Integrating single-cell and spatial omics identifies a prognostic ferroptosis signature in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most lethal malignancies, and limited treatment options available for advanced-stage cancer highlight the need to identify new therapeutic targets. Ferroptosis is an iron-dependent form of programmed cell death characterized by lipid peroxidation. It may serve as an attractive therapeutic target due to its unique form of death and the high susceptibility of HCC cells because of iron and lipid metabolism overexpression. However, the full expression spectrum, regulatory network, and prognostic impact of the ferroptosis-associated genes (FRGs) in HCC are not yet well established. The Cancer Genome Atlas database provided mRNA expression and clinical information for 374 patients with HCC. mRNA of differentially expressed genes (DEGs) of ferroptosis was obtained by intersecting DEGs between tumor and corresponding normal tissues with the known FRG set from GeneCards. We performed functional enrichment analysis, protein-protein interaction network construction, and survival analysis. A prognostic model was constructed using the least absolute shrinkage and selection operator and multivariate Cox regression analysis. Single-cell RNA-seq analysis (GSE242889) and spatial transcriptomic analysis (GSE203612) data were used to verify the expression patterns and functional associations of signature genes. We identified 183 ferroptosis-related DEGs in HCC, which were greatly enriched in the oxidative stress response and the ferroptosis pathway. Consequently, we constructed a powerful prognostic signature based on three genes ( TPX2 , KIF20A , and HJURP ). High expression of these three genes is predictive of a high risk and poor overall survival. Single-cell sequencing analyzed the expression of these genes in different cell types and identified their expression with important oncogenic pathways such as the phosphatidylinositol 3-kinase-protein kinase B-mammalian target of rapamycin pathway, E2F targets, and the G2M checkpoint. Spatial transcriptome sequencing verified their specific expression within the tumor region and identified their very strong positive correlations with each other. This multi-omics study analyzed and validated a new ferroptosis-related gene signature ( TPX2 , KIF20A , and HJURP ) as a strong prognostic biomarker for HCC. Our findings, which incorporate bulk, single-cell, and spatial transcriptomic sequencing data, reveal a remarkable association between these genes and ferroptosis-related oxidative stress pathways, cell cycle processes, and core oncogenic cascades. Dysregulation of these pathways may accelerate HCC malignant development, providing preliminary bioinformatic evidence for ferroptosis-related targeted precision therapy research for HCC.