The epigenetic basis of hepatocellular carcinoma - mechanisms and potential directions for biomarkers and therapeutics

Abstract

Hepatocellular carcinoma (HCC) is the sixth leading cancer worldwide and has complex pathogenesis due to its heterogeneity, along with poor prognoses. Diagnosis is often late as current screening methods have limited sensitivity for early HCC. Moreover, current treatment regimens for intermediate-to-advanced HCC have high resistance rates, no robust predictive biomarkers, and limited survival benefits. A deeper understanding of the molecular biology of HCC may enhance tumor characterization and targeting of key carcinogenic signatures. The epigenetic landscape of HCC includes complex hallmarks of 1) global DNA hypomethylation of oncogenes and hypermethylation of tumor suppressors; 2) histone modifications, altering chromatin accessibility to upregulate oncogene expression, and/or suppress tumor suppressor gene expression; 3) genome-wide rearrangement of chromatin loops facilitating distal enhancer-promoter oncogenic interactions; and 4) RNA regulation via translational repression by microRNAs (miRNAs) and RNA modifications. Additionally, it is useful to consider etiology-specific epigenetic aberrancies, especially in viral hepatitis and metabolic dysfunction-associated steatotic liver disease (MASLD), which are the main risk factors of HCC. This article comprehensively explores the epigenetic signatures in HCC, highlighting their potential as biomarkers and therapeutic targets. Additionally, we examine how etiology-specific epigenetic patterns and the integration of epigenetic therapies with immunotherapy could advance personalized HCC treatment strategies.

Fig. 1. DNA methylation patterns associated with hepatocarcinogenesis.

In non-cancerous hepatocytes, the genome-wide methylation and relatively unmethylated CpG island in the promoter of tumor suppressor genes suppress oncogenic expression and enable the expression of tumor suppressive pathways, respectively. In contrast, HCC is characterized by global hypomethylation, which may lead to the activation of oncogenes, e.g., the C/EBPβ gene, contributing to tumor progression as demonstrated by greater histopathological grades and tumor sizes. Additionally, hypermethylation at the promoter regions results in the silencing of tumor suppressor genes, e.g., ZNF334, HIC1, GSTP1, SOCS1, RASSF1, CDKN2A, APC, RUNX3, PRDM2. Hypermethylation at genomic regions known as methylated-in-tumor (MINT) 1, 2, 12, 31 loci are associated with hepatocarcinogenesis. These methylation changes underscore the complex regulatory mechanisms that drive the transition from normal liver function to malignant transformation.

Fig. 2. The interplay of specific histone post-translational modifications (PTMs) in HCC illustrates a complex but targeted landscape of epigenetic regulation that influences various aspects of tumor behavior and pathology.

PTMs contribute to aberrant oncogenic upregulation and tumor suppressor gene repression that characterizes HCC. Activating histone PTMs (e.g., H3K27ac, H3K4me3) and erasers of repressive PTMs (e.g., KDM6B) facilitate open chromatin, leading to proto-oncogene upregulation, thereby promoting hepatocarcinogenesis. Conversely, the downregulation of tumor suppressor genes and miRNAs can be attributed to changes in chromatin accessibility induced by repressive PTMs (e.g., H3K9me2, H3K9me3, H3K27me3). Moreover, various erasers of PTM (e.g., HDAC1, KDM5B) suppress key tumor-suppressive pathways by removing activating methylation or acetylation marks. Overall, these result in increased tumor proliferation, vascular invasion, distal metastasis, and poorer overall survival.

Fig. 3. Transcriptional activation of proto-oncogenes from distal promoter-enhancer interaction.

In some cases of HCC, aberrant chromatin loop formation brings de novo distal enhancers in close proximity to the promoter of several proto-oncogenes. The chromatin loop is stabilized by the CCCTC-binding factor (CTCF) and the cohesin complex to facilitate gene transcription. These interactions are associated with increased neovascularization, tumor growth, invasion, and metastasis in HCC.

Fig. 4. Mechanisms of epigenetic regulation by direct interference by microRNAs (miRNA) and epitranscriptomic RNA modifications.

In HCC, direct miRNA interference contributes to HCC in two mechanisms. Firstly, oncogenic miRNAs degrade tumor-suppressive mRNAs and inhibit ribosomal translation. Secondly, tumor-suppressive miRNAs, which normally suppress the expression of proto-oncogenes in normal cells, are downregulated in HCC. Additionally, some epitranscriptomic changes include hypermethylation of tumor suppressor mRNA, which hinders ribosomal translation. Interestingly, hypomethylation of tumor suppressor mRNA can result in a loss in function through destabilization and degradation of mRNA. These result in increased translation of oncogenic mRNAs. Altogether, these might lead to HCC development through hepatic inflammation and metabolic dysregulation, evasion of cell death, unregulated proliferation, invasion, metastasis, and tumor microenvironment remodeling that favors hepatocarcinogenesis.