Table 2_Unveiling ammonia-induced cell death: a new frontier in clear cell renal cell carcinoma prognosis.xls

BackgroundClear cell renal cell carcinoma (KIRC) is the most aggressive renal carcinoma subtype of renal carcinoma, characterized by high mortality, early metastasis, and resistance to treatment. Ammonia-induced cell death (AICD) has recently been identified as a novel metabolic mechanism influencing tumor progression, yet its prognostic implication and regulatory networks in KIRC remain underexplored.
MethodsTranscriptomic and clinical information from the TCGA-KIRC cohort and the validation cohort (E-MTAB-1980) were analyzed. Differentially expressed AICD-related genes were identified through differential expression analysis, univariate Cox regression, and machine learning algorithms (LASSO, random forest, and CoxBoost). A prognostic risk model was developed via multivariate Cox regression. Spatial and single-cell transcriptomics were employed to characterize the immune microenvironment heterogeneity. Cell-based experiments were performed to investigate the potential involvement of ATP1A1 in KIRC. Molecular docking and pan-cancer analyses were conducted to identify therapeutic candidates and ATP1A1-related mechanisms.
ResultsFive AICD-related genes (FOXM1, ANK3, ATP1A1, HADH, and PLG) were identified and selected to construct a risk score model. The model demonstrated high accuracy and was integrated into a nomogram for clinical application. High-risk (HR) patients exhibited immunosuppressive microenvironments, elevated tumor mutational burden (TMB), and genomic instability. In vitro functional assays confirmed that ATP1A1 knockdown significantly enhanced the proliferative, migratory, and invasive capabilities of renal carcinoma cells (A498 and 786-O), suggesting a suppressive role for ATP1A1 in malignant tumor progression. ATP1A1, a core gene, was associated with metabolic reprogramming and chemotherapy sensitivity across multiple cancers. Molecular docking revealed Emodinanthrone as a high-affinity ligand for ATP1A1 (−6.8 kcal/mol).
ConclusionThis study identifies an AICD-associated gene signature as a robust prognostic tool for KIRC, revealing its interactions with immune evasion and genomic instability. ATP1A1 is proposed as a promising therapeutic target, with Emodinanthrone emerging as a novel drug candidate. These findings contribute to the advancement of personalized treatment strategies for KIRC patients.

背景 透明细胞肾细胞癌（clear cell renal cell carcinoma, KIRC）是肾癌中恶性程度最高的亚型，以高死亡率、早期转移及治疗耐药为典型特征。氨诱导细胞死亡（ammonia-induced cell death, AICD）作为一种新型调控肿瘤进展的代谢机制，近年已被证实，但其在KIRC中的预后价值与调控网络仍有待深入探索。
方法 本研究分析了TCGA-KIRC队列与验证队列（E-MTAB-1980）的转录组学与临床信息。通过差异表达分析、单因素Cox回归及机器学习算法（LASSO、随机森林、CoxBoost）筛选得到差异表达的AICD相关基因。采用多因素Cox回归构建预后风险模型。借助空间转录组与单细胞转录组技术解析肿瘤免疫微环境的异质性。开展细胞实验以探究ATP1A1在KIRC发生发展中的潜在作用。通过分子对接与泛癌分析筛选潜在治疗靶点并阐明ATP1A1相关调控机制。
结果 本研究筛选得到5个AICD相关基因（FOXM1、ANK3、ATP1A1、HADH及PLG），并以此构建风险评分模型。该模型具有较高预测精度，后续整合至列线图以用于临床实践。高风险（HR）患者呈现免疫抑制性肿瘤微环境、较高的肿瘤突变负荷（tumor mutational burden, TMB）及基因组不稳定性。体外功能实验证实，敲低ATP1A1可显著增强肾癌细胞（A498与786-O）的增殖、迁移与侵袭能力，提示ATP1A1在肿瘤恶性进展中发挥抑癌作用。作为核心基因，ATP1A1在多种癌症中均与代谢重编程及化疗敏感性密切相关。分子对接结果显示，大黄素蒽酮（Emodinanthrone）是ATP1A1的高亲和力配体（结合能为-6.8 kcal/mol）。
结论 本研究鉴定得到的AICD相关基因特征可作为KIRC可靠的预后评估工具，并揭示其与肿瘤免疫逃逸及基因组不稳定性的关联。ATP1A1有望成为KIRC潜在治疗靶点，而大黄素蒽酮则是新型候选抗肿瘤药物。本研究结果可为KIRC患者的个性化治疗策略优化提供理论依据。