鼻咽癌转移中线粒体稳态相关基因的生物信息学鉴定与功能验证

文献信息

中文摘要

引言： 转移扩散仍是鼻咽癌（NPC）死亡的主要原因；然而，线粒体稳态在这一过程中的作用在很大程度上仍不清楚。
目的： 本研究旨在鉴定与线粒体稳态和NPC转移相关的关键基因，并进一步探索其潜在调控机制、与免疫微环境的相关性以及预后价值。
方法： 聚焦于转移和线粒体稳态相关基因（MMHRGs），我们依次进行枢纽基因筛选、构建调控网络、预测药物结合、探索与免疫和预后的相关性，并进行体外功能验证。候选枢纽基因通过LASSO回归结合随机森林进行优先排序。通过药物基因相互作用数据库（DGIdb）鉴定靶向这些基因的潜在可成药化合物，并通过分子对接进一步检查。进行免疫浸润和肿瘤免疫功能障碍与排斥（TIDE）分析，以表征肿瘤免疫微环境并预测免疫治疗反应。开发了包含这些基因的预后列线图，并使用时间依赖性ROC曲线分析评估其预测准确性。最后，使用伤口愈合实验和透射电子显微镜在NPC细胞系中实验验证了枢纽基因的功能作用。
结果： 在NPC转移中鉴定出一个以四个枢纽基因（FKBP4、ATN1、CDKAL1、GPR25）为突出特征的线粒体稳态相关基因特征。这些基因嵌入广泛的转录后和转录调控网络（ceRNA、RNA结合蛋白、转录因子、蛋白质-蛋白质相互作用）中，以深入阐明NPC的分子机制。分子对接显示SAR260301与FKBP4具有高结合亲和力，提示潜在的结合线索。共识聚类将NPC分为两个亚型（Cluster_A/B），其中Cluster_B显示出增强的免疫检查点表达和基于TIDE的特征。包含HNMT、TAGLN3、CSF2RA和LYZ的预后模型对NPC显示出高预测准确性，在训练队列中1年、2年和3年总生存期的AUC值分别为0.854、0.860和0.920，在内部验证队列中分别为0.778、0.914和0.846。关键的是，功能验证显示GPR25过表达或ATN1、CDKAL1或FKBP4敲低显著抑制NPC细胞迁移并破坏线粒体形态。
讨论： 该研究证明线粒体稳态相关基因FKBP4、ATN1、CDKAL1和GPR25是NPC转移中的候选枢纽基因。
结论： 本研究鉴定了四个参与NPC转移的新型线粒体稳态相关枢纽基因，建立了基于线粒体的分子分型方案，并为未来转移性NPC的机制和转化研究提供了初步的预后生物标志物和潜在治疗靶点。

英文摘要

INTRODUCTION: Metastatic spread remains the leading cause of death in Nasopharyngeal Carcinoma (NPC); however, the role of mitochondrial homeostasis in this process remains largely unclear.
OBJECTIVE: This study aims to identify key genes associated with mitochondrial homeostasis and NPC metastasis, and to further explore their potential regulatory mechanisms, correlations with the immune microenvironment, and prognostic values.
METHODS: Focusing on metastasis- and mitochondrial homeostasis-related genes (MMHRGs), we sequentially conduct screening for hub genes, construct regulatory networks, predict drug binding, explore correlations with immunity and prognosis, and perform in vitro functional verification. Candidate hub genes were prioritized using LASSO regression combined with Random Forests. Putative druggable compounds targeting these genes were identified through the Drug Gene Interaction Database (DGIdb) and further examined by molecular docking. Immune infiltration and Tumor Immune Dysfunction and Exclusion (TIDE) analyses were performed to characterize the tumor immune microenvironment and predict immunotherapy response. A prognostic nomogram incorporating these genes was developed, and its predictive accuracy was assessed using time-dependent ROC curve analysis. Finally, the functional roles of the hub genes were experimentally validated in NPC cell lines using wound-healing assays and transmission electron microscopy.
RESULTS: A mitochondrial homeostasis-related gene signature, highlighted by four hub genes (FKBP4, ATN1, CDKAL1, GPR25), was identified in NPC metastasis. These genes were embedded within extensive post-transcriptional and transcriptional regulatory networks (ceRNA, RNA-binding proteins, TFs, PPIs) to deeply illustrate the molecular mechanism in NPC. Molecular docking revealed SAR260301 with high binding affinity to FKBP4, suggesting potential binding clues. Consensus clustering stratified NPC into two subtypes (Cluster_A/B), with Cluster_B showing enhanced immune checkpoint expression and TIDE-based features. A prognostic model incorporating HNMT, TAGLN3, CSF2RA, and LYZ demonstrated high predictive accuracy for NPC with AUC values of 0.854, 0.860, and 0.920 for 1-, 2-, and 3-year overall survival in the training cohort, and 0.778, 0.914, and 0.846 in the internal validation cohort. Crucially, functional validation showed that overexpression of GPR25 or knockdown of ATN1, CDKAL1, or FKBP4 significantly inhibited NPC cell migration and disrupted mitochondrial morphology.
DISCUSSION: The study demonstrated mitochondrial homeostasis-related genes- FKBP4, ATN1, CDKAL1, and GPR25 as candidate hub genes in NPC metastasis.
CONCLUSION: This study identified four novel mitochondrial homeostasis-associated hub genes involved in NPC metastasis, established a mitochondria-based molecular subtyping scheme, and provided preliminary prognostic biomarkers and potential therapeutic targets for future mechanistic and translational investigations of metastatic NPC.