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A novel immune-related LncRNA prognostic signature for cutaneous melanoma

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Abstract

Backgrounds

Among tumor microenvironment, the immune components in it have an important influence on gene expression and clinical efficacy. We aim to find out the role of those in skin cutaneous melanoma (SKCM).

Objectives

Gene expression profile and homologous clinical information of SKCM patients were obtained by TCGA (The Cancer Genome Atlas) and UCSC Toil. SsGSEA method was used to evaluate the immune cell infiltration of 468 TCGA-SKCM samples divided into high immune cell infiltration group (HICI) and low immune cell infiltration group (LICI). We used the Edger packet to conduct difference analysis on normal samples (GTEx) and cancer samples (TCGA), and combined it with the difference of the HICI group and LICI group, to find out the common differential expression of lncRNA in both groups. The prognostic value of immune-related lncRNAs was studied by univariate Cox, Lasso-Cox and multivariate Cox regression analysis, and a prognostic model was established. C index and calibration diagram were used to judge the accuracy of the model, and DCA was used to judge the net benefit.

Results

Six prognostic markers of immune-related lncRNA genes were established, which could be used as independent prognostic factors. The net benefit and prediction accuracy are significantly higher than TNM Stage.

Conclusion

The prognostic model identified in this study is a reliable biomarker for SKCM. The Nomogram survival prediction model based on it is a reliable way to predict the median survival time of patients, which may lay the foundation for future treatment of this disease.

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Data availability

The datasets analyzed in this study were obtained from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/).

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Acknowledgements

We gratefully acknowledge Chengcheng He for his technical support on this manuscript.

Funding

This study was supported by the Luzhou Science and Technology Department Project (2020-JYJ-44), Sichuan Science and Technology of Traditional Chinese Medicine Administration Project (2020JC0134), and the Science Foundation of Southwest Medical University (2020ZRZD001).

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Authors and Affiliations

  1. Department of Dermatology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Road, Luzhou, 646000, China

    Nan Hu, Cancan Huang, Jingyi Yuan, Guishu Zhong & Yan Chen

  2. School of Medicine and Rehabilitation, Jiangyang City Construction College, Luzhou, 646000, Sichuan, People’s Republic of China

    Yancheng He

  3. Sichuan Provincial Laboratory of Orthopaedic Engineering, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China

    Shuyang Li

Authors
  1. Nan Hu
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  2. Cancan Huang
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  3. Yancheng He
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  4. Shuyang Li
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  5. Jingyi Yuan
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  6. Guishu Zhong
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  7. Yan Chen
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Contributions

YC and GZ conceived and designed the study; NH, CH and YH performed data analysis; SL and JY assisted in data curation and analyzed the references; NH and YC wrote the paper; all authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Guishu Zhong or Yan Chen.

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This article does not contain any studies with human participants or animals performed by any of the authors; thus, ethical approval and informed consent are not required.

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Hu, N., Huang, C., He, Y. et al. A novel immune-related LncRNA prognostic signature for cutaneous melanoma. Mol. Cell. Toxicol. 20, 377–387 (2024). https://doi.org/10.1007/s13273-023-00351-4

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