Prognostic evaluation and experimental validation of cuproptosis-related hub genes identified through weighted gene co-expression network analysis in uveal melanoma

Background: Uveal melanoma (UVM) is the most common primary intraocular malignancy, poses a formidable challenge due to its high metastatic potential and grim prognosis, but limited treatment options for UVM have prompted studies on immunotherapies. Cuproptosis is a recently discovered form of regulated cell death that has emerged as a potential regulator of the tumor microenvironment (TME) and a modulator of Cancer development. However, the association between Cuproptosis and UVM remains unclear.

Methods: Weighted gene co-expression network analysis (WGCNA) was used to identify Cuproptosis genes. Transcriptome correlation analysis and differential analysis were conducted following consensus clustering on 221 UVM samples. The objective was to identify cuproptosis-related genes (CRGs). Employing the LASSO COX regression method, the identified CRGs were utilized to formulate a prognostic model termed CRG_score. Functional enrichment analysis was conducted to explore the biological processes linked to the CRG_score. Additionally, the research delved into the association between CRG_score and the responsiveness to chemotherapy drugs like docetaxel and etoposide. We also explored the effect of Cuproptosis on UVM at the cellular level.

Results: UVM patients were classified into two distinct Cuproptosis clusters, each exhibiting unique clinicopathological characteristics, prognostic outcomes, immune checkpoint expression levels, and immune infiltration patterns. CRGs were used to develop a prognostic model, CRG_score, with eight pivotal CRGs that accurately predicted the prognosis of UVM (AUC = 0.895). The single-cell RNA Sequencing (scRNA-seq) analysis further confirmed the high tumor cell specificity of these eight model genes, validating the rationale for constructing the CRG_score. Functional enrichment analysis demonstrated that the CRG_score is associated with pathways involving cell signaling, immune responses, and metabolic regulation. A low CRG_score was associated with a favorable response to chemotherapy drugs such as docetaxel and etoposide. In cellular experiments, it was observed that the Cuproptosis Inducer elesclomol can impede the growth and proliferation of UVM cells, causing cell cycle arrest at the G2/M phase, as well as prompting Apoptosis and the accumulation of Reactive Oxygen Species (ROS).

Conclusion: Compared to several previous studies, we have extended the search for CRGs very rigorously in order to increase the value of Cuproptosis in the prognosis and treatment of UVM. This whole transcriptome analysis elucidates the crucial role of cuproptosis-related molecular subtypes in the prognosis of UVM, highlights its association with the TME, and provides a scientific basis for clinical drug decisions.

Cuproptosis; Immune checkpoint inhibitors; Molecular subtypes; Tumor microenvironment; Uveal melanoma prognosis.