The lncRNAs in HBV-Related HCCs: Targeting Chromatin Dynamics and Beyond

Abstract

Hepatocellular carcinoma (HCC) represents the fourth leading and fastest rising cause of cancer death (841,000 new cases and 782,000 deaths annually), and hepatitis B (HBV), with 250 million people chronically infected at risk of developing HCC, accounts for >50% of the cases worldwide. Long non-coding RNAs (lncRNAs), untranslated transcripts longer than 200 nucleotides, are implicated in gene regulation at the transcriptional and post-transcriptional levels, exerting their activities both in the nuclear and cytoplasmic compartments. Thanks to high-throughput sequencing techniques, several lncRNAs have been shown to favor the establishment of chronic HBV infection, to change the host transcriptome to establish a pro-carcinogenic environment, and to directly participate in HCC development and progression. In this review, we summarize current knowledge on the role of lncRNAs in HBV infection and HBV-related liver carcinogenesis and discuss the potential of lncRNAs as predictive or diagnostic biomarkers.

Keywords: HBV; HCC; LncRNAs; biomarkers; epigenetic regulation.

Figure 1

LncRNAs functions in HBV-related HCCs. The nuclear or cytoplasmic localization of lncRNAs reflects their mode of action. Nuclear lncRNAs are involved in nuclear organization, chromatin function by sequestering (decoy), guiding toward their target loci (guide) or tethering (scaffold) transcription factors or chromatin-modifying complexes and RNA maturation (splicing). In the cytoplasm, lncRNAs are involved in post-transcriptional mechanisms of gene regulation by: (a) binding to complementary sequences on miRNAs and relieving the repression of targeted mRNAs (Competing Endogenous RNA or ceRNAs); (b) binding to cytoplasmic proteins and affecting their stability; (c) acting as precursors of miRNAs; and (d) coding for small peptides through small open reading frames (smORFs). Circulating lncRNAs in extracellular fluids are found complexed to proteins (free circulating lncRNAs) or in extracellular microvescicles (exMVs), comprising both exosomes and larger MVs.

Figure 2

LncRNAs/PRC2 interactome in HBV-related HCCs. (A) Schematic representation of the PRC2 complex and its interaction with lncRNAs. The PRC2 complex proteins EED1, SUZ12, and EZH2 have a high affinity to G-quadruplex sequences, an intermediate affinity to unstructured G-rich RNA, and a lower affinity to stem-loop RNA structures on lncRNAs. The lncRNAs deregulated in HBV-related HCCs that bind the PRC2 complex are listed in (A). In (B) to (E) are shown the functional consequences of their interaction and HBV infection on the activity of the PRC2 complex. (B) The lncRNA HOTAIR interacts with the PRC2 complex and the RNA helicase DDX5. HBV infection promotes the activation of PLK1, which phosphorylates SUZ12 and DDX5 . The downregulation of DDX5 in HBV-infected cells and in HBV-related HCCs allows the preferential association of HOTAIR with the E3-ligase Mex3b, the ubiquitination of SUZ12 and its proteasomal degradation . The functional significance of the phosphorylation of DDX5 by PLK1 remains to be determined but the transcriptional repression exerted by the DDX5/PRC2/HOTAIR complex is impaired, leading to the transcriptional activation of PRC2/HOTAIR target genes, including EpCAM and other genes related to the hepatic progenitor cells (HPCs) phenotype. (C) The lncRNA DLEU2, activated by HBV infection and upregulated in HCC, directly binds HBx and EZH2 . By increasing DLEU2 levels and by binding to DLEU2, HBx interferes with EZH2/PRC2 repressive functions and activates transcription. HBx interaction with DLEU2 either evicts EZH2, a modality prevalent on cccDNA, or displaces the PRC2/EZH2 complex from close contact with chromatin in the case of host genes. PCR2 subunits are still immunoprecipitated with their target chromatin sequences . The precise mechanisms underlying the removal of the repressive H3K27me3 mark imposed by the PRC2 complex, the deposition of active H3K27Ac marks, and the conversion of PRC2 complexes to transcriptional activation are still unclear. (D) The upregulation of the lncRNA PVT1 in HBV-related HCCs and its interaction with the PRC2 leads to a loss of EZH2 recruitment to the c-Myc oncogene promoter and the concomitant reduction of the H3K27me3 mark. Interestingly, this leads to cell proliferation and the acquisition of stem cell-like properties . (E) The lncRNAs ANRIL and UCA1, both upregulated in HBV-related HCCs, guide PRC2 to the Kruppel-like factor 2 (KLF2) and the P27/Kip1 promoters, leading to an increase of H3K27 tri-methylation and their transcriptional repression.

Figure 3

LncRNA involved in the development and progression of HBV-related HCCs. The biological functions targeted by lncRNAs deregulated in HBV-related HCCs and involved in HCC development and progression are shown. The lncRNA are grouped according to their up- or downregulation in the tumor and their activity in the nucleus or in the cytoplasm.