Currently, the most common treatment for HCC patients is surgical operation. However, approximately half of HCC patients with hepatectomy experience recurrence within 3 years, even at stage A [15,16,17,18]. Furthermore, metastasis before diagnosis and incomplete resection for HCC patients further reduce the 5-year survival rate. To facilitate the identification of HCC patients with poor prognosis and timely intervention implementation, the identification of predictors related to OS is urgent.
Based on the characteristic of the reversibility of DNA methylation, a large number of drugs for DNA methylation and demethylation are currently being researched. Azacitidine (AZA), a hypomethylating agent, has been suggested to be beneficial to myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) patients [19,20,21], and the drug is licensed for clinical treatment in the US, Europe and China. Our study used stricter criteria to identify methylation-driven genes and integrated more comprehensive clinical information, including BMI, new cancer events, surgical method, cancer state, and HCC risk factors, to predict an individual’s prognosis, which further improved the reliability of the study.
In this study, we tried to explore the biological targets of HCC that can be applied by methylation-targeted drugs. After differentially expressed genes and differentially methylated genes were identified, we found more hypomethylated genes than hypermethylated genes (2828 vs 977) and more highly expressed genes than lowly expressed genes (1821 vs 1493). Interestingly, the numbers of hypomethylated genes and highly expressed genes were greater than those in the control group, which is roughly consistent with the fact that methylation is negatively correlated with gene expression. Univariate and multivariable Cox regression analyses filtered three independent predictive genes. The high-risk group and low-risk group were separated into HCC patients using the three central methylation-driven genes. In this study, LCAT was expressed at low levels and hypermethylated in HCC samples. Lecithin-cholesterol acyltransferase (LCAT) is an important gene that is correlated with poor prognosis in many cancers, such as ovarian cancer , Hodgkin lymphoma , and breast cancer . LCAT is related to fatty metabolism in males, and its activity is reduced in patients with liver disease . Ribosomal protein S6 kinase A6 (RPS6KA6) is a protein in the 90-kDa ribosomal protein S6 kinase (RSK) family that participates in a series of cellular biological processes, such as cellular survival, proliferation, differentiation, mobility, nuclear signaling and protein synthesis [26,27,28]. RPS6KA6 plays a differential role in cancers and was reported to be an oncogene in lung squamous cell carcinoma and renal cell carcinoma [29, 30]. In contrast, RPS6KA6 works as a tumor suppressor in endometrial cancer, acute myeloid leukemia, ovarian cancer, and breast cancer [31,32,33,34]. Furthermore, the low expression of RPS6KA6 was the result of DNA hypermethylation in endometrial cancers . However, the role of RPS6KA6 in HCC has not been reported in previous studies. In our study, RPS6KA6, is a hypermethylated and lowly expressed gene, was identified as a core methylation-driven gene correlated with prognosis in HCC patients. Consistent with RPS6KA6, chromosome 5 open reading frame 58 (C5orf58) was hypermethylated and expressed at low levels in HCC. However, the roles of C5orf58 have not been previously reported. C5orf58 maps on chromosome 5 at 5q35.1 according to Entrez Gene . The roles of these three genes, especially RPS6KA6 and C5orf58, have not been sufficiently elucidated in HCC. Given the potentially reversible characteristic of DNA methylation, we filtered the three core methylation-driven genes to identify high-risk HCC patients, which might be therapeutic targets of epigenetic drugs and reduce the risk score of HCC patients.
There are several comprehensive studies related to methylation-driven genes in HCC. However, few studies have integrated clinical parameters and core methylation-driven genes in HCC. The advantage of the study was that stricter criteria were used to obtain more precise methylation-driven genes. Then, the prognosis module based on three genes was built, and the number of genes to build the module increased the feasibility and reduced the clinical cost. The expression, methylation and clinical data were retrieve from matched HCC patients, the feature strengthens the persuasiveness of the prognostic module based on the methylation-driven genes in HCC patients. The internal and external validation of the prognostic module also shown optimistic predictive capacities. Next, we first included more comprehensive clinical information than that included in previous studies to construct a nomogram and calculate an individual’s prognosis. The nomogram to predict prognosis in HCC patients was more accurate than that in a previous study (C-index: 0.75 vs 0.717, 0.676) [36, 37]. Furthermore, T stage, new tumor event, surgical method and risk score were filtered to be the independent prognosticators, which further strengthens the result that risk score might be utilized to calculate the prognosis in HCC patients. Finally, LCAT was found to be correlated with T stage and new tumor events, and RPS6KA6 was found to be related to T stage. It is worth further exploring whether the T stage and new cancer events were reversed by regulating LCAT and RPS6KA6. Overall, the nomogram, independent prognosticators and potential treatment targets are beneficial for individualized treatment of HCC patients.
Certainly, the potential limitations of the study should be noted. The biological mechanisms of LCAT, RPS6KA6 and C5orf58 remain to be explored. In addition, the study was based only on research data from the TCGA database, which might contribute to selection bias. Therefore, a multicenter and large-scale study should be implemented to further validate our model.