Skip to main content
PMC home page
NIHPA Author Manuscripts logoLink to NIHPA Author Manuscripts
. Author manuscript; available in PMC: 2021 Jun 10.
Published in final edited form as: Antiviral Res. 2019 Jun 25;170:104540. doi: 10.1016/j.antiviral.2019.104540

Distinct dual antiviral mechanism that enhances hepatitis B virus mutagenesis and reduces viral DNA synthesis

Yumeng Z McDaniel a,b, Steven E Patterson a,f, Louis M Mansky a,b,c,d,e,f,*
PMCID: PMC8191393  NIHMSID: NIHMS1695728  PMID: 31247245

Abstract

Reverse transcriptase (RT) is an essential enzyme for the replication of retroviruses and hepadnaviruses. Current therapies do not eliminate the intracellular viral replication intermediate termed covalently closed circular (ccc) DNA, which has enhanced interest in hepatitis B virus (HBV) reverse transcription and cccDNA formation. The HBV cccDNA is generated as a plasmid-like episome in the host cell nucleus from the protein-linked relaxed circular (rc) DNA genome in incoming virions during HBV replication. The creation of the cccDNA via conversion from rcDNA remains not fully understood. Here, we sought to investigate whether viral mutagens can effect HBV replication. In particular, we investigated whether nucleoside analogs that act as viral mutagens with retroviruses could impact hepadnaviral DNA synthesis. We observed that a viral mutagen (e.g., 5-aza-2’-deoxycytidine, 5-aza-dC or 5-azacytidine, 5-aza-C) severely diminished the ability of a HBV vector to express a reporter gene following virus transfer and infection of target cells. As predicted, the treatment of 5-aza-dC or 5-aza-C elevated the HBV rcDNA mutation frequency, primarily by increasing the frequency of G-to-C transversion mutations. A reduction in rcDNA synthesis was also observed. Intriguingly, the ccc DNA nick/gap region transcription was diminished by 5-aza-dC, but did not enhance viral mutagenesis. Taken together, our results demonstrate that viral mutagens can impact HBV reverse transcription, and propose a model in which viral mutagens can induce mutagenesis during rcDNA formation and diminish viral DNA synthesis during the conversion of rcDNA to cccDNA.

Keywords: Hepadnavirus, reverse transcription, lethal mutagenesis, polymerase

1. Introduction

Nearly 257 million people worldwide are chronically infected with hepatitis B virus (HBV), a number 8 times greater than the number of people infected with human immunodeficiency virus type 1 (HIV-1) (Choi et al., 2018; Hutin et al., 2018). Chronic HBV infection can develop into serious liver disease, including cirrhosis or liver cancer. Although infection is preventable by vaccination and some antiviral treatments are available, there are up to 1 million deaths per year from HBV-associated hepatocellular carcinoma and complications of cirrhosis. The currently approved therapeutics for chronic HBV infection cannot cure HBV infection and efficiently eliminate HBV covalently closed circular (ccc) DNA (Lucifora and Protzer, 2016; Tang et al., 2017). Therefore, there is a need for basic research to better understand HBV biology, in order to help develop effective drug treatments. Since antiviral drug development is a time-consuming and costly process, drug repositioning has been applied for treatment of many conditions, which has been utilized to identify potential anti-HIV-1 drug treatments (Ashburn and Thor, 2004; Clouser et al., 2010). Decitabine (5-aza-dC), 5-azacytidine (5-aza-C) and gemcitabine, commercially used as anti-cancer drugs, are reported to have anti-HIV-1 activity, mainly through targeting reverse transcription (Clouser et al., 2011; Clouser et al., 2010; Dapp et al., 2009). Reverse transcription is a characteristic step for the replication life cycle of retroviruses. Importantly, reverse transcription is also a crucial step in the life cycle of hepadnaviruses (Tang et al., 2017). HBV is a hepadnavirus and upon infection of a permissive target cell, the rcDNA enters into the nucleus, and is converted into covalently closed circular (ccc) DNA, which exists as a minichromosome that can transcribe HBV mRNAs. These HBV mRNAs are translated into viral proteins, including reverse transcriptase (RT). The pre-genomic RNA (pgRNA) and RT are packaged into HBV capsids. Reverse transcriptase (RT) activity generates a minus DNA strand synthesized from the pgRNA, which allows the synthesis of plus strand DNA to produce the rcDNA. Two nucleoside reverse transcriptase inhibitors (NRTIs), lamivudine (3TC) and tenofovir, have been used for the treatment of both HIV-1 and HBV infection. Given the similarities between HIV-1 and HBV reverse transcription, we hypothesized that 5-aza-dC, 5-aza-C and gemcitabine may target HBV reverse transcription.

5-aza-dC and 5-aza-C are cytidine analogs that are clinically approved for the treatment of myelodysplastic syndromes and acute myeloid leukemia (AML). Initial reports indicated that 5-aza-C and 5-aza-dC were found to inhibit HIV-1 infection in cell culture (Bouchard et al., 1990). More recent studies have shown that 5-aza-dC and 5-aza-C can induce G-to-C hypermutation in HIV-1, increasing the mutational load and extinguishing viral infectivity (Dapp et al., 2009; Rawson et al., 2015). Furthermore, 5-aza-C was reported to enhance HIV-1 mutagenesis by reduction of 5-aza-C to 5-aza-dC (Rawson et al., 2016). While the high rates of mutation can enable immune evasion and drive the emergence of drug resistance, quasispecies theory predicts that there is a maximum “error threshold” above which genetic information is not maintained, thus leading to virus extinction (i.e., production of non-infectious virus particles). This type of collapse in a viral population infectivity can be achieved through the use of viral mutagens, via lethal mutagenesis (Domingo et al., 2012). While hepatitis C virus, poliovirus, vesicular stomatitis virus, influenza virus, hepatitis E virus, herpes simplex virus and HIV-1 have been shown to be susceptible to lethal mutagenesis (de Avila et al., 2016; Graci et al., 2007; Greggs et al., 2012; Jiang et al., 2016; Moreno et al., 2012; Reina and Reina, 2017; Todt et al., 2016), no studies to date have been reported for HBV.

In this study, we have observed that the viral mutagens 5-aza-dC and 5-aza-C can cause an increase in viral mutagenesis concomitantly with reduced viral DNA synthesis. In particular, our observations support a model in which viral mutagens can induce mutagenesis during rcDNA formation and diminish viral DNA synthesis during the conversion of rcDNA to cccDNA.

