Integrating multiple key molecules in uveal melanoma to uncover metastatic and immune microenvironment-related gene signatures
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Lu Ye. Shaanxi Eye Hospital, Xi’an People’s Hospital (Xi’an Fourth Hospital), Affiliated People’s Hospital of Northwest University, Xi’an 710004, Shaanxi Province, China. YL0618@med.nwu.edu.cn; Yang Liu. People’s Hospital of Ningxia Hui Autonomous Region, Ningxia Medical University, Ningxia Clinical Research Institute, Yinchuan 750000, Ningxia Hui Autonomous Region, China. herbliuyang@163.com

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Supported by the National Natural Science Foundation of China (No.82460215); National Natural Science Foundation of China Pre-experimental Project (No.2025GZRYSY006); 2025 Youth Training Project of the Xi’an Municipal Health Commission (No.2025qn05); Xi’an Medical Research-Discipline Capacity Building Project (No.23YXYJ0002); Key R&D Plan of Shaanxi Province: Key Industrial Innovation Chain (Cluster)-Social Development Field (No.2022ZDLSF03-10); Research Incubation Fund of Xi’an People’s Hospital (Xi’an Fourth Hospital; No.LH-13).

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    Abstract:

    AIM: To identify metastasis-associated prognostic genes and construct a robust molecular signature for survival prediction in uveal melanoma (UVM) patients. METHODS: Transcriptomic data and clinical information from 80 UVM patients in the Cancer Genome Atlas (TCGA)-UVM cohort and an external Gene Expression Omnibus (GEO) microarray dataset (GSE73652; 8 non-metastatic vs 5 metastatic cases) were analyzed to identify differentially expressed genes (DEGs). Functional enrichment, protein-protein interaction (PPI) network construction, and survival analyses identified seven metastasis- and prognosis-related genes. Their expression was further examined using public single-cell RNA-seq data (GSE139829; 11 tumors). Experimental validation was performed in UVM cell lines (92.1, OMM1, MEL270) and adult retinal pigment epithelial (ARPE-19) cells using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting to confirm transcriptomic trends. A LASSO Cox model was applied to construct a metastasis-related risk Score signature. Tumor immune microenvironment characteristics were evaluated via single-sample gene set enrichment analysis (ssGSEA) and ESTIMATE. Somatic mutation and copy number variation (CNV) profiles were also examined. RESULTS: Seven key genes (UBE2T, KIF20A, DLGAP5, KLC3, TPX2, UBE2C, AURKA) were significantly associated with overall survival and used to construct a metastasis-related riskScore signature, which effectively stratified patients into high- and low-risk groups and served as an independent prognostic factor. qRT-PCR and Western blot results confirmed that the expression levels of selected key genes in UVM cell lines showed significant differences compared to ARPE-19 cells, which were largely consistent with the transcriptomic findings. The high-risk group exhibited reduced immune infiltration and stromal activity. Single-cell analysis revealed these genes were predominantly expressed in a tumor cell cluster characterized by BAP1 loss and high metastatic potential. Mutation and CNV analyses further supported the relevance of these genes to UVM progression. CONCLUSION: This study establishes and validates a seven-gene signature associated with metastasis and prognosis in UVM. The findings provide a framework for understanding molecular determinants of tumor progression and immune microenvironment alterations, and may offer guidance for future mechanistic studies and therapeutic exploration.

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Yi-Ming Guo, Zhan-Pei Bai, Jia-Qi Wang, et al. Integrating multiple key molecules in uveal melanoma to uncover metastatic and immune microenvironment-related gene signatures. Int J Ophthalmol, 2026,(1):11-24

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Publication History
  • Received:July 04,2025
  • Revised:September 05,2025
  • Adopted:
  • Online: December 16,2025
  • Published: