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Construction of cuproptosis signature based on bioinformatics and experimental validation in clear cell renal cell carcinoma

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Abstract

Background

Cuproptosis was defined as a novel nonapoptotic cell death pathway and its potential function in clear cell renal cell carcinoma (ccRCC) remains unclear.

Methods

We obtained gene expression profiles, somatic mutation and corresponding clinical information of 881 ccRCC samples from 3 cohorts including the cancer genome atlas cohort, GSE29609 cohort and CheckMate 025 cohort. As described in the latest published article, we enrolled 16 genes as cuproptosis-related genes (CRGs). We explored the expression level, variants and copy number variation of the CRGs. Univariate and multi-variate regression were utilized to assess the prognostic significance of the CRGs. Non-negative matrix factorization was used to identify potential subgroup and gene set variation analysis was used to explore the potential biological functions. CIBERSORT, ESTIMATE algorithm and single sample gene set enrichment analysis were used to evaluate the tumor microenvironment. In vitro experiments including CCK-8, transwell and wound healing assays were utilized to explore the potential biological function of DLAT in ccRCC.

Results

We found that except for CDKN2A, the CRGs were positively associated with patients’ OS. Cuproptosis cluster, cuproptosis gene cluster and cuproptosis score were established, respectively, and higher cuproptosis score was significantly associated with a worse OS in ccRCC (p < 0.001). The area under the receiver operating characteristic curve of the cuproptosis-related nomogram at 1 year, 3 years, 5 years was 0.858, 0.821 and 0.78, respectively. In addition, we found that the cuproptosis score was positively associated with PDCD1, CTLA4 expression level, thus the cuproptosis score may also reflect the dysfunction of tumor infiltrating immune cells. In vitro experiments indicated that overexpression of DLAT could inhibited the migration and proliferation ability of ccRCC cells.

Conclusion

Our findings identify a novel cuproptosis-related signature and the cuproptosis characteristics may influence the anti-tumor immunity though complex regulating networks, and thus cuproptosis may play a role in developing novel therapeutic target of ccRCC.

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Data availability

Gene expression and corresponding clinical information of 881 ccRCC samples from 3 cohorts as follow: 531 ccRCC samples from TCGA cohort (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga), 39 ccRCC samples from GSE29609 cohort (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi), 311 ccRCC samples from patients treated with Everolism or Nivolumab were also obtained from the the online supplemental data (online supplemental table S4) appended to the published paper (https://www.nature.com/articles/s41591-020-0839-y#Sec27).

Abbreviations

AUC:

Area under curve

ccRCC:

Clear cell renal cell carcinoma

CRGs:

Cuproptosis-related genes

CNV:

Copy number variations

DEG:

Differentially expressed genes

GSVA:

Gene set variation analysis

OS:

Overall survival

PFS:

Progression-free survival

RCC:

Renal cell carcinoma

ROC:

Receiver operating characteristic

ssGSEA:

Single sample gene set enrichment analysis

TCGA:

The cancer genome atlas

TME:

Tumor microenvironment

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Acknowledgements

We thank the TCGA, GEO database for providing NGS data and clinical information of ccRCC.

Funding

This work is supported by Grants from the National Key Research and Development Program of China (No. 2019YFC1316005), National Natural Science Foundation of China (Nos. 81772706, 81802525 and 81902568), Shanghai Science and Technology Committee (Nos. 20ZR1413100, 18511108000), and Shanghai Sailing Program (No. 19YF1409700).

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Author notes

  1. Xi Tian, Shuxuan Zhu, Cong Chen, Xinrui Wu and Gaomeng Wei contributed equally.

Authors and Affiliations

  1. Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China

    Xi Tian, Shuxuan Zhu, Ji Zhang, Aihetaimujiang Anwaier, Shiqi Ye, Xiangxian Che, Wenhao Xu, Yuanyuan Qu, Hailiang Zhang & Dingwei Ye

  2. Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People’s Republic of China

    Wangrui Liu

  3. Department of Clinical Medicine, Medical School of Nantong University, Nantong, 226001, People’s Republic of China

    Xinrui Wu

  4. Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, People’s Republic of China

    Gaomeng Wei

  5. Department of Nursing, Fudan University Shanghai Cancer Cente, Shanghai, China

    Cong chen

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  1. Xi Tian
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Contributions

The work reported in the paper has been performed by the authors, unless clearly specified in the text. Conceptualization: XT, SZ, WX, GW, and CC. Data curation and formal analysis: XT, WL, SZ, XW, WX, AA, GW, and JZ. Funding acquisition: HZ and DY. Investigation and methodology: XT, XW, WL, WX, AA, SY and XC. Resources and software: WX, YQ, HZ and DY. Supervision: GW, YQ, HZ and DY. Validation and visualization: WX, AA and WL. Original draft: XT, SZ, CC, XW, and GW. Editing: WX, YQ, HZ and DY.

Corresponding authors

Correspondence to Wenhao Xu, Yuanyuan Qu, Hailiang Zhang or Dingwei Ye.

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Tian, X., Zhu, S., Liu, W. et al. Construction of cuproptosis signature based on bioinformatics and experimental validation in clear cell renal cell carcinoma. J Cancer Res Clin Oncol 149, 17451–17466 (2023). https://doi.org/10.1007/s00432-023-05259-z

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