Cuproptosis gene‐related, neural network‐based prognosis prediction and drug‐target prediction for KIRC
Authors: Liu Yixin , Shao Yuan , Hao Zezhou , Lei Xuanzi , Liang Pengchen , Chang Qing , Wang Xianjin 
Published: December 2023

Background

Kidney renal clear cell carcinoma (KIRC), as a common case in renal cell carcinoma (RCC), has the risk of postoperative recurrence, thus its prognosis is poor and its prognostic markers are usually based on imaging methods, which have the problem of low specificity. In addition, cuproptosis, as a novel mode of cell death, has been used as a biomarker to predict disease in many cancers in recent years, which also provides an important basis for prognostic prediction in KIRC. For postoperative patients with KIRC, an important means of preventing disease recurrence is pharmacological treatment, and thus matching the appropriate drug to the specific patient's target is also particularly important. With the development of neural networks, their predictive performance in the field of medical big data has surpassed that of traditional methods, and this also applies to the field of prognosis prediction and drug‐target prediction.

Objective

The purpose of this study is to screen for cuproptosis genes related to the prognosis of KIRC and to establish a deep neural network (DNN) model for patient risk prediction, while also developing a personalized nomogram model for predicting patient survival. In addition, sensitivity drugs for KIRC were screened, and a graph neural network (GNN) model was established to predict the targets of the drugs, in order to discover potential drug action sites and provide new treatment ideas for KIRC.

Methods

We used the Cancer Genome Atlas (TCGA) database, International Cancer Genome Consortium (ICGC) database, and DrugBank database for our study. Differentially expressed genes (DEGs) were screened using TCGA data, and then a DNN‐based risk prediction model was built and validated using ICGC data. Subsequently, the differences between high‐ and low‐risk groups were analyzed and KIRC‐sensitive drugs were screened, and finally a GNN model was trained using DrugBank data to predict the relevant targets of these drugs.

Results

A prognostic model was built by screening 10 significantly different cuproptosis‐related genes, the model had an AUC of 0.739 on the training set (TCGA data) and an AUC of 0.707 on the validation set (ICGC data), which demonstrated a good predictive performance. Based on the prognostic model in this paper, patients were also classified into high‐ and low‐risk groups, and functional analyses were performed. In addition, 251 drugs were screened for sensitivity, and four drugs were ultimately found to have high sensitivity, with 5‐Fluorouracil having the best inhibitory effect, and subsequently their corresponding targets were also predicted by GraphSAGE, with the most prominent targets including Cytochrome P450 2D6, UDP‐glucuronosyltransferase 1A, and Proto‐oncogene tyrosine‐protein kinase receptor Ret. Notably, the average accuracy of GraphSAGE was 0.817 ± 0.013, which was higher than that of GAT and GTN.

Conclusion

Our KIRC risk prediction model, constructed using 10 cuproptosis‐related genes, had good independent prognostic ability. In addition, we screened four highly sensitive drugs and predicted relevant targets for these four drugs that might treat KIRC. Finally, literature research revealed that four drug‐target interactions have been demonstrated in previous studies and the remaining targets are potential sites of drug action for future research.