2. Materials and methods

2.1. Cell lines, plasmids and drugs.

The HepG2 and HepAD38 cell lines were a kind gift from Dr. Daniel D. Loeb (University of Wisconsin-Madison, Madison, WI). The HepG2-NTCP cell line was generously offered by Dr. Haitao Guo (Indiana University, Indianapolis, IN). The pUC1.2xHBV/NL and pUCxHBV-D plasmids were provided by Dr. Kunitada Shimotohno (National Center for Global Health and Medicine, Ichikawa, Japan). 5-aza-C (Sigma-Aldrich, St. Louis, MO), gemcitabine (TCI, Tokyo, Japan), and 3TC (NIH-ARP, Germantown, MD) were obtained from the indicated sources. 5-aza-dC divalerate (abbreviated as 5-aza-dC), a more stable prodrug form of 5-aza-dC, was synthesized by the Center for Drug Design at the University of Minnesota as described previously (Clouser et al., 2014). All drugs were dissolved and were stored in aliquots at −20°C.

2.2. Cell culture.

HepG2 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal clone 3 (FC3) serum (HyClone, Logan, UT), 100 U/ml penicillin, 100 μg/ml streptomycin and 100 U/ml MEM-NEAA (Life Technologies). HepAD38 cells were maintained in RPMI-1640 with 10% FC3 serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 100 U/ml MEM-NEAA, 10 mM HEPES, 0.4 mg/ml G418 and 0.3 μg/ml tetracycline. HepG2-NTCP cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM)-F12 supplemented with 10% FC3, 100 U/ml penicillin, 100 μg/ml streptomycin and 8 μg/ml blasticidin (Yan et al., 2015). All cell lines were maintained at 37°C in 5% CO2.

2.3. Production of virus stocks.

HBV/NL virus was produced as described previously (Nishitsuji et al., 2015). Briefly, the pUC1.2xHBV/NL plasmids were co-transfected with pUCxHBV-D into HepG2 cells using Lipofectamine 3000 (Life Technologies). Media was replaced one day post-transfection and cells were treated with drugs or vehicle. Cell culture supernatants were collected five days post- transfection and concentrated to 24X by using a Vivaspin 20 ml 100,000 MWCO (Sartorius) centrifuged at 1000 × g at 20o C. Virus was then aliquoted and stored at −80 °C until use.

2.4. Drug treatment and virus transfer to target cells.

HepG2-NTCP cells were treated with drugs 2 hours before adding virus to the cell cultures. HepG2-NTCP cells were infected with HBV/NL virus in the presence of 4% PEG8000 and 2% dimethyl sulfoxide (DMSO) overnight. After 24 hours, media was replaced with fresh media containing 2% DMSO and drugs. Drugs were removed and media was changed at three days post-infection. At six or seven days post-infection, cells were washed with PBS once and lysed in 1X passive lysis buffer (Promega Corp., Madison, WI). The lysate was measured for Nano luciferase activity with the NL Luciferase Assay Kit (Promega) according to the manufacturer’s protocol. The HepG2-NTCP cell viability was also measured with the lysate using CellTiter-Glo® Luminescent Cell Viability Assay Kit (Promega).

2.5. Cellular proliferation.

HepG2 cells (50,000 cells per well) or HepAD38 cells (4,500 cells per well) were plated in a 96-well plate 24 hours prior to drug treatment. Cells were treated individually or in combination for five days, and proliferation was quantified using the CellTiter-Glo® kit from Promega according to the manufacturer’s instructions. Cells treated with DMSO were used as an untreated control. The data were expressed as a percentage of the untreated control to normalize for differences in luciferase activity between experiments.

2.6. qPCR of rcDNA in released viral particles.

The HepAD38 cell line produces HBV particles under control of a tetracycline operator/CMV promoter (Ladner et al., 1997). Five days following removal of tetracycline and drug treatment of cells, HBV rcDNA was purified from cell culture supernatants using the E.Z.N.A. ○RBlood DNA Mini Kit (Omega Bio-tek). The purified DNA was quantified by qPCR as previously described (Pas et al., 2000). Primers were designed to amplify an 89 bp product in the pre-S gene (F: 5’-GGA CCC CTG CTC GTG TTA CA-3’ (nucleotides 184 to 203), R: 5’-GAG AGA AGT CCA CCA CGA GTC TAG A-3’ (nucleotides 273 to 249)). HBV DNA was calculated by dividing the relative DNA copy number of the drug-treated group by that of the no-drug-treated group. A series of drug concentrations were tested, and each experiment was independently repeated three times.

2.7. qPCR of cccDNA.

At seven days post-infection, HepG2-NTCP cells were lysed in 50 mM Tris/0.5% NP-40/ 150 mM NaCl (pH 7.4) as previously described (Ni et al., 2014). Cytosolic and nuclear fractions were separated by centrifugation (4000 rpm for 5 minutes). HBV cccDNA was extracted from the nuclear fractions by using the E.Z.N.A. ○RBlood DNA mini kit (Omega Bio-tek). Extracted cccDNA was treated for 2 hours at 37o C with plasmid safe DNase I (Epicentre Inc, Madison, WI), which was subsequently inactivated by incubation at 70o C for 30 minutes. The extracted DNA was quantified by qPCR as described above using primers in the nick/gap region of the HBV minus-strand cccDNA generating a 308 bp product (F: 5’-CCG TGT GCA CTT CGC TTC A-3’ (nucleotides 1575 to 1593), R: 5’-GCA CAG CTT GGA GGC TTG A-3’ (nucleotides 1864 to 1882).

2.8. RT-qPCR of RNA from HepG2-NTCP cells infected with HBV vector.

RNA was extracted from infected HepG2-NTCP cells with the High Pure RNA isolation Kit (Roche). Next, cDNA synthesis was performed using the iScript Select cDNA Synthesis Kit (Bio-Rad) according to the manufacturer’s instructions. The synthesized cDNA was diluted 10-fold and quantified by qPCR using iTaq Universal SYBR Green Supermix (Bio-Rad). RNA was quantified by both nick/gap gene (nucleotides 1575–1882) and pre S gene (nucleotides 184–249) primer sets.

