:data:geo:GSE54236 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ves were used to evaluate model performance. 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