Development of a prognostic risk model of uveal melanoma based on N7-methylguanosine-related regulators.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38987843", "kind": "science-record", "revision": 2, "content_hash": "sha256:d000b8fa306464a7262d83adc9e594e6ae20ed5e365286d736c87717617c3bf7", "created_at": "2026-11-01T20:29:03Z", "updated_at": "2026-11-01T21:33:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of a prognostic risk model of uveal melanoma based on N7-methylguanosine-related regulators.", "doi": "10.1186/s41065-024-00324-0", "pmid": "38987843", "authors": ["Pingfan Wu", "Qian Zhang", "Peng Zhong", "Li Chai", "Qiong Luo", "Chengyou Jia"], "journal": "Hereditas", "year": 2024, "abstract": "BACKGROUND: Uveal melanoma (UVM) stands as the predominant type of primary intraocular malignancy among adults. The clinical significance of N7-methylguanosine (m7G), a prevalent RNA modifications, in UVM remains unclear.\nMETHODS: Primary information from 80 UVM patients were analyzed as the training set, incorporating clinical information, mutation annotations and mRNA expression obtained from The Cancer Genome Atlas (TCGA) website. The validation set was carried out using Gene Expression Omnibus (GEO) database GSE22138 and GSE84976. Kaplan-Meier and Cox regression of univariate analyses were subjected to identify m7G-related regulators as prognostic genes.\nRESULT: A prognostic risk model comprising EIF4E2, NUDT16, SNUPN and WDR4 was established through Cox regression of LASSO. Evaluation of the model's predictability for UVM patients' prognosis by Receiver Operating Characteristic (ROC) curves in the training set, demonstrated excellent performance Area Under the Curve (AUC) > 0.75. The high-risk prognosis within the TCGA cohort exhibit a notable worse outcome. Additionally, an independent correlation between the risk score and overall survival (OS) among UVM patients were identified. External validation of this model was carried out using the validation sets (GSE22138 and GSE84976). Immune-related analysis revealed that patients with high score of m7G-related risk model exhibited elevated level of immune infiltration and immune checkpoint gene expression.\nCONCLUSION: We have developed a risk prediction model based on four m7G-related regulators, facilitating effective estimate UVM patients' survival by clinicians. Our findings shed novel light on essential role of m7G-related regulators in UVM and suggest potential novel targets for the diagnosis, prognosis and therapy of UVM.", "claims": [{"id": "claim-method", "statement": "Integrating the nine genes into Cox regression of LASSO, the LASSO coefficient curve consisting of four m7G-related prognostic genes was obtained, with the minimum parameter serve as the penalty regularization parameter lambda (λmin = 0.0411, Fig. 2a-b and Supplemental Table 1–3).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38987843", "locator": "sections[9] \"The prognostic risk model is developed and validated on the basis of m7G-related regulators\" paragraph 2", "quote": "Integrating the nine genes into Cox regression of LASSO, the LASSO coefficient curve consisting of four m7G-related prognostic genes was obtained, with the minimum parameter serve as the penalty regularization parameter lambda (λmin = 0.0411, Fig. 2a-b and Supplemental Table 1–3)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original data involved in this work comes from the website: https://portal.gdc.cancer.gov; https://www.ncbi.nlm.nih.gov/geo; http://www.gsea-msigdb.org. The code and results used to support the findings of this study are available from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38987843", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The original data involved in this work comes from the website: https://portal.gdc.cancer.gov; https://www.ncbi.nlm.nih.gov/geo; http://www.gsea-msigdb.org. The code and results used to support the findings of this study are available from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "An m7G-related prognostic risk model based on EIF4E2, NUDT16, SNUPN, and WDR4 was developed in 80 TCGA UVM patients and externally validated in 91 integrated GEO patients, with 1-, 3-, and 5-year AUCs of 0.770, 0.856, and 0.869 in the training cohort and 0.632, 0.808, and 0.828 in the validation cohort.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Consistent with the training set, the Kaplan–Meier curve for the validation set showed poor prognosis in the high risk cohort (p < 0.001, Fig. 2d), Additionally, Fig. 2f was generated through ROC analysis, displaying AUC value at 1, 3 and 5-years (0.632, 0.808 and 0.828, respectively)."}, "evidence": [{"asset": "source:pmid:38987843", "locator": "sections[9] \"The prognostic risk model is developed and validated on the basis of m7G-related regulators\" paragraph 2", "quote": "The LASSO Cox regression model is: Risk score = (1.170190103 × mRNA expression of EIF4E2) + (-0.470940387 × mRNA expression of NUDT16) + (0.55003035 × mRNA expression of SNUPN) + (0.945486337 × mRNA expression of WDR4) (Table 3)."}, {"asset": "source:pmid:38987843", "locator": "sections[9] \"The prognostic risk model is developed and validated on the basis of m7G-related regulators\" paragraph 3", "quote": "Subsequently, the risk model’s predictive ability the OS prognosis by calculating 1, 3 and 5-years AUC values (AUC at 1, 3 and 5-years was 0.770, 0.856, and 0.869, respectively, as shown in Fig. 2e)."}, {"asset": "source:pmid:38987843", "locator": "sections[9] \"The prognostic risk model is developed and validated on the basis of m7G-related regulators\" paragraph 3", "quote": "Consistent with the training set, the Kaplan–Meier curve for the validation set showed poor prognosis in the high risk cohort (p < 0.001, Fig. 2d), Additionally, Fig. 2f was generated through ROC analysis, displaying AUC value at 1, 3 and 5-years (0.632, 0.808 and 0.828, respectively)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "An m7G-related prognostic risk model based on EIF4E2, NUDT16, SNUPN, and WDR4 was developed in 80 TCGA UVM patients and externally validated in 91 integrated GEO patients, with 1-, 3-, and 5-year AUCs of 0.770, 0.856, and 0.869 in the training cohort and 0.632, 0.808, and 0.828 in the validation cohort.", "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:38987843"], "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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