2.9. DNA sequencing.

A portion of the pol/s gene was chosen for sequencing from the rcDNA and the cccDNA, respectively. The primers used, F: 5’-ACC CTG TTC TGA CTA CTG CC-3’ (nucleotides 87 to 106), and R: 5’ -ACA GCG GTA AAA AGG GAC TCA-3’ (nucleotides 800 to 780), were designed to overlap a region of both the polymerase and surface antigen genes and generated a product of 714 bp. The primers designed in the nick/gap region in cccDNA were also used as described above. Phusion Hot Start II High-Fidelity DNA Polymerase (Thermo Scientific) was used for PCR reactions, and the initial PCR reaction was purified with QIAquick○R Gel Extraction Kit (Qiagen). Amplicons were verified for correct size and purity by DNA gel imaging prior to ligation into the pGEM-T vector (Promega). Plasmids were transformed into E. coli, and insert-containing vectors were purified (DirectPrep 96 Miniprep Kit, Qiagen) and sequenced. Sequence alignments were performed using SeqMan assembler of Lasergene 7 software package (DNAStar; Madison, WI). DMSO-treated HepAD38 or HepG2-NTCP cells were used as a untreated, negative control.

2.10. Statistical analysis.

Statistical analyses were, in part, implemented with GraphPad Prism, version 5.0 (GraphPad Software, Inc., La Jolla, CA). To determine the half maximal inhibitory concentration (IC50), and the 50% cytotoxic concentration (CC50) of 5-aza-dC, 5-aza-C, and gemcitabine, infectivity data were normalized to the data for the untreated control, plotted against log-transformed drug concentrations, and subjected to nonlinear regression in GraphPad Prism (GraphPad Software, Inc., La Jolla, CA). The MacSynergy II program was used for isobologram analysis in order to determine the nature of drug interactions between two compounds, e.g., additive, antagonistic, or synergistic (Clouser et al., 2012; Prichard and Shipman, 1990). Data were analyzed by calculating the mean ± standard deviation. Differences between groups were analyzed by either a one-way ANOVA test or by a “N-1” Chi-squared test, as indicated.

3. Results

3.1. Treatment of HBV-producing cells with 5-aza-dC, 5-aza-C, or gemcitabine virus transfer to target cells.

Viral mutagens and ribonucleotide reductase inhibitors (RNRIs) have been shown to be effective antivirals with several viruses, but have not been tested to date against HBV. HBV is difficult to study in cell culture. To determine the effect of viral mutagens on HBV transfer to permissive cells, we used a reporter system that was recently developed to look at the early stage of the HBV viral life cycle (Nishitsuji et al., 2015). The HBV/NL plasmid contains the small NanoLuc luciferase gene in place of part of the core and pol region of the HBV genome. The HBV/D plasmid expresses all HBV protein but is not packaged into virus particles. Therefore, virus producer cells (HepG2) are co-transfected with HBV/NL and the HBV/D plasmid, resulting in generating reporter virus that can only progress to pgRNA during virus transfer to HBV-susceptible cell line HepG2-NTCP. Virus transfer to permissive target cells can be measured by analyzing luciferase activity in these cells.

To determine if 5-aza-dC, 5-aza-C, or gemcitabine could inhibit HBV transfer, HepG2 cells were co-transfected with HBV/NL and HBV/D plasmids; one day later they were treated with 5-aza-dC, 5-aza-C, or gemcitabine at the concentrations shown in Figure 1. Virus was collected 5 days post-transfection and used to infect the HBV-susceptible cell line HepG2-NTCP. Virus transfer was quantified at 6 days post infection using the NL Luciferase Assay Kit (Promega). As expected, we found that virus transfer of HBV/NL virus treated with 3TC, a known RT-inhibitor, was almost completely ablated (Figure 1A). Virus produced in the presence of 5-aza-dC, 5-aza-C, or gemcitabine also showed significant and concentration-dependent reductions in virus transfer. As RNRIs can potentiate the activity of 5-aza-dC and 5-aza-C (Clouser et al., 2010; Rawson et al., 2013), producer cells were also treated with these drugs in combination with gemcitabine. This resulted in virus that had reduced degree of virus transfer compared to either drug alone, indicating potentiation.

Figure 1. Treatment of HBV-producing cells with 5-aza-dC, 5-aza-C and/or gemcitabine reduce viral infectivity. A. HBV/NL infectivity to HepG2-NTCP cells.

Figure 1.

Open in a new tab

HepG2 cells (1.4 X 106 cells per well) were plated in a 6-well plate 24 h prior to transfection. HBV/NL vector virus is produced by the co-transfection of HBV/NL and HBV/D plasmids into HepG2 cells. One day post-transfection, the HepG2 cells were treated with 3TC (10 μM), 5-aza-dC (10, 50 μM), 5-aza-C (10, 50 μM), gemcitabine (10, 50 nM), 5-aza-dC (10 μM) & gem (10 nM) or 5-aza-C (10 μM) & gem (10 nM). Virus was collected 5 days post-transfection. HepG2-NTCP cells (5.0 X 104 cells/well) were plated in a 96-well plate 24 h prior to infection. Next, HepG2-NTCP cells were infected with vector virus. At 6 days post infection, the infectivity was tested by using a luciferase assay and normalized to infected, untreated cells. B. Relative number of HepG2 cells with drug treatments. Cell proliferation was examined using the CellTiter-Glo kit from Promega according to the manufacturer’s instructions. HepG2 (50,000 cells/well) cells were plated in a 96-well plate 24 h prior to drug treatment. Cells were treated with either an individual drug or a combination of two drugs for 5 days, and then cell proliferation was assessed. Cells were treated with the equivalent volume of dimethyl sulfoxide (DMSO) for the untreated group. Data is shown with the average ± standard deviation from 3 independent replicate experiments. The number in the graph bar indicates the mean value. All drug-treated groups were compared to that of the untreated group and statistical analysis is shown. A one-way ANOVA test was used; “****” = p ≤ 0.0001; “**” = p ≤ 0.01; “*” = p ≤ 0.05. Abbreviation: gem = gemcitabine.

To exclude the possibility that the reduced expression of the NL reporter gene was caused by cytotoxicity, HepG2 cell proliferation was quantified in the presence of the drugs. Neither 5-aza-C nor gemcitabine treatment resulted in any significant cytotoxicity (Figure 1B). Although 5-aza-dC did cause significantly decreased cell proliferation, the 25% decrease in proliferation caused by 50 μM 5-aza-dC does not account for the 91% reduction in reporter expression seen at that drug concentration. These findings indicate that 5-aza-dC, 5-aza-C, and gemcitabine are able to directly inhibit HBV virus transfer.

3.2. HBV rcDNA mutation frequency is significantly increased in the presence of 5-aza-dC, 5-aza-C, or the combination of 5-aza-dC and gemcitabine.

