One single nucleotide difference alters the differential expression of spliced RNAs between HBV genotypes A and D

Huang, Chien Chiao; Kuo, Tzer Min; Yeh, Chau Ting; Hu, Cheng; Chen, Ya Ling; Tsai, Yue Lin; Chen, Mong Liang; Chou, Yi-Chun; Chang, Chung-Ming

doi:10.1016/j.virusres.2013.02.004

Cited by 23 publications

(25 citation statements)

References 46 publications

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“…2C,D) of intracellular core particle-associated viral RNAs and DNAs. Interestingly, in addition to the known spliced RNA species7911515253545556, we identified 8 novel species of spliced mini-RNA encapsidated in arginine-deficient mutants III + IV and I + II + III + IV (red color in Fig. 2E).…”

Section: Resultsmentioning

confidence: 92%

HBV maintains electrostatic homeostasis by modulating negative charges from phosphoserine and encapsidated nucleic acids

Yang

Chu

et al. 2016

Sci Rep

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Capsid assembly and stability of hepatitis B virus (HBV) core protein (HBc) particles depend on balanced electrostatic interactions between encapsidated nucleic acids and an arginine-rich domain (ARD) of HBc in the capsid interior. Arginine-deficient ARD mutants preferentially encapsidated spliced viral RNA and shorter DNA, which can be fully or partially rescued by reducing the negative charges from acidic residues or serine phosphorylation of HBc, dose-dependently. Similarly, empty capsids without RNA encapsidation can be generated by ARD hyper-phosphorylation in insect, bacteria, and human hepatocytes. De-phosphorylation of empty capsids by phosphatase induced capsid disassembly. Empty capsids can convert into RNA-containing capsids by increasing HBc serine de-phosphorylation. In an HBV replicon system, we observed a reciprocal relationship between viral and non-viral RNA encapsidation, suggesting both non-viral RNA and serine-phosphorylation could serve as a charge balance buffer in maintaining electrostatic homeostasis. In addition, by comparing the biochemistry assay results between a replicon and a non-replicon system, we observed a correlation between HBc de-phosphorylation and viral replication. Balanced electrostatic interactions may be important to other icosahedral particles in nature.

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Section: Resultsmentioning

confidence: 92%

HBV maintains electrostatic homeostasis by modulating negative charges from phosphoserine and encapsidated nucleic acids

Yang

Chu

et al. 2016

Sci Rep

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“…Our prior study found that relatively high levels of 2.2DS-RNAs were present in CHB patients with genotype A infection but not in those with genotype D infection (25). These results indicated that the expression of 2.2DS-RNA could be induced and regulated differently in CHB patients than it is in tissue culture.…”

Section: Discussionmentioning

confidence: 93%

“…A plasmid expressing HBV with a G2335A mutation (HBV G2335A ) plasmid was generated from an HBV genotype A plasmid (34) by site-directed mutagenesis, as described previously (25). The mutation in HBV G2335A causes a nucleotide substitution at position 2335 within the polypyrimidine tract of a splice acceptor site, which alters the splicing pattern of genotype A to that of genotype D, rendering it 2.2DS-RNA deficient.…”

Section: Methodsmentioning

confidence: 99%

“…The cells were transfected with a plasmid encoding the genome of HBV genotype A, from which the 2.2DS-RNA is transcribed. We also transfected cells with a plasmid encoding the mutant HBV G2335A genome, which is 2.2DS-RNA deficient (25). The results of the Northern blotting of the cells transfected with the HBV genotype A expression plasmid showed that the level of pgRNA was lower than that in the cells transfected with the HBV G2335A expression plasmid ( Fig.…”

Section: 2ds-rna Suppresses Hbv Transcription In Vitro and In Vivomentioning

confidence: 97%

“…A 2.2-kb doubly spliced RNA (2.2DS-RNA) which lacks splice donor and acceptor sites, respectively, at nucleotides 2067 and 2350 and at nucleotides 2447 and 282 is produced by HBV genotypes A and B only (19,24). Our prior study found that the expression levels of 2.2DS-RNAs in chronic hepatitis B (CHB) patients are very different, with relatively high levels of 2.2DS-RNAs present in a portion of liver biopsy specimens from the CHB patients of genotype A (25). The detailed mechanisms that modulate the level of 2.2DS-RNA in the CHB patients have not yet been elucidated.…”

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confidence: 99%

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Doubly Spliced RNA of Hepatitis B Virus Suppresses Viral Transcription via TATA-Binding Protein and Induces Stress Granule Assembly

Tsai

Chong

Chou

et al. 2015

J Virol

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The risk of liver cancer in patients infected with the hepatitis B virus (HBV) and their clinical response to interferon alpha therapy vary based on the HBV genotype. The mechanisms underlying these differences in HBV pathogenesis remain unclear. In HepG2 cells transfected with a mutant HBV G2335A expression plasmid that does not transcribe the 2.2-kb doubly spliced RNA (2.2DS-RNA) expressed by wild-type HBV genotype A, the level of HBV pregenomic RNA (pgRNA) was higher than that in cells transfected with an HBV genotype A expression plasmid. By using cotransfection with HBV genotype D and 2.2DS-RNA expression plasmids, we found that a reduction of pgRNA was observed in the cells even in the presence of small amounts of the 2. T he hepatitis B virus (HBV) causes acute and chronic liver diseases in humans. Millions of people worldwide suffer from HBV-induced liver disorders, and HBV infection increases the risk of hepatic cirrhosis and hepatocellular carcinoma (1, 2). Type I interferons (IFNs), including IFN-␣ and IFN-␤, exert antiviral activity and important immunomodulatory effects in the innate immune response against HBV infection (3-5). However, the mechanism through which HBV evades the host immune response in chronically infected patients has not been fully elucidated.In addition to the factors such as viral load and naturally occurring mutants, the HBV genotype, classified as A through J based on genomic sequence, has been shown to be associated with disease progression and responses to IFN-based therapy (6). Previous studies have shown that chronic hepatitis B patients infected with genotype A or B exhibit higher rates of seroclearance of HBV e antigen (HBeAg) and viral DNA in response to IFN-␣ therapy than patients with genotype C or D infection (7-9) and that chronically infected children with HBV genotype A infection have lower viral DNA loads and exhibit less severe symptoms than patients with genotype D infection (10, 11). Clinical studies have also shown that differences between HBV genotypes correlate with deoxycytidine analog resistance (12) and hepatic pathogenesis (13).

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Serum hepatitis B virus spliced RNA proportion increases with liver disease progression in patients with chronic hepatitis B

Lu,

Li,

Deng

et al. 2024

Journal of Medical Virology

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Serum hepatitis B virus (HBV) spliced RNAs (spRNAs) are ubiquitous in HBV‐infected patients; however, their clinical significance remains unknown. Therefore, we aimed to explore the relationship between HBV spRNAs and liver disease progression in chronic hepatitis B (CHB) patients; in vitro cell line assessment was also performed. The serum HBV wild‐type RNA (wtRNA) and spRNA levels were individually quantified in a cohort of 279 treatment‐naïve, hepatitis B e antigen positive CHB patients with or without cirrhosis. The spRNA proportion was determined as (spRNA × 100%)/(spRNAs + wtRNA). 20 patients' serum samples underwent spRNA species profiling using next‐generation sequencing. Serum spRNA species 1, 2, 3, 4, and 5 were the most common variants. The spRNA proportion varied from 0.00% to 19.02%, with higher levels in HBV genotype C patients than in those with genotype B (1.76% vs. 0.84%, p < 0.001). The spRNA proportion was positively associated with the alanine aminotransferase levels (r = 0.144, p = 0.053) and significantly higher in cirrhotic than in non‐cirrhotic patients (1.69% vs. 1.04%, p = 0.001). Multivariate analysis revealed a 2.566‐fold higher risk of cirrhosis in patients with elevated spRNA proportion (p = 0.024). In vitro experiments confirmed that spRNAs contributed to hepatic stellate cell activation, which is critical in liver fibrosis development. Therefore, increased HBV spRNA expression poses a risk for liver disease progression. Quantifying serum HBV spRNAs can aid in monitoring liver disease progression. Furthermore, the therapeutic targeting of spRNAs may improve the prognosis of patients with CHB.

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One single nucleotide difference alters the differential expression of spliced RNAs between HBV genotypes A and D

Cited by 23 publications

References 46 publications

HBV maintains electrostatic homeostasis by modulating negative charges from phosphoserine and encapsidated nucleic acids

HBV maintains electrostatic homeostasis by modulating negative charges from phosphoserine and encapsidated nucleic acids

Doubly Spliced RNA of Hepatitis B Virus Suppresses Viral Transcription via TATA-Binding Protein and Induces Stress Granule Assembly

Serum hepatitis B virus spliced RNA proportion increases with liver disease progression in patients with chronic hepatitis B

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