Immune implication of an autophagy-related prognostic signature in uveal melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34374416", "kind": "science-record", "revision": 7, "content_hash": "sha256:0e11fe1409281c141d16fc5e7217b4a3edd015cbbdfcfc1c4e27730f899b36dc", "created_at": "2026-11-01T15:41:47Z", "updated_at": "2026-11-01T21:26:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immune implication of an autophagy-related prognostic signature in uveal melanoma.", "doi": "10.1042/BSR20211098", "pmid": "34374416", "authors": ["Samuel Chuah", "Valerie Chew"], "journal": "Bioscience reports", "year": 2021, "abstract": "Uveal Melanoma (UM) is a rare cancer deriving from melanocytes within the uvea. It has a high rate of metastasis, especially to the liver, and a poor prognosis thereafter. Autophagy, an intracellular programmed digestive process, has been associated with the development and progression of cancers, with controversial pro- and anti-tumour roles. Although previous studies have been conducted on autophagy-related genes (ARGs) in various cancer types, its role in UM requires a deeper understanding for improved diagnosis and development of novel therapeutics. In the present study, Zheng et al. used univariate Cox regression followed by least absolute shrinkage and selection operator (Lasso) regression to identify a robust 9-ARG signature prognostic of survival in a total of 230 patients with UM. The authors used the Cancer Genome Atlas (TCGA) UM cohort as a training cohort (n=80) to identify the signature and validated it in another four independent cohorts of 150 UM patients from the Gene Expression Omnibus (GEO) repository (GSE22138, GSE27831, GSE44295 and GSE84976). This 9-ARG signature was also significantly associated with the enrichment of cancer hallmarks, including angiogenesis, IL6-KJAK-STAT3 signalling, reactive oxygen species pathway and oxidative phosphorylation. More importantly, this signature is associated with immune-related functional pathways and immune cell infiltration. Thus, this 9-ARG signature predicts prognosis and provides deeper insights into the immune mechanisms in UM, with potential implications for future immunotherapy.", "claims": [{"id": "claim-method", "statement": "Using the TCGA cohort (n=80) as the training cohort, univariate Cox regression analysis narrowed this list down to 133 ARGs, which were associated with overall survival (OS). From these ARGs, a final prognostic signature of 9-ARGs was then established using Lasso Cox regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34374416", "locator": "sections[2] \"Identification of an ARGs signature predictive of UM prognosis\" paragraph 2", "quote": "Using the TCGA cohort (n=80) as the training cohort, univariate Cox regression analysis narrowed this list down to 133 ARGs, which were associated with overall survival (OS). From these ARGs, a final prognostic signature of 9-ARGs was then established using Lasso Cox regression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Zheng et al. [17] first obtained bulk RNAseq data from five UM cohorts: The Cancer Genome Atlas (TCGA) cohort, and four others from the Gene Expression Omnibus (GEO) repository (GSE22138, GSE27831, GSE44295 and GSE84976), and identified 423 ARGs which were expressed across all the cohorts.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34374416", "locator": "sections[2] \"Identification of an ARGs signature predictive of UM prognosis\" paragraph 2", "quote": "Zheng et al. [17] first obtained bulk RNAseq data from five UM cohorts: The Cancer Genome Atlas (TCGA) cohort, and four others from the Gene Expression Omnibus (GEO) repository (GSE22138, GSE27831, GSE44295 and GSE84976), and identified 423 ARGs which were expressed across all the cohorts."}], "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:34374416"], "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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