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构建包含铁死亡/铜死亡相关特征和突变景观分析的肌层浸润性膀胱癌预后模型。

Development of prognostic model incorporating a ferroptosis/cuproptosis-related signature and mutational landscape analysis in muscle-invasive bladder cancer.

机构信息

Department of Urology, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, 310003Zhejiang , China.

Department of Urology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.

出版信息

BMC Cancer. 2024 Aug 6;24(1):958. doi: 10.1186/s12885-024-12741-5.


DOI:10.1186/s12885-024-12741-5
PMID:39107713
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11302292/
Abstract

BACKGROUND: Muscle-invasive bladder cancer (MIBC) is a prevalent and aggressive malignancy. Ferroptosis and cuproptosis are recently discovered forms of programmed cell death (PCD) that have attracted much attention. However, their interactions and impacts on MIBC overall survival (OS) and treatment outcomes remain unclear. METHODS: Data from the TCGA-BLCA project (as the training set), cBioPortal database, and GEO datasets (GSE13507 and GSE32894, as the test sets) were utilized to identify hub ferroptosis/cuproptosis-related genes (FRGs and CRGs) and develop a prognostic signature. Differential expression analysis (DEA) was conducted, followed by univariate and multivariate Cox's regression analyses and multiple machine learning (ML) techniques to select genetic features. The performance of the ferroptosis/cuproptosis-related signature was evaluated using Kaplan-Meier (K-M) survival analysis and receiver-operating characteristics (ROC) curves. Mutational and tumour immune microenvironment landscapes were also explored. Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) experiments confirmed the expression patterns of the hub genes, and functional assays assessed the effects of SCD knockdown on cell viability, proliferation, and migration. RESULTS: DEA revealed dysregulated FRGs and CRGs in the TCGA MIBC cohort. SCD, DDR2, and MT1A were identified as hub genes. A prognostic signature based on the sum of the weighted expression of these genes demonstrated strong predictive efficacy in the training and test sets. Nomogram incorporating this signature accurately predicted 1-, 3-, and 5-year survival probabilities in the TCGA cohort and GSE13507 dataset. Copy number variation (CNV) and tumour immune microenvironment analysis revealed that high risk score level groups were associated with immunosuppression and lower tumour purity. The associations of risk scores with immunotherapy and chemical drugs were also explored, indicating their potential for guiding treatment for MIBC patients. The dysregulated expression patterns of three hub genes were validated by RT-qPCR experiments. CONCLUSIONS: Targeting hub FRGs and CRGs could be a promising therapeutic approach for MIBC. Our prognostic model offers a new framework for MIBC subtyping and can inform personalized therapeutic strategies.

摘要

背景:肌层浸润性膀胱癌(MIBC)是一种常见且侵袭性的恶性肿瘤。铁死亡和铜死亡是最近发现的程序性细胞死亡(PCD)形式,引起了广泛关注。然而,它们在 MIBC 总生存期(OS)和治疗结果中的相互作用和影响尚不清楚。

方法:利用 TCGA-BLCA 项目(作为训练集)、cBioPortal 数据库和 GEO 数据集(GSE13507 和 GSE32894,作为测试集)的数据,鉴定铁死亡/铜死亡相关基因(FRGs 和 CRGs)的枢纽基因,并建立一个预后特征。进行差异表达分析(DEA),然后进行单因素和多因素 Cox 回归分析以及多种机器学习(ML)技术来选择遗传特征。使用 Kaplan-Meier(K-M)生存分析和接收器操作特征(ROC)曲线评估铁死亡/铜死亡相关特征的性能。还探索了突变和肿瘤免疫微环境图谱。实时定量逆转录聚合酶链反应(RT-qPCR)实验证实了枢纽基因的表达模式,功能测定评估了 SCD 敲低对细胞活力、增殖和迁移的影响。

结果:DEA 显示 TCGA MIBC 队列中 FRGs 和 CRGs 失调。SCD、DDR2 和 MT1A 被鉴定为枢纽基因。基于这些基因加权表达之和的预后特征在训练集和测试集中具有很强的预测效果。包含该特征的列线图准确预测了 TCGA 队列和 GSE13507 数据集的 1、3 和 5 年生存率。拷贝数变异(CNV)和肿瘤免疫微环境分析显示,高风险评分组与免疫抑制和肿瘤纯度降低有关。还探讨了风险评分与免疫治疗和化学药物的关联,表明它们有可能指导 MIBC 患者的治疗。通过 RT-qPCR 实验验证了三个枢纽基因的失调表达模式。

结论:靶向枢纽 FRGs 和 CRGs 可能是 MIBC 的一种有前途的治疗方法。我们的预后模型为 MIBC 提供了一个新的亚型框架,并可以为个性化治疗策略提供信息。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/9c0b6cdb9ea7/12885_2024_12741_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/a2aef15ec63d/12885_2024_12741_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/50cc5f5aed0a/12885_2024_12741_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/b9785d169aea/12885_2024_12741_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/79506339a3bb/12885_2024_12741_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/c5d353ff6726/12885_2024_12741_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/8f1ebd156020/12885_2024_12741_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/3ed80ddffefb/12885_2024_12741_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/9c0b6cdb9ea7/12885_2024_12741_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/a2aef15ec63d/12885_2024_12741_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/1174706654d0/12885_2024_12741_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/35f664d49571/12885_2024_12741_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/50cc5f5aed0a/12885_2024_12741_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/b9785d169aea/12885_2024_12741_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/79506339a3bb/12885_2024_12741_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/c5d353ff6726/12885_2024_12741_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/8f1ebd156020/12885_2024_12741_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/3ed80ddffefb/12885_2024_12741_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4776/11302292/9c0b6cdb9ea7/12885_2024_12741_Fig10_HTML.jpg

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引用本文的文献

[1]
Identification and validation of a 9-RBPs-related gene signature associated with prognosis and immune infiltration in bladder cancer based on bioinformatics analysis and machine learning.

Transl Androl Urol. 2025-4-30

[2]
Harnessing ferroptosis for precision oncology: challenges and prospects.

BMC Biol. 2025-2-24

[3]
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Front Oncol. 2024-11-1

本文引用的文献

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