Previous studies have shown that 5-aza-dC and 5-aza-C disrupt reverse transcription in HIV-1, inducing G-to-C and C-to-G transition mutations that lead to lethal mutagenesis, and that this can be potentiated by gemcitabine (Clouser et al., 2010; Dapp et al., 2009; Rawson et al., 2016). We thus sought to determine whether this mechanism of action also applied to HBV. As the majority of HBV reverse transcription takes place in the producer cells, we used the treated chronically infected HepAD38 cells, where expression of HBV particles is inhibited by tetracycline (Ladner et al., 1997). Production of virus was initiated by removing tetracycline at the same time that cells were treated with 5-aza-dC, 5-aza-C, gemcitabine, or the combination of azacytidines and gemcitabine. Supernatant containing viral particles was harvested 5 days later and HBV rcDNA was extracted from the supernatants and used as a template for Sanger Sequencing. We sequenced a portion of the pol/s gene (nucleotides 87–800) of rcDNA to determine if these drugs are able to increase the virus mutation frequency.

We found that 5-aza-C increased HBV rcDNA mutation frequency almost three-fold, while 5-aza-dC increased it by five-fold (Figure 2 and Supplemental Table 1). Gemcitabine, as an RNRI, did not impact the mutation frequency of HBV rcDNA, as predicted. However, the addition of gemcitabine to 5-aza-dC increased the mutation frequency to eight times that of the no-drug control, indicating that gemcitabine enhances 5-aza-dC-mediated mutagenesis. This gemcitabine-mediated enhancement in mutagenesis was not seen with 5-aza-C. As predicted, the treatment of 5-aza-dC and 5-aza-C significantly enhanced the level of G-to-C and C-to-G transition mutations (Figure 2). Interestingly, G-to-T transition mutations were also observed at an increased frequency. These results indicate that 5-aza-dC and 5-aza-C inhibit HBV replication at least in part by increasing the mutation frequency in rcDNA.

Figure 2. Significant increase in HBV rcDNA mutation frequency in the presence of either 5-aza-dC or 5-aza-C.

Figure 2.

Open in a new tab

HepAD38 cells (1.0 X 105 cells per well) were plated in a 24-well plate 24 h prior to virus-producing induction. Five days following removal of tetracycline from cultured HepAD38 cells and cell treatment with 10 nM gemcitabine, 50 μM 5-aza-dC, 200 μM 5-aza-C or the combination of 5-aza-dC/5-aza-C with gemcitabine, HBV rcDNA was purified from cell culture supernatants. A DNA product of 714 bp (HBV sequence 87–800) was amplified by PCR. After gel purification, the 714 bp product was ligated to the pGEM-T vector. Ligated DNAs introduced into E. coli by transformation, and insert containing-vectors were subjected to DNA sequencing, with 70 −100 colonies were sequenced per each treatment (see Supplemental Table 1). Sequence alignments were done by using SeqMan assembly tool in the Lasergene 7 software package (DNAStar; Madison, WI). A. Mutation frequency analysis. Mutation frequency was calculated by the number of mutations divided by the total number of bases sequenced. The mutation frequency of the untreated was 1.46 × 10−4 mutations per basepair (see Supplemental Table 1). B. Mutation spectra analysis. The spectra of mutations from each experimental group is depected by a pie chart, which shows the main mutation types and percentages observed. The size of the pie chart was normalized to the mutation frequency of untreated controls. Results are shown from 3 independent experiments. The gray asterisks and brackets associating any two bars indicate the significant difference between the experimental pairs. The statistical significance compared to the untreated control is shown above the bar with black asterisks. Significance was analyzed with the “N-1” Chi-squared test; “ns” = not significant; “****” = p ≤ 0.0001; “**” = p ≤ 0.01; “*” = p ≤ 0.05. Abbreviation: gem = gemcitabine.

3.3. 5-aza-dC, 5-aza-C, and gemcitabine inhibit HBV rcDNA synthesis with minimal cytotoxicity and demonstrate anti-HBV synergy.

To further assess the effects of 5-aza-dC, 5-aza-C, and gemcitabine on reverse transcription, rcDNA from viral particles produced from drug-treated HepAD38 cells was quantified by using qPCR. Similar to 3TC, 5-aza-dC inhibited rcDNA synthesis with minimal cytotoxicity (Figure 3A). The half maximal inhibitory concentration (IC50) of 5-aza-dC was found to be 15 μM. Inhibition of rcDNA synthesis was also observed for 5-aza-C, however, both the IC50 and 50% cytotoxic concentration (CC50) were high (180 μM and 411μM, respectively) (Figure 3B). Gemcitabine caused inhibition of rcDNA synthesis with a 47 nM IC50 (Figure 3C). Gemcitabine and 5-aza-dC or 5-aza-C have previously been observed to possess synergistic antiviral activity against HIV-1 (Clouser et al., 2010). To determine if drug synergy occurs with HBV, HepAD38 cells were treated with increasing concentrations of gemcitabine (1–100 nM) and 5-aza-dC (1–50 μM). The addition of 1nM gemcitabine to 5-aza-dC treatment did not have a significant difference on antiviral activity compared to individual 5-aza-dC treatment, while an increased inhibition of rcDNA synthesis was observed in combinations with gemcitabine concentrations over 5 nM (Figure 4A). MacSynergy II plot analysis confirmed the synergistic activity of gemcitabine and 5-aza-dC against HBV rcDNA synthesis (Figure 4B). This synergy was also observed between 5-aza-C and gemcitabine (Figure 5A and 5B). In particular, the combination of 5 nM gemcitabine with 100 μM 5-aza-dC showed significantly higher inhibition of rcDNA synthesis than that caused by the same amount of each drug individually. Moreover, cytotoxicity analysis indicated that there is no enhancement in cytotoxicity between 5-aza-dC or 5-aza-C and gemcitabine (Figure 4C, 4D, 5C and 5D). These results indicate that 5-aza-dC or 5-aza-C and gemcitabine synergistically inhibit HBV rcDNA synthesis with no enhancement in cytotoxicity.

Figure 3. 5-aza-dC, 5-aza-C and gemcitabine inhibit HBV rcDNA synthesis.

Figure 3.

Open in a new tab

HepAD38 cells (1.0 X 105 cells per well) were plated in a 24-well plate 24 h prior to virus-producing induction. Following removal of tetracycline, HepAD38 cells were treated with 3TC (1, 10, 100 μM), 5-aza-dC (0.001, 0.01, 0.1, 1, 10, 50, 100, 200 μM), 5-aza-C (10, 20, 50, 100, 150, 200, 400, 600 μM), or gemcitabine (gem) (0.1, 1, 10, 20, 50, 100, 200 nM). At 5 days post-induction of virus particle production, HBV rcDNA was purified from cell culture supernatants. The extracted rcDNA was quantified by qPCR. HBV DNA synthesis was normalized by dividing the DNA relative copy number from the drug-treated experiment by that of the untreated experiment. Cell proliferation was determined by using the CellTiter-Glo kit from Promega according to the manufacturer’s instructions. HepAD38 cells (4,500 cells per well) cells were plated in a 96-well plate 24 h prior to drug treatment. Cells were treated with 3TC (10, 100, 1000 μM), 5-aza-dC (0.1, 1, 10, 50, 100, 200, 400, 800 μM), 5-aza-C (0.1, 1, 10, 20, 50, 100, 150, 200, 400, 600 μM) or gem (0.1, 1, 10, 50, 100, 200, 800, 1000, 10000 nM) for 5 days, and cell proliferation was then assessed. Cells were treated with an equivalent volume of DMSO for the untreated (i.e., no drug) group. The data were converted to relative cell numbers by setting the value for untreated cells at 100 for each experiment and then multiplying the data for the other samples by the number used to convert the untreated cells to 100. The data represents the average ± standard deviation for 3 independent replicate experiments. To determine the half-maximal inhibitory concentration (IC50) and 50% cytotoxic concentration (CC50) of 5-aza-C, 5-aza-dC, and gemcitabine, the infectivity data were normalized to the data for the untreated control, plotted against log-transformed drug concentrations, and subjected to nonlinear regression. IC50s are indicated for each drug, with 3TC as a positive control.

Figure 4. Anti-HBV drug synergy of 5-aza-dC and gemcitabine. A. rcDNA synthesis.

Figure 4.

Open in a new tab

HepAD38 cells (1.0 X 105 cells per well) cells were plated in a 24-well plate 24 h prior to induction of virus production. Following removal of tetracycline, HepAD38 cells were treated with various concentrations of combinations of gem (1, 5, 10, 50, 100 nM) and 5-aza-dC (1, 10, 50 μM) in combination. At 5 days post-virus induction, HBV rcDNA was purified from cell culture supernatants, and the rcDNA was analyzed by qPCR. HBV DNA synthesis was normalized by dividing the relative DNA copy number of the drug-treated group to that of the untreated group. B. Isobologram analysis of drug synergy. Analysis of drug synergy was determined by using the MacSynergy II program. C. Cell proliferation analysis. HepAD38 cells (4,500 cells per well) were plated in a 96-well plate 24 h prior to drug treatment. HepAD38 cells were treated with various concentrations of gem (1, 5, 10, 50, 100 nM) and 5-aza-dC (1, 10, 50 μM) for 5 days, and cell proliferation was then assessed. DMSO-treated cells were used as an untreated control. The data was converted to relative cell numbers by setting the value for untreated cells at 100. D. Isobologram analysis of drug synergy in cell toxicity. Analysis of drug synergy was determined by using the MacSynergy II program. The results are presented as the average ± standard deviation from 3 independent experiments. Abbreviation: gem = gemcitabine.

Figure 5. Anti-HBV drug synergy of 5-aza-C and gemcitabine. A. rcDNA synthesis.

Figure 5.

Open in a new tab

HepAD38 cells (1.0 X 105 cells per well) were plated in a 24-well plate 24 h prior to induction of virus production. Following removal of tetracycline, HepAD38 cells were treated with various concentrations of gem (1, 5, 10, 50, 100 nM) and 5-aza-C (10, 100, 200 μM) in combination. At 5 days post-virus-induction, HBV rcDNA was purified from cell culture supernatants. The extracted rcDNA was quantified by qPCR, and the rcDNA was analyzed by qPCR. HBV DNA synthesis was normalized by dividing the relative DNA copy number of the drug-treated group to that of the untreated group. B. Isobologram analysis of drug synergy. Analysis of drug synergy was determined by using the MacSynergy II program. C. Cell proliferation analysis. HepAD38 cells (4,500 cells per well) were plated in a 96-well plate 24 h prior to drug treatment. HepAD38 cells were treated with various concentrations of combination of gem (1, 5, 10, 50, 100 nM) and 5-aza-dC (1, 10, 50 μM) for 5 days, and cell proliferation was then assessed. DMSO-treated cells were used as an untreated control. The data were converted to relative cell numbers by setting the value for untreated cells at 100. D. Isobologram analysis of drug synergy in cell toxicity. The results are presented as the average ± standard deviation from 3 independent experiments. Abbreviation: gem = gemcitabine.

3.4. 5-aza-dC, 5-aza-C, and gemcitabine have antiviral effects on HBV early-stage replication.

In addition to their effects on reverse transcription, the effects of 5-aza-dC, 5-aza-C, and gemcitabine on the early stages of HBV replication was determined, particularly the generation and function of cccDNA. As state above, infection of HepG2-NTCP cells using the HBV/NL reporter virus is an ex vivo model of early-stage HBV replication, since the HBV/NL reporter virus has defective pol and preC/C genes needed for reverse transcription (Nishitsuji et al., 2015). With a defective polymerase and capsid, HBV infection can progress only to the HBV pgRNA stage. Therefore, HepG2-NTCP cells were treated during HBV/NL virus replication to study the effects on HBV early-stage replication. HepG2-NTCP cells were treated with 3TC, 5-aza-dC, 5-aza-C, gemcitabine, or the drugs in combination for three days during HBV/NL replication. Six- or seven-days post-replication, NanoLuc luciferase activity in the lysate was measured using the NL Luciferase Assay Kit. 5-aza-dC, 5-aza-C, and gemcitabine were all found to be able to inhibit HBV early-stage replication, though to a lesser extent than late stages of replication (Figure 6A). For example, treatment of 100 μM 5-aza-dC resulted in 50% loss of virus replication; while treatment of 10 nM gemcitabine led to virus replication that was about 40% that of the no-drug treated group. Both 5-aza-dC and gemcitabine showed no significant toxicity to HepG2-NTCP cells under functional concentrations (Figure 6B). Although high concentrations of 5-aza-C showed strong toxicity to HepG2-NTCP cells, lower concentrations, e.g., 50 μM, can potently inhibit early-stage HBV infection (63% reduction of infectivity) with limited cytotoxic effect (26% reduction of cellular proliferation) (Figure 6B). It was also observed that synergy occurred between gemcitabine and low concentrations of 5-aza-dC (10 μM). In contrast, drug synergy was not observed between 5-aza-C (10 μM) and gemcitabine, likely due to the low 5-aza-C concentrations.

