An autophagy-related prognostic signature associated with immune microenvironment features of uveal melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33682883", "kind": "science-record", "revision": 7, "content_hash": "sha256:3ef45c9a270811dfe3bcd0a14e87bd8ba2eb02befe414a5de0caa93722180a37", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T22:03:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An autophagy-related prognostic signature associated with immune microenvironment features of uveal melanoma.", "doi": "10.1042/BSR20203812", "pmid": "33682883", "authors": ["Zhuotao Zheng", "Lingyue Zhang", "Zewei Tu", "Yan Deng", "Xiaolong Yin"], "journal": "Bioscience reports", "year": 2021, "abstract": "Autophagy is involved in cancer initiation and progression but its role in uveal melanoma (UM) was rarely investigated. Herein, we built an autophagy-related gene (ARG) risk model of UM patients by univariate Cox regression and least absolute shrinkage and selection operator (Lasso) regression model and filtrated out nine prognostic ARGs in The Cancer Genome Atlas (TCGA) cohort. Survival and Receiver Operating Characteristic (ROC) Curve analysis in the TCGA and other four independent UM cohorts (GSE22138, GSE27831, GSE44295 and GSE84976) proved that the ARG-signature possessed robust and steady prognosis predictive ability. We calculated risk scores for patients included in our study and patients with higher risk scores showed worse clinical outcomes. We found the expressions of the nine ARGs were significantly associated with clinical and molecular features (including risk score) and overall survival (OS) of UM patients. Furthermore, we utilized univariate and multivariate Cox regression analyses to determine the independent prognostic ability of the ARG-signature. Functional enrichment analysis showed the ARG-signature was correlated with several immune-related processes and pathways like T-cell activation and T-cell receptor signaling pathway. Gene set enrichment analysis (GSEA) found tumor hallmarks including angiogenesis, IL6-JAK-STAT3-signaling, reactive oxygen species pathway and oxidative phosphorylation were enriched in high-risk UM patients. Finally, infiltrations of several immune cells and immune-related scores were found significantly associated with the ARG-signature. In conclusion, the ARG-signature might be a strong predictor for evaluating the prognosis and immune infiltration of UM patients.", "claims": [{"id": "claim-method", "statement": "Based on the clinical and survival information, univariate and multivariate Cox regression were the vital analytical methods to decide the independent prognostic role of the ARG-signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33682883", "locator": "sections[8] \"Statistical methods\" paragraph 2", "quote": "Based on the clinical and survival information, univariate and multivariate Cox regression were the vital analytical methods to decide the independent prognostic role of the ARG-signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data analyzed in the present study can be accessed the TCGA (http://cancergenome.nih.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) websites.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33682883", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The data analyzed in the present study can be accessed the TCGA (http://cancergenome.nih.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) websites."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33682883"], "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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(40.00%)", "/", "/", "/", "/"], ["", "No", "48 (60.00%)", "/", "/", "/", "/"], ["", "NA", "0 (0)", "/", "/", "/", "/"], ["Chr1 loss", "", "", "", "", "", ""], ["", "Yes", "9 (11.25%)", "/", "/", "/", "/"], ["", "No", "71 (88.75%)", "/", "/", "/", "/"], ["", "NA", "0 (0)", "/", "/", "/", "/"], ["Chr3 loss", "", "", "", "", "", ""], ["", "Yes", "31 (38.75%)", "37 (58.73%)", "/", "14 (50.00%)", "/"], ["", "No", "49 (61.25%)", "18 (28.57%)", "/", "14 (50.00%)", "/"], ["", "NA", "0 (0)", "8 (12.70%)", "/", "/", "/"]], "row_count": 50, "column_count": 7, "numeric_cells": 83, "header_rows": 2, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33682883:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:81b6d7e952b4b7de96ec2daedb81d65088e857e019bfd1f3093d7063c91c041b", "bytes": 794, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:33682883", "data:geo:GSE22138", "asset:table:pmid:33682883:1", "asset:table:pmid:33682883:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22138"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 20673, "completion_tokens": 2980, "cached_tokens": 784}}, "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:33682883", "type": "paper", "label": "pmid:33682883"}, {"id": "source:pmid:33682883", "type": "manuscript", "label": "PMID 33682883 full text"}, {"id": "data:geo:GSE22138", "type": "dataset", "label": "GEO GSE22138"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33682883", "type": "paper", "label": "pmid:33682883"}, {"id": "source:pmid:33682883", "type": "manuscript", "label": "PMID 33682883 full text"}, {"id": "data:geo:GSE22138", "type": "dataset", "label": "GEO GSE22138"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33682883", "type": "extraction", "used": ["source:pmid:33682883"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22138", "type": "accession_resolution", "used": ["data:geo:GSE22138"], "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:33682883", "parent_hash": "sha256:db6f2ea250597f1f44007b295026d2b861ff8481dc27a32fb0217154e80eb265", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE22138 licence not read", "asset:data:geo:GSE22138 not downloaded", "asset:data:geo:GSE27831 licence not read", "asset:data:geo:GSE27831 not downloaded", "asset:data:geo:GSE44295 licence not read", "asset:data:geo:GSE44295 not downloaded", "asset:data:geo:GSE84976 licence not read", "asset:data:geo:GSE84976 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["red in published researches [16,17]. For the microarray data in the GSE22138, GSE27831, GSE44295 and", "quantile normalization were performed on the microarray raw data using a robust multiarray averaging"], "order_basis": "paper_text_order:2080", "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": ["Based on the clinical and survival information, univariate and multivariate Cox regression were the vital analytical methods to decide the independent prognostic role of the ARG-signature."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}