Data_Sheet_1_PLEK2: a potential biomarker for metastasis and prognostic evaluation in uveal melanoma.zip

BackgroundUveal melanoma (UVM) is an aggressive tumor known for its high metastatic rate, making it necessary to delineate potential molecules that may promote the development of UVM. PLEK2 has been found to promote the progression and metastasis of some tumors, but its role in UVM has not yet been reported. Through this study, we hope to explore the effect of PLEK2 on the prognosis of UVM patients and to discover the potential functional role and intrinsic mechanism of PLEK2.
MethodsThe GEO datasets GSE211763 and GSE149920 were analyzed using GEO2R to identify differentially expressed genes that may be associated with UVM progression and metastasis. A Protein-Protein Interaction Network (PPI) was constructed to identify key molecules. The correlation between PLEK2 expression and overall survival was evaluated via GEPIA2, and clinical characteristics of UVM patients were compared based on PLEK2 levels. PLEK2 expression in UVM cell lines was assessed using the CCLE database and confirmed by qPCR and western blot. A weighted correlation network analysis (WGCNA) was performed, followed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, a search for miRNAs potentially regulating PLEK2 expression was performed using TargetScan, miRWalk, and TarBase databases.
ResultsComparative analysis of the GEO datasets unveiled 79 commonly up-regulated genes and 238 commonly down-regulated genes. The PPI network identified 9 hub genes, with PLEK2 significantly linked to reduced overall survival. Clinical comparisons indicated significant differences in cancer status (p = 0.013) and tumor diameter (p = 0.039) between high and low PLEK2 expression groups. Elevated PLEK2 mRNA levels were confirmed in UVM cell lines compared to retinal pigment epithelial cells. PLEK2 was enriched in the calcium signaling pathway and associated with the Wnt/Ca2+ signaling pathway. A total of 21 miRNAs potentially regulating PLEK2 were predicted.
ConclusionPLEK2 is upregulated in UVM and correlates with poor patient prognosis, likely influencing the calcium signaling pathway. PLEK2 represents a promising prognostic biomarker and therapeutic target for UVM.

研究背景：葡萄膜黑色素瘤（Uveal melanoma, UVM）是一种侵袭性极强的肿瘤，以极高的转移率为典型特征，因此亟需明确可促进其发生发展的潜在分子机制。已有研究发现，PLEK2可推动部分肿瘤的进展与转移，但目前尚无其在葡萄膜黑色素瘤中作用的相关报道。本研究旨在探讨PLEK2对葡萄膜黑色素瘤患者预后的影响，并揭示PLEK2潜在的功能角色与内在作用机制。
研究方法：本研究通过GEO2R工具分析基因表达综合（Gene Expression Omnibus, GEO）数据库中GSE211763与GSE149920数据集，筛选出与葡萄膜黑色素瘤进展及转移相关的差异表达基因。构建蛋白质相互作用网络（Protein-Protein Interaction Network, PPI）以识别关键分子。借助基因表达谱交互分析2（Gene Expression Profiling Interactive Analysis 2, GEPIA2）平台评估PLEK2表达与患者总生存期的相关性，并基于PLEK2表达水平对葡萄膜黑色素瘤患者的临床特征进行分组比较。通过癌症细胞系百科全书（Cancer Cell Line Encyclopedia, CCLE）数据库分析葡萄膜黑色素瘤细胞系中PLEK2的表达情况，并采用实时定量聚合酶链反应（quantitative real-time polymerase chain reaction, qPCR）与蛋白质印迹（western blot）实验进行验证。随后开展加权基因共表达网络分析（weighted correlation network analysis, WGCNA），并进行基因本体（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析。最后通过TargetScan、miRWalk及TarBase数据库预测靶向调控PLEK2表达的微小RNA（microRNA, miRNA）。
研究结果：对GEO数据集的对比分析共筛选得到79个共同上调基因与238个共同下调基因。PPI网络筛选出9个核心基因，其中PLEK2与患者总生存期缩短显著相关。临床分组比较结果显示，PLEK2高表达组与低表达组在肿瘤状态（p = 0.013）与肿瘤直径（p = 0.039）上存在显著差异。相较于视网膜色素上皮细胞，葡萄膜黑色素瘤细胞系中PLEK2的mRNA水平显著升高。富集分析结果表明，PLEK2富集于钙信号通路，并与Wnt/Ca2+信号通路密切相关。最终共预测得到21个潜在调控PLEK2表达的miRNA。
研究结论：PLEK2在葡萄膜黑色素瘤中呈高表达状态，且与患者不良预后显著相关，其可能通过调控钙信号通路发挥作用。PLEK2有望成为葡萄膜黑色素瘤极具潜力的预后生物标志物与治疗靶点。