Table 1_Comprehensive analysis based on the ubiquitination- and deubiquitylation-related genes reveals the function of NEURL3 in esophageal squamous cell carcinoma.docx

BackgroundAs a highly invasive gastrointestinal malignancy, esophageal squamous cell carcinoma (ESCC) carries with its high morbidity and mortality. Accumulating evidence indicates that abnormal activation of ubiquitination and deubiquitylation has been implicated in pathophysiology of ESCC. However, rare prognostic models for ubiquitination-related genes (URGs) and deubiquitylation-related genes (DRGs) have been built up in ESCC.
MethodsFrom training dataset GSE53624, the differentially expressed prognostic URGs and DRGs were identified to develop a prognostic signature, which was validated in GSE53622 and TCGA-ESCC dataset to show the robustness of the signature. To further confirm their prognosis value, the unsupervised clustering analysis was used to develop the molecular subtypes based on the prognostic URGs and DRGs. Differences in terms of biological function, immune status, and drug sensitivity were evaluated between high- and low-risk groups. The nomogram was constructed by combining the URGs and DRGs prognostic signature and clinical characteristics to improve prediction efficacy. Loss-of-function studies were conducted to explore the biological function of NEURL3 in ESCC.
ResultsThe URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient. Based on these 11 URGs and DRGs, two molecular subtypes of ESCC (C1 and C2) were identified, of which C2 subtype had significantly shorter overall survival time than that of C1 subtype. The function enrichment analysis showed that these genes play key roles in essential processes such as tumor metastasis and immune response. Moreover, the risk score was closely related to infiltration abundance of some types of immune cells, gene markers of immune cells and immune checkpoint-related markers. The drug sensitivity analysis showed that dacomitinib and talazoparib may serve as anti-ESCC drugs through targeting MAPK14. The nomogram was established by combining the URGs and DRGs signature with age and TNM stage, and it also showed enhanced prognostic predictive accuracy. The in vitro experiments showed that knockdown of NEURL3 inhibited the proliferation and motility of ESCC cells.
ConclusionsBased on the URGs and DRGs prognostic signature, a novel nomogram was constructed that could serve as a potentially reliable prognostic model and provide theoretical basis for uncovering potential therapeutic target in the treatment of ESCC.

背景：食管鳞状细胞癌（esophageal squamous cell carcinoma, ESCC）是一种高侵袭性胃肠道恶性肿瘤，具有较高的发病率与死亡率。大量研究证据表明，泛素化与去泛素化的异常激活与食管鳞状细胞癌的病理生理过程密切相关。然而，目前针对食管鳞状细胞癌中泛素化相关基因（ubiquitination-related genes, URGs）与去泛素化相关基因（deubiquitylation-related genes, DRGs）的预后模型仍较为少见。
方法：本研究以训练数据集GSE53624为基础，筛选差异表达的预后相关泛素化相关基因与去泛素化相关基因，以构建预后特征，并在GSE53622及TCGA-ESCC数据集中进行验证，以证实该预后特征的稳健性。为进一步验证这些基因的预后价值，本研究基于上述预后相关泛素化相关基因与去泛素化相关基因，通过无监督聚类分析构建食管鳞状细胞癌的分子亚型。同时，本研究评估了高低风险组间的生物学功能、免疫状态以及药物敏感性差异。此外，本研究将泛素化相关基因与去泛素化相关基因的预后特征与临床特征相结合，构建列线图以提升预后预测效能。本研究还通过功能丧失实验，探讨了NEURL3在食管鳞状细胞癌中的生物学功能。
结果：本研究构建的泛素化相关基因与去泛素化相关基因预后特征包含11个基因，可较为精准地预测食管鳞状细胞癌患者的预后。基于这11个基因，本研究鉴定出两种食管鳞状细胞癌分子亚型（C1与C2），其中C2亚型患者的总生存期显著短于C1亚型。功能富集分析显示，这些基因在肿瘤转移、免疫应答等核心生物学过程中发挥关键作用。此外，风险评分与多种免疫细胞浸润丰度、免疫细胞基因标志物及免疫检查点相关标志物密切相关。药物敏感性分析表明，达可替尼（dacomitinib）与他拉唑帕利（talazoparib）或可通过靶向MAPK14成为抗食管鳞状细胞癌治疗药物。本研究将泛素化相关基因与去泛素化相关基因的预后特征与患者年龄、TNM分期相结合，构建了列线图，该列线图同样展现出更高的预后预测准确性。体外实验结果显示，敲低NEURL3可抑制食管鳞状细胞癌细胞的增殖与迁移能力。
结论：本研究基于泛素化相关基因与去泛素化相关基因的预后特征构建了一种新型列线图，该列线图可作为一款潜在可靠的预后模型，为揭示食管鳞状细胞癌治疗的潜在治疗靶点提供理论依据。