Figure 6. Antiviral activity of 5-aza-dC, 5-aza-C and/or gemcitabine on the early phase of HBV infection.

Figure 6.

Open in a new tab

HepG2-NTCP cells (5.0 X 104 cells per well) were plated in a 96-well plate 24 h prior to infection. HepG2-NTCP cells were treated with 3TC (10 or 100 μM), 5-aza-dC (10, 50, 100 or 200 μM), 5-aza-C (10, 50, 100 or 200 μM), gem (10 or 50 nM), 5-aza-dC (10 μM) & gem (10 nM) or 5-aza-C (10 μM) & gem (10 nM) for 2 h, then infected with HBV/NL vector virus in the presence of 4% PEG8000 and 2% DMSO and incubated overnight at 37o C. At 24 h post-infection, fresh media and drugs. At 3 days post-infection, media was changed again, and at 6 or 7 days post-infection, cells were washed once with PBS and cells lysed. A. Analysis of virus infectivity To analyze virus infectivity, the cell lysates were tested for Nanoluciferase activity (NL Luciferase Assay), and normalized compared to that of untreated cells. B. Cell proliferation analysis. Cell lysates was also examined for cell proliferation (CellTiter-Glo assay). Shown are the average values ± standard deviation from 3 independent experiments. The number in each bar graph represents the mean value. Drug-treated experiments were compared to untreated controls. Statistical analysis was done using a one-way ANOVA; “ns” = not significant; “****” = p≤0.0001; “***” = p≤0.001; “**” = p≤0.01; “*” = p≤0.05. Abbreviation: gem = gemcitabine.

3.5. Inhibition of HBV cccDNA transcription in the presence of 5-aza-dC.

The mechanism by which 5-aza-dC and 5-aza-C inhibit early stage HBV virus transfer was investigated by testing whether these drugs could impact cccDNA synthesis and transcription. To address this question, cccDNA in the infected HepG2-NTCP cells was quantified by using qPCR. It was observed that 50 μM 5-aza-dC led to a trend towards reduced cccDNA synthesis, which was not statistically significant (Figure 7). While 10 μM 3TC inhibited early-stage virus transfer at nearly the same level as 50 μM 5-aza-dC, it was observed to have no impact on cccDNA synthesis (Figure 6 and 7). Intriguingly, gemcitabine increased the cccDNA synthesis. Viral RNA from infected cells was quantified by using RT-qPCR with primer sets in both the nick/gap region and pre S gene. 50 μM 5-aza-dC decreased nick/gap region transcription by 43%, but did not affect pre S gene RNA synthesis (Figure 7). As expected, 3TC and gemcitabine did not affect the viral RNA synthesis in cells where HBV was transferred to via replication. It was observed that 5-aza-C did not inhibit cccDNA or RNA synthesis. These results demonstrate that 5-aza-dC can impact cccDNA synthesis and transcription, while 5-aza-C and gemcitabine were not observed to have effects on cccDNA synthesis or RNA transcription.

Figure 7. Inhibition of HBV cccDNA transcription by 5-aza-dC.

Figure 7.

Open in a new tab

HepG2-NTCP cells (5.0 X 105 cells per well) were plated in a 24-well plate 24 h prior to infection. The HepG2-NTCP cells were treated with either 10 μM 3TC, 50 μM 5-aza-dC, 50 μM 5-aza-C, 50 nM gem or untreated (DMSO only), respectively. At 2 h post-drug treatment, cells were infected by HBV/NL vector virus, and at 3 days post-infection, fresh media with drug was added. At 6 to 7 days post-infection, HepG2-NTCP cells were lysed, and nucleic acids were purified. The amount of cccDNA was quantified by qPCR using nick/gap gene primer sets (1575–1882). Viral RNA was quantified by qRT-PCR using both nick/gap gene and pre S gene (184–249) primer sets. Nucleic acids values were normalized to untreated, infected HepG2-NTCP cells. Nucleic acids from non-infected or heat-inactivated, virus-infected HepG2-NTCP cells were used as negative controls. Data is shown as the average ± standard deviation of 3 independent experiments. Statistical analysis was determined with a one-way ANOVA test; “****” = p≤0.0001; “***” = p≤0.001; “**” = p≤0.01; “*” = p≤0.05. Abbreviation: gem = gemcitabine.

3.6. 5-aza-dC and 5-aza-C do not increase the mutation frequency of cccDNA.

The formation of cccDNA from rcDNA is poorly understood. 5-aza-dC can be incorporated into DNA during production of either plus- or minus-strand DNA. Incorporation of 5-aza-dC into the plus strand DNA may lead to the destabilization of cccDNA, which would lead to decrease of RNA transcription of both the preS and nick/gap genes. However, only a reduction of nick/gap gene transcription was observed. Therefore, it was speculated that 5-aza-dC might interfere with the completion of minus stand DNA synthesis, which would result only in a decrease of nick/gap gene cccDNA synthesis and transcription. The completion of minus strand DNA synthesis includes RNA primer removal, polymerase removal, the terminal redundancy removal and DNA ligation (Guo et al., 2007). Except for DNA ligation, these processes are poorly understood (Long et al., 2017). One hypothesis is that 5-aza-dC incorporates into the nick/gap region during synthesis, which would affect transcription of the nick/gap region but not the preS gene. To test this, the nick/gap region was sequenced, as well as a partially overlapping region of the polymerase and surface envelope of cccDNA from infected HepG2-NTCP cells. Interestingly, few mutations were observed in either the nick/gap region or partial pol/s gene in the 5-aza-dC, 5-aza-C or untreated experiments, with no significant difference mutation frequencies observed (Table 1 and 2). These results suggest that while 5-aza-dC and 5-aza-C can induce mutations in rcDNA, they do not increase cccDNA mutagenesis.

Table 1.

Lack of increased mutation frequency in cccDNA pol/s gene in the presence of 5-aza-dC or 5-aza-C.

cccDNA pol/s gene
No. of mutants / cloned sequence No. of mutations / bases sequenced Mutation frequency Statistical significance (p≤0.05)
untreated 2 / 55 2/41,939 4.77 × 10−5
5-aza-dC 3 / 65 4/47,007 8.51 × 10−5 ns
5-aza-C 4 / 63 4/45,726 8.75 × 10−5 ns
Open in a new tab
a

ns = not significant

Table 2.

Lack of increased mutation frequency in cccDNA nick/gap gene in the presence of 5-aza-dC or 5-aza-C.

cccDNA nick/gap gene
No. of mutants / cloned sequence No. of mutations / bases sequenced Mutation frequency Statistical significance (p≤0.05)
untreated 2 / 47 2/14,417 1.36 × 10−4 -
5-aza-dC 0 / 45 0/12,440 0 nsa
5-aza-C 1 / 60 1/18,233 5.31 × 10−5 Ns
Open in a new tab
a

ns = not significant

4. Discussion

In 2016, the World Health Organization set a goal for global reduction of 90% in incidence and 65% in mortality for hepatitis B and C by 2030 (Hutin et al., 2018). Developing new therapeutics is therefore an important goal. Mutagens and RNRIs have been shown to have anti-HIV-1 activity through targeting of reverse transcription, which is a shared step in the lifecycle of HIV-1 and HBV. In this study, we found that the viral mutagens 5-aza-dC and 5-aza-C lead to a significant reduction in virus transfer to permissive target cells. In particular, 5-aza-dC or 5-aza-C elevated the HBV rcDNA mutation frequency, due primarily to an increase in the G-to-C transversion mutation frequency. Also, rcDNA synthesis was reduced. Intriguingly, cccDNA nick/gap region transcription was reduced by 5-aza-dC, but was found to not impact viral mutagenesis. Together, these observations demonstrate that viral mutagens are efficient for extinguishing HBV virus transfer to target cells, and supports a model in which viral mutagens can induce mutagenesis and synthesis reduction during rcDNA formation and diminish viral DNA synthesis during the conversion of rcDNA to cccDNA.

Lethal mutagenesis caused by mutagens, like 5-aza-dC and 5-aza-C, has been shown to be a promising antiviral strategy for HIV-1. After entering the cell, 5-aza-C is phosphorylated to 5-aza-CMP and then 5-aza-CDP. 5-aza-CDP can incorporate into the viral genome via one of two mechanisms (Rawson et al., 2016). The first is to incorporate into HIV-1 vRNA as 5-aza-CTP, causing C-to-G transversions. 5-aza-CDP can also be reduced to 5-aza-dCDP by ribonucleotide reductase and then phosphorylated to 5-aza-dCTP, which incorporate into viral DNA during reverse transcription, and leads to G-to-C or C-to-G transversions, depending on which strand it is incorporated into. The latter is believed to be the primary mechanism by which 5-aza-C incorporates into the HIV-1 genome. 5-aza-dC, on the other hand, exclusively incorporates into viral DNA directly after phosphorylation, also causing G-to-C and C-to-G transversions. Consistent with these findings on HIV-1, we observed significantly increased G-to-C and C-to-G mutations in HBV rcDNA treated with azacytidines, among which G-to-C is the most frequently observed mutation type. Surprisingly, a large portion of G-to-T mutations were also seen in HBV rcDNA with azacytidines treatment, which has not been reported for HIV-1. While we do not know the mechanisms for this type of mutagenesis at present, we suspect that this occurs during the incorporation of 5-aza-dCTP into viral DNA since there was an obvious reduction in the ratio of G-to-T mutations after the addition of gemcitabine (Figure 2). For example, 200 μM 5-aza-C treatment resulted in 19% G-to-T mutations in rcDNA, while the addition of 10 nM gemcitabine to it led to only 4% G-to-T mutations. We also observed that mutations occur randomly throughout the pol/s (HBV sequence 87–800) of rcDNA, with no evidence of specific mutational “hot spots” (Supplemental Data 1). This is consistent with what has been observed within the HIV-1 genome (Rawson et al., 2015).

Interestingly, 5-aza-dC was found to inhibit the transcription of cccDNA nick/gap region while 5-aza-C did not. It is possible that a higher concentration of 5-aza-C is needed to successfully inhibit cccDNA transcription than was used here, as our data suggested that 5-aza-C typically has a higher functional concentration than that of 5-aza-dC (Figure 3). However, since 100 μM 5-aza-C treatment of HepG2-NTCP cells resulted in a nearly 80% reduction in cell proliferation, we have not tested higher concentrations of 5-aza-C to date. Nevertheless, our data demonstrate for the first time that a nucleotide analog is capable of interfering with cccDNA synthesis. The conversion from rcDNA to cccDNA involves completion of both plus and minus strand DNA, the latter of which requires RNA primer removal, polymerase removal, the terminal redundancy removal, and DNA ligation (Guo et al., 2007). The mechanism for this conversion is unclear. One recent study reported that host DNA polymerase κ contributes to cccDNA formation during de novo HBV replication (Qi et al., 2016). Given the high fidelity of the host polymerase, the possibility that 5-aza-dC incorporates into the plus strand of cccDNA is therefore low. Furthermore, even if 5-aza-dC could be incorporated into the plus strand DNA, the effect would be trivial as pgRNA is transcribed from minus strand DNA. It is also possible, however, that incorporation of 5-aza-dC into plus strand cccDNA destabilizes the cccDNA (due to the aza-C base inducing conformational changes in the DNA), thus resulting in defective or degraded cccDNA. This possibility could explain the decrease of cccDNA with 5-aza-dC treatment, but does not explain the unchanging amount of preS gene RNA. Therefore, we posit that 5-aza-dC incorporates during completion of minus strand cccDNA. To date, only host DNA ligases have been reported to be utilized by hepadnaviruses for cccDNA minus strand formation (Long et al., 2017). Other involved enzymes are not known yet. This incorporation may result in either a mutated or incomplete cccDNA. Both of these outcomes can explain the decrease in cccDNA nick/gap gene RNA observed. Nevertheless, we did not observe an increase in the mutation frequency of cccDNA after treatment with 5-aza-dC. However, given the limited size of our sequencing samples, we cannot conclude that 5-aza-dC does not cause mutagenesis of cccDNA. The nick/gap region of cccDNA is small, and a larger sample size as well as deep sequencing would help increase the sensitivity of mutation detection. 5-aza-dC incorporation may also lead to defective cccDNA formation, which could help explain the decreased nick/gap cccDNA synthesis and RNA with unchanged preS RNA levels.

While 5-aza-dC and 5-aza-C are both known to be viral mutagens, their mechanisms of action are not identical. As a deoxyribonucleoside, 5-aza-dC is only able to incorporate into DNA. However, 5-aza-C is a ribonucleoside, and is incorporated into RNA. However, 5-aza-C can be reduced to 5-aza-dC by ribonucleoside reductase, and can thus be incorporated into DNA as well (Rawson et al., 2016). These differences in template specificity likely explain why 5-aza-C inhibited the synthesis and increased the mutation frequency of rcDNA exclusively while 5-aza-dC also inhibited the synthesis and transcription of cccDNA. These results imply a difference in the anti-HBV mechanisms between 5-aza-dC and 5-aza-C (Figure 8). In this model, 5-aza-dC incorporates into cccDNA minus strand nick/gap region during the conversion of rcDNA to cccDNA, resulting in formation of defective cccDNA. During rcDNA formation, 5-aza-dC incorporates into rcDNA, and leads to either chain termination or mutagenesis. In contrast, 5-aza-C interferes with gene translation of cccDNA and results in reduction of gene expression. During rcDNA formation, a majority of 5-aza-C is reduced to 5-aza-dC and then incorporated into rcDNA, with only a minority of 5-aza-C incorporating into rcDNA directly. This would explain why 5-aza-C has a much higher IC50 than that of 5-aza-dC in rcDNA synthesis. Gemcitabine was observed to inhibit rcDNA synthesis and inhibit early-stage HBV replication as well. It has been reported that the main mechanism of action of gemcitabine include masked chain termination and inducing dNTP pool imbalances in the cell (de Sousa Cavalcante and Monteiro, 2014). Given these activities, gemcitabine inhibit HBV cccDNA gene translation and cause rcDNA chain termination during reverse transcription.

Figure 8. Summary and model of observed antiviral activities of 5-aza-dC, 5-aza-C and gemcitabine against HBV. A. Drug structures.

Figure 8.

Open in a new tab

The chemical structures of 5-aza-dC divalerate, gemcitabine, and 5-aza-C are shown. The colored symbols, ● = 5-aza-dC; ■ = 5-aza-C and ▲ = gemcitabine, are indicated and refer to antiviral effects at particular steps in the HBV life cycle (see panel B. ). B. HBV life cycle and antiviral activities. The HBV life cycle is shown, with the key steps where antiviral activity of 5-aza-dC, gemcitabine and 5-aza-C are indicated (colored symbols). The numbers in the symbols refer to particular drug action targets (see panel C). C. Drug action targets. The drug action targets of 5-aza-dC, gemcitabine, and 5-aza-C in the HBV life cycle are indicated. D. Antiviral drug synergy. The observed anti-HBV drug synergy between 5-aza-dC and gemcitabine and between 5-aza-C and gemcitabine are indicated.

Consistent with HIV-1, anti-HBV drug synergy between 5-aza-dC or 5-aza-C and gemcitabine was observed (Figures 4 and 5) (Clouser et al., 2010). According to the synergistic analysis of mutagens and RNRIs on HIV-1 replication, it is thought that this synergy is due to induction of dNTP pool imbalances by RNRIs, which promotes the incorporation of mutagens. The results in our study are consistent with this model, as 5-aza-dC or 5-aza-C and gemcitabine acted together in synergy for inhibiting rcDNA synthesis. Gemcitabine was also observed to promote the mutagenesis caused by 5-aza-dC, but not 5-aza-C. This is likely due to 5-aza-C being primarily incorporated as the reduced form; thus, inhibiting reduction with gemcitabine prevents incorporation and mutagenesis. This would also help explain why a lower mutation frequency of rcDNA was observed with the combined treatment of 5-aza-C (200μM) and gemcitabine (10nM) compared to individual treatment (Figure 2 and Supplemental Table 1). Similarly, 5-aza-dC and gemcitabine exhibited synergistic activity in the inhibition of early-stage HBV replication, while 5-aza-C and gemcitabine did not. This is likely due to the lower functional concentration of 5-aza-C used.

Overall, our findings provide the first demonstration of the anti-HBV activity of viral mutagens and RNRIs. We found that the elevation of the HBV mutation rate can extinguish the virus transfer to target cells. Additionally, the anti-HBV synergy between mutagens and RNRIs should help to expand the application of both types of drugs in antiviral therapy. Notably, we propose a model in which viral mutagens like 5-aza-dC can induce mutagenesis and reduce rcDNA formation, as well as diminish viral DNA synthesis during the conversion of rcDNA to cccDNA. Taken together, these findings lay the foundation for future studies directed at studies of HBV DNA synthesis.

Supplementary Material

Supplemental Figure 1

Supplemental Figure 1. Location of mutations in the pol/s of rcDNA in the presence of 5-aza-dC treatment. HepAD38 cells (1.0 × 105 cells per well) were plated in a 24-well plate 24 h prior to induction of virus production. Five days following removal of tetracycline from cultured HepAD38 cells and cell treatment with 50 μM 5-aza-dC, HBV rcDNA was purified from cell culture supernatants. A portion of the pol/s gene (HBV sequence 87-800) was analyzed by DNA sequence by amplifying a 714 bp product by PCR, ligating to a pGEM-T vector, and transforming E. coli. Recombinant plasmid DNAs were purified and sequenced, with alignments being done by using the SeqMan assembler of the Lasergene 7 software package (DNAStar; Madison, WI). Sequencing results are from 3 independent experiments. Mutations are shown above the sequence. Individual mutations are represented as colored dots, as indicated.

Supplemental Table 1

Supplemental Table 1. Significant increase in HBV rcDNA mutation frequency in the presence of either 5-aza-dC or 5-aza-C.

Supplemental Figure 1 legend

Highlights.

  • Viral mutagens can diminish HBV replication

  • G-to-C transversion mutations predominated

  • Viral DNA synthesis was dramatically reduced

  • Dual antiviral mechanism impacts viral replication

Acknowledgments

Support for these studies was provided by NIH R01 GM105876. We thank Dr. Daniel D. Loeb for sharing with us the HepG2 and HepAD38 cell line, Dr. Haitao Guo for the kind gift of the HepG2-NTCP cell line, and Dr. Kunitada Shimotohno for pUC1.2xHBV/NL and pUCxHBV-D plasmid DNAs.

List of abbreviations

5-aza-C

5-azacytidine

5-aza-dC

decitabine

AML

acute myeloid leukemia

cccDNA

covalently closed circular DNA

HBV

hepatitis B virus

HIV-1

human immunodeficiency virus type 1

pgRNA

pre-genomic RNA

rcDNA

relaxed circular DNA

RT

reverse transcriptase

RNRI

ribonucleotide reductase inhibitors

References

  1. Ashburn TT, Thor