Construction of oxidative phosphorylation-related prognostic risk score model in uveal melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38698303", "kind": "science-record", "revision": 3, "content_hash": "sha256:647592dd9f07eec6fbc69e0fbb0afeec33c5408325391bac3a1d9c13a600fe95", "created_at": "2026-11-01T19:20:39Z", "updated_at": "2026-11-01T22:11:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of oxidative phosphorylation-related prognostic risk score model in uveal melanoma.", "doi": "10.1186/s12886-024-03441-6", "pmid": "38698303", "authors": ["Zhiyun Zhan", "Kun Lin", "Tingting Wang"], "journal": "BMC ophthalmology", "year": 2024, "abstract": "BACKGROUND: Uveal melanoma (UVM) is a malignant intraocular tumor in adults. Targeting genes related to oxidative phosphorylation (OXPHOS) may play a role in anti-tumor therapy. However, the clinical significance of oxidative phosphorylation in UVM is unclear.\nMETHOD: The 134 OXPHOS-related genes were obtained from the KEGG pathway, the TCGA UVM dataset contained 80 samples, served as the training set, while GSE22138 and GSE39717 was used as the validation set. LASSO regression was carried out to identify OXPHOS-related prognostic genes. The coefficients obtained from Cox multivariate regression analysis were used to calculate a risk score, which facilitated the construction of a prognostic model. Kaplan-Meier survival analysis, logrank test and ROC curve using the time \"timeROC\" package were conducted. The immune cell frequency in low- and high-risk group was analyzed through Cibersort tool. The specific genomic alterations were analyzed by \"maftools\" R package. The differential expressed genes between low- or high-risk group were analyzed and performed Gene Ontology (GO) and GSEA. Finally, we verified the function of CYC1 in UVM by gene silencing in vitro.\nRESULTS: A total of 9 OXPHOS-related prognostic genes were identified, including NDUFB1, NDUFB8, ATP12A, NDUFA3, CYC1, COX6B1, ATP6V1G2, ATP4B and NDUFB4. The UVM prognostic risk model was constructed based on the 9 OXPHOS-related prognostic genes. The prognosis of patients in the high-risk group was poorer than low-risk group. Besides, the ROC curve demonstrated that the area under the curve of the model for predicting the 1 to 5-year survival rate of UVM patients were all more than 0.88. External validation in GSE22138 and GSE39717 dataset revealed that these 9 genes could also be utilized to evaluate and predict the overall survival of patients with UVM. The risk score levels related to immune cell frequency and specific genomic alterations. The DEGs between the low- and high- risk group were enriched in tumor OXPHOS and immune related pathway. In vitro experiments, CYC1 silencing significantly inhibited UVM cell proliferation and invasion, induced cell apoptosis.\nCONCLUSION: In sum, a prognostic risk score model based on oxidative phosphorylation-related genes in UVM was developed to enhance understanding of the disease. This prognostic risk score model may help to find potential therapeutic targets for UVM patients. CYC1 acts as an oncogene role in UVM.", "claims": [{"id": "claim-method", "statement": "LASSO regression was carried out to identify OXPHOS-related prognostic genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38698303", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "LASSO regression was carried out to identify OXPHOS-related prognostic genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data can be accessed by contacting the corresponding author.\nThe datasets generated and/or analysed during the current study are available in the UCXC Xena (https://xenabrowser.net/datapages/) and GEO database (GSE22138, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22138), (GSE39717, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39717) repository.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38698303", "locator": "sections[27] \"Data availability\" paragraphs 1-3", "quote": "All data can be accessed by contacting the corresponding author.\nThe datasets generated and/or analysed during the current study are available in the UCXC Xena (https://xenabrowser.net/datapages/) and GEO database (GSE22138, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22138), (GSE39717, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39717) repository."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 9 OXPHOS-related prognostic genes were identified, including NDUFB1, NDUFB8, ATP12A, NDUFA3, CYC1, COX6B1, ATP6V1G2, ATP4B and NDUFB4.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38698303", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 9 OXPHOS-related prognostic genes were identified, including NDUFB1, NDUFB8, ATP12A, NDUFA3, CYC1, COX6B1, ATP6V1G2, ATP4B and NDUFB4."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 9 OXPHOS-related prognostic genes were identified, including NDUFB1, NDUFB8, ATP12A, NDUFA3, CYC1, COX6B1, ATP6V1G2, ATP4B and NDUFB4.", "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:38698303"], "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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