Perspectives on NcRNAs in HBV/cccDNA-driven HCC progression

Abstract

Hepatitis B virus (HBV) integration, the HBx protein (and its mutants), and covalently closed circular DNA (cccDNA) are critical for HBV replication, packaging, and transmission to new host cells. Although nucleos(t)ide analogs (NAs) are a class of antiviral drugs that effectively suppress HBV replication, they do not eliminate cccDNA. This persistent cccDNA, often referred to as an "invisible bullet", plays a pivotal role not only in the horizontal transmission of HBV but also within the context of hepatocellular carcinoma (HCC). Growing evidence reveals that noncoding RNAs (ncRNAs) are deeply involved in cancer progression, as well as the HBV life cycle and related pathogenesis, including liver inflammation, fibrosis, and HCC. This involvement occurs through various mechanisms, as ncRNAs regulate gene transcription, act as miRNA sponges, modulate signaling pathways, and influence downstream effects. These functions depend on the proper formation of RNA structures, which are critical for maintaining the biological activity of ncRNAs. The structure of RNAs appears to play a pivotal role in their functional capacity. Moreover, both ncRNAs and viral nucleotides contribute to G-quadruplex structure formation, which is essential for the HBV life cycle and cancer progression. In this review, we provide an updated overview of the mechanisms by which key ncRNAs mediate HBV/cccDNA actions in HCC progression and focus on their roles in gene expression and structural formation/modification.

Keywords: Cancer progression; CccDNA; Epigenetic regulation; G-quadruplex; HBV; HBx; HCC; NcRNAs; Nucleos(t)ide analogue; Paraspeckle.

Fig. 1

Schematic illustration of miRNA and lncRNA biogenesis and their functional roles in the nucleus and cytoplasm. Inside the nucleus, miRNA is transcribed into pri-miRNA from DNA by RNA polymerase (RNA p), which is then processed into pre-miRNA by the DROSHA-DGCR8 complex. Pre-miRNA is imported into the cytoplasm, where it undergoes further processing through Dicer, leading to the production of mature miRNA. After processing, the mature miRNA becomes associated with Argonaute 2 (AGO2) to form the RNA-induced silencing complex (RISC), which binds to complementary mRNAs to mediate mRNA degradation or translational inhibition. Like mRNAs, lncRNAs are also transcribed by RNA polymerase and can regulate gene expression by different means: (1) Through interactions with specific regions of mRNAs, lncRNAs alter mRNA stability and affect mRNA translation. (2) Functioning as miRNA sponges that inhibit miRNA function. (3) Regulating processes such as phosphorylation (e.g., phosphorylation of p-STAT3) by disrupting phosphatase SHP-1-mediated dephosphorylation. (4) Acting as scaffolds to facilitate molecular interactions. Created with BioRender.com

Fig. 2

Schematic diagram of the HBV life cycle and the functions of ncRNAs in HBV replication. HBV infects host cells and converts relaxed circular DNA (rcDNA) into cccDNA in the nucleus. As a transcriptional template, cccDNA produces pgRNA. In the cytoplasm, these RNAs are translated into HBV proteins, including HBV polymerase, core protein (core), HBsAg, HBeAg and HBx proteins. HBV particles are then assembled and released from the cell. In contrast, HBx affects downstream target gene expression. Different ncRNAs facilitate the control of HBV replication via different mechanisms; for example, HBV replication is inhibited by miRNAs such as miR-125 and miR-101. NcRNAs regulate the epigenetic state of cccDNA in the nucleus. NcRNAs also regulate transcription factors (TFs), which in turn modulate the expression of viral genes and replication. This figure depicts the balancing effect of HBV replication and host ncRNA-mediated regulation. Created with BioRender.com

Fig. 3

Interplay among G4 structures, lncRNAs and HBV. (A) The interaction of MALAT1 with the G4 structure is facilitated by NPM and NCL to induce paraspeckle formation, which facilitates the establishment of HBV replication. (B) G4 structures in the promoter region of NRP1 regulate the expression of the NRP1 gene. (C) The viral genome of HBV functions as cccDNA, an intermediary structure required for HBV replication, as it contains G4 structures. Created with BioRender.com