Department of Urology, Jiangxi Province, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang City, 330000, People's Republic of China.
Jiangxi Institute of Urology, Nanchang City, Jiangxi Province, 330000, China.
BMC Cancer. 2023 Jan 30;23(1):105. doi: 10.1186/s12885-023-10584-0.
BACKGROUND: Cuproptosis, an emerging form of programmed cell death, has recently been identified. However, the association between cuproptosis-related long non-coding RNA (lncRNA) signature and the prognosis in prostate carcinoma remains elusive. This study aims to develop the novel cuproptosis-related lncRNA signature in prostate cancer and explore its latent molecular function. METHODS: RNA-seq data and clinical information were downloaded from the TCGA datasets. Then, cuproptosis-related gene was identified from the previous literature and further applied to screen the cuproptosis-related differentially expressed lncRNAs. Patients were randomly assigned to the training cohort or the validation cohort with a 1:1 ratio. Subsequently, the machine learning algorithms (Lasso and stepwise Cox (direction = both)) were used to construct a novel prognostic signature in the training cohorts, which was validated by the validation and the entire TCGA cohorts. The nomogram base on the lncRNA signature and several clinicopathological traits were constructed to predict the prognosis. Functional enrichment and immune analysis were performed to evaluate its potential mechanism. Furthermore, differences in the landscape of gene mutation, tumour mutational burden (TMB), microsatellite instability (MSI), drug sensitivity between both risk groups were also assessed to explicit their relationships. RESULTS: The cuproptosis-related lncRNA signature was constructed based on the differentially expressed cuproptosis-related lncRNAs, including AC005790.1, AC011472.4, AC099791.2, AC144450.1, LIPE-AS1, and STPG3-AS1. Kaplan-Meier survival and ROC curves demonstrate that the prognosis signature as an independent risk indicator had excellent potential to predict the prognosis in prostate cancer. The signature was closely associated with age, T stage, N stage, and the Gleason score. Immune analysis shows that the high-risk group was in an immunosuppressive microenvironment. Additionally, the significant difference in landscape of gene mutation, tumour mutational burden, microsatellite instability, and drug sensitivity between both risk groups was observed. CONCLUSIONS: A novel cuproptosis-related lncRNA signature was constructed using machine learning algorithms to predict the prognosis of prostate cancer. It was closely with associated with several common clinical traits, immune cell infiltration, immune-related functions, immune checkpoints, gene mutation, TMB, MSI, and the drug sensitivity, which may be useful to improve the clinical outcome.
背景:细胞铜死亡是一种新发现的程序性细胞死亡形式。然而,前列腺癌中铜死亡相关长链非编码 RNA(lncRNA)特征与预后的关系仍不清楚。本研究旨在建立前列腺癌新的铜死亡相关 lncRNA 特征,并探讨其潜在的分子功能。
方法:从 TCGA 数据集下载 RNA-seq 数据和临床信息。然后,从先前的文献中确定铜死亡相关基因,并进一步筛选铜死亡相关差异表达的 lncRNA。患者以 1:1 的比例随机分配到训练队列或验证队列。随后,使用机器学习算法(Lasso 和逐步 Cox(方向=两者))在训练队列中构建新的预后签名,并在验证队列和整个 TCGA 队列中进行验证。基于 lncRNA 特征和几个临床病理特征构建列线图来预测预后。进行功能富集和免疫分析以评估其潜在机制。此外,还评估了两组之间基因突变、肿瘤突变负荷(TMB)、微卫星不稳定性(MSI)和药物敏感性的差异,以明确它们之间的关系。
结果:基于差异表达的铜死亡相关 lncRNA,构建了铜死亡相关 lncRNA 特征,包括 AC005790.1、AC011472.4、AC099791.2、AC144450.1、LIPE-AS1 和 STPG3-AS1。Kaplan-Meier 生存和 ROC 曲线表明,预后签名作为独立的风险指标具有很好的预测前列腺癌预后的潜力。该特征与年龄、T 分期、N 分期和 Gleason 评分密切相关。免疫分析表明,高危组处于免疫抑制微环境中。此外,两组之间的基因突变、肿瘤突变负荷、微卫星不稳定性和药物敏感性的差异具有统计学意义。
结论:使用机器学习算法构建了一种新的铜死亡相关 lncRNA 特征,用于预测前列腺癌的预后。它与几个常见的临床特征、免疫细胞浸润、免疫相关功能、免疫检查点、基因突变、TMB、MSI 和药物敏感性密切相关,这可能有助于改善临床结局。
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