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Cuproptosis-related LncRNA signatures as a prognostic model for head and neck squamous cell carcinoma

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Abstract

Cuproptosis is a novel, distinct form of regulated cell death. However, little is known about the role of cuproptosis-related lncRNAs (CRlncRNAs) in head and neck squamous cell carcinoma (HNSCC). This study aimed to identify a CRlncRNAs signature, explore its prognostic value in HNSCC. RNA-seq data and relevant clinical data were downloaded from The Cancer Genome Atlas (TCGA) database, and cuproptosis-related genes were identified from a search of the relevant candidate-gene literature. Analysis of differentially expressed lncRNAs (DElncRNAs) was performed using the R package “edgeR”. The intersection of the lncRNAs between DElncRNAs and CRlncRNAs was obtained using the R package “Venn Diagram”. Univariate Cox regression was used to identify cuproptosis-related prognostic lncRNAs. LASSO-Cox method was used to narrow these cuproptosis-related prognostic lncRNAs and construct a prognostic model. Multiple statistical methods were used to evaluate the predictive ability of the model. Moreover, the relationships between the model and immune cell subpopulations, related functions and pathways and drug sensitivity were explored. Then, two risk groups were established according to the risk score calculated by the CRlncRNAs signature included three lncRNAs. In HNSCC patients, the risk score was a better predictor of survival than traditional clinicopathological features. In addition, significant differences in immune cells such as B cells, T cells and macrophages were observed between the two groups. Finally, the high-risk group had a lower IC50 for certain chemotherapeutic agents, such as cisplatin and cetuximab. This 3 CRlncRNAs signature is a powerful prognostic biomarker for predicting clinical outcomes and therapeutic responses in HNSCC patients.

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Data availability

The dataset analyzed in this study is available from the TCGA database. These data can be found here: https://portal.gdc.cancer.gov/. More detailed data is available from the corresponding author on reasonable request.

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Acknowledgements

We acknowledge the TCGA database for providing their platforms and the contributors for uploading their meaningful datasets.

Funding

This work was supported by the Hospital-level Project of QingPu Branch of Zhongshan Hospital Affiliated to Fudan University (QYT2021-02) and the Project of Health Commission (W2021-09, QingPu District, Shanghai, P.R. China).

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Author notes

  1. Qing Sun, Xuemei Qin and Jing Zhao are first authors and have contributed equally to this study.

Authors and Affiliations

  1. Department of Otolaryngology-Head and Neck Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Park Road (E), Qingpu, Shanghai, 201700, People’s Republic of China

    Qing Sun, Xuemei Qin, Jing Zhao, Tianle Gao, Yinwei Xu, Guohui Chen, Guangping Bai, Zhiqiang Guo & Jian Liu

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  1. Qing Sun
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Contributions

JL and QS designed the study and drafted the manuscript. XQ, JZ, and TG provided the statistical software and performed the data analysis. YX and GC arranged the figures and tables. GB and ZG reviewed and revised the manuscript. All authors contributed to the article and approved the submitted version.

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Correspondence to Jian Liu.

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Sun, Q., Qin, X., Zhao, J. et al. Cuproptosis-related LncRNA signatures as a prognostic model for head and neck squamous cell carcinoma. Apoptosis 28, 247–262 (2023). https://doi.org/10.1007/s10495-022-01790-5

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