Independent prognostic value of ISCU and a multi‑gene signature of cuproptosis‑related genes in glioblastoma multiforme: a TCGA‑based study
Abstract
Background: Cuproptosis is a recently identified copper‑dependent form of regulated cell death, but its clinical significance in glioblastoma multiforme (GBM) remains poorly understood. This study aimed to systematically characterize the expression and prognostic value of cuproptosis‑related genes (CRGs) in GBM using data from The Cancer Genome Atlas (TCGA).
Methods: RNA‑seq and corresponding clinical data of 194 GBM patients were downloaded from TCGA. Differentially expressed CRGs were identified using the limma‑voom pipeline (|log₂FC|>1, FDR<0.05). Kaplan‑Meier survival analysis and multivariate Cox regression were performed to evaluate the prognostic significance of individual CRGs. A LASSO‑Cox regression model with 10‑fold cross‑validation was constructed to develop a multi‑gene risk score, whose predictive accuracy was assessed by time‑dependent ROC at 1/3‑year, 2/3‑year and 1‑year. All analyses were computational (dry‑lab) and focused on biomarker discovery.
Results: Among 28 CRGs, 26 were differentially expressed in GBM. High expression of ISCU was significantly associated with worse overall survival (log‑rank p = 0.0354). After adjusting for age and sex, ISCU remained an independent adverse prognostic factor (HR = 1.61, 95% CI 1.21–2.16, p = 0.0013). A LASSO‑Cox risk score incorporating ten other CRGs – including key genes such as SLC31A1, ATP7A and MT2A – achieved time‑dependent AUC values of 0.678, 0.673 and 0.678 at 1/3‑year, 2/3‑year and 1‑year, respectively. Notably, ISCU was not selected in this multi‑gene signature, indicating that its prognostic information is partially shared with other functionally related CRGs involved in copper transport and metal detoxification. Consequently, the multi‑gene score provides complementary prognostic value, whereas ISCU alone remains a practical single‑gene biomarker.
Conclusion: ISCU is a novel independent prognostic biomarker in GBM, with high expression predicting poor survival. The multi‑gene risk score offers additional predictive information, and both approaches together may facilitate risk stratification in GBM patients. Nevertheless, both approaches are dry‑lab based and require further validation in independent cohorts.
References
1. Stupp, R. et al. Radiotherapy plus Concomitant and Adjuvant Temozolomide for Glioblastoma. N Engl J Med 352, 987–996 (2005).
2. Ostrom, Q. T. et al. CBTRUS Statistical Report: Primary Brain and Other Central Nervous System Tumors Diagnosed in the United States in 2013–2017. Neuro-Oncology 22, iv1–iv96 (2020).
3. Tsvetkov, P. et al. Copper induces cell death by targeting lipoylated TCA cycle proteins. Science 375, 1254–1261 (2022).
4. Li, S.-R., Bu, L.-L. & Cai, L. Cuproptosis: lipoylated TCA cycle proteins-mediated novel cell death pathway. Sig Transduct Target Ther 7, 158 (2022).
5. Wang, L., Chen, X., Yu, H., Wang, G. & Han, D. Identification Cuproptosis-related Genes Signature to Predict the Prognosis of Lung Cancer. Cell Biochem Biophys 83, 4807–4818 (2025).
6. He, Y., Liu, F., Li, Q. & Jiang, Z. Identification of cuproptosis and ferroptosis-related subtypes and development of a prognostic signature in colon cancer. PLoS ONE 20, e0307013 (2025).
7. Guo, Z. et al. The molecular mechanism and therapeutic landscape of copper and cuproptosis in cancer. Sig Transduct Target Ther 10, 149 (2025).
8. Jiang, D., Zhuang, L., Koong, A. C. & Gan, B. Cuproptosis in cancer: from molecular mechanisms to therapeutic intervention. Trends in Cancer 12, 275–286 (2026).
9. Zhao, Z., Ma, Y., Liu, Y., Chen, Z. & Zheng, J. A cuproptosis-based prognostic model for predicting survival in low-grade glioma. Aging 16, 8697–8716 (2024).
10. Wang, L. et al. Identification of cuproptosis‐related lncRNAs for prognosis and immunotherapy in glioma. J Cellular Molecular Medi 26, 5820–5831 (2022).
11. Maio, N., Kim, K. S., Singh, A. & Rouault, T. A. A Single Adaptable Cochaperone-Scaffold Complex Delivers Nascent Iron-Sulfur Clusters to Mammalian Respiratory Chain Complexes I–III. Cell Metabolism 25, 945-953.e6 (2017).
12. Favaro, E. et al. MicroRNA-210 Regulates Mitochondrial Free Radical Response to Hypoxia and Krebs Cycle in Cancer Cells by Targeting Iron Sulfur Cluster Protein ISCU. PLoS ONE 5, e10345 (2010).
13. Colaprico, A. et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Research 44, e71–e71 (2016).
14. Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 15, R29 (2014).
15. Kaplan, E. L. & Meier, P. Nonparametric Estimation from Incomplete Observations. Journal of the American Statistical Association 53, 457–481 (1958).
16. Tibshirani, R. THE LASSO METHOD FOR VARIABLE SELECTION IN THE COX MODEL. Statist. Med. 16, 385–395 (1997).
17. Blanche, P., Dartigues, J. & Jacqmin‐Gadda, H. Estimating and comparing time‐dependent areas under receiver operating characteristic curves for censored event times with competing risks. Statistics in Medicine 32, 5381–5397 (2013).
18. Chen, Y., Zhang, J., Zheng, W. & Xu, H. Cuproptosis-related lncRNAs and genes: Potential markers for glioblastoma prognosis and treatment. PLoS ONE 20, e0315927 (2025).
19. Yao, S., Guan, H., Chai, J. & Liu, X. Regulatory networks of iron sulfur cluster biology in cancer mechanisms and therapeutic perspectives. iScience 29, 115256 (2026).
20. Ciscar, M., Rodríguez-Santana, C. & Santana-Codina, N. Iron and metabolic rewiring in cancer. Oncogenesis 15, 1 (2026).
21. Yun, D. et al. A Novel Prognostic Signature Based on Glioma Essential Ferroptosis-Related Genes Predicts Clinical Outcomes and Indicates Treatment in Glioma. Front. Oncol. 12, 897702 (2022).
22. Xie, D. et al. Integrated profiling identifies ferredoxin 1 as an immune-related biomarker of malignant phenotype in glioma. Heliyon 10, e26976 (2024).
23. Al-Majali, G. et al. Identification of the cuproptosis-related gene signature associated with the tumor environment and prognosis of patients with glioblastoma multiforme (GBM) (S17.003). Neurology 100, 4090 (2023).
24. Markouli, M., Skouras, P. & Piperi, C. Impact of cuproptosis in gliomas pathogenesis with targeting options. Chemico-Biological Interactions 408, 111394 (2025).
25. Saddozai, U. A. K. et al. Prognostic value of metal-based ferroptosis and cuproptosis genes and score in lower grade gliomas. Front. Immunol. 16, 1608077 (2025).
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