m5C-Related Regulators Define Tumor Microenvironment and Predict Prognosis in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a highly lethal cancer and a leading cause of cancer-related deaths globally. RNA 5-methylcytosine (m5C) modification plays a vital role in epigenetic regulation, yet its impact on prognosis and the tumor immune microenvironment (TIME) in HCC remains unclear.

RNA sequencing and clinical data were obtained from the Cancer Genome Atlas (TCGA) database. We applied an unsupervised clustering algorithm for the cluster analysis of m5C RNA methylation regulators, and then performed survival analyses to determine the best prognosis for HCC samples. Univariate and multivariate Cox regression analyses were conducted to construct a prognostic model. HCC patients were classified into high- and low-risk groups based on risk scores. Model performance was evaluated using ROC curves and validated with the ICGC cohort. Immune infiltration, clinicopathological features, and functional enrichment analyses were also performed.

We analyzed the differential expression patterns of the m5C-related regulators between HCC and normal tissue samples. Based on consensus clustering of these regulators, three distinct molecular subgroups were identified, each associated with differences in patient survival and immune cell infiltration. Furthermore, we developed a prognostic signature comprising NSUN3, NSUN5, and YBX1, and stratified HCC patients into low- and high-risk groups. Patients in the low-risk group exhibited significantly better overall survival (OS) than those in the high-risk group. The robustness of this risk model was validated using the ICGC database. When integrated with clinicopathological characteristics, the risk score emerged as an independent prognostic factor. Additionally, we performed functional annotation and enrichment analyses based on differentially expressed genes (DEGs) between the two risk subgroups to explore potential underlying biological mechanisms.

Our study revealed the potential roles of these m5C-related regulators in TIME and identified their prognosis value and therapeutic potential for HCC patients.