Comprehensive Analysis of Cuproptosis-Related Genes in Prognosis and Immune Infiltration of Hepatocellular Carcinoma Based on Bulk and Single-Cell RNA Sequencing Data

SIMPLE SUMMARY: Hepatocellular carcinoma (HCC) is a common malignant tumor with high mortality. Cuproptosis is a newly discovered mechanism of cell death. Numerous cuproptosis-related-genes are reported; however, the studies on the role of cuproptosis-related genes in the prognosis of HCC are limited. This study aimed to establish a prognosis model of HCC related to cuproptosis-related genes and explore the correlations between cuproptosis-related genes and the immune microenvironment of HCC. These findings might aid in studying the cuproptosis and tumor immune microenvironment of HCC patients for improving their treatment outcomes and prognosis. ABSTRACT: Background: Studies on prognostic potential and tumor immune microenvironment (TIME) characteristics of cuproptosis-related genes (CRGs) in hepatocellular carcinoma (HCC) are limited. Methods: A multigene signature model was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis. The cuproptosis-related multivariate cox regression analysis and bulk RNA-seq-based immune infiltration analysis were performed. The results were verified using two cohorts. The enrichment of CRGs in T cells based on single-cell RNA sequencing (scRNA-seq) was performed. Real-time polymerase chain reaction (RT-PCR) and multiplex immunofluorescence staining were performed to verify the reliability of the conclusions. Results: A four-gene risk scoring model was constructed. Kaplan–Meier curve analysis showed that the high-risk group had a worse prognosis (p < 0.001). The time-dependent receiver operating characteristic (ROC) curve showed that the OS risk score prediction performance was good. These results were further confirmed in the validation queue. Meanwhile, the Tregs and macrophages were enriched in the cuproptosis-related TIME of HCC. Conclusions: The CRGs-based signature model could predict the prognosis of HCC. Treg and macrophages were significantly enriched in cuproptosis-related HCC, which was associated with the depletion of proliferating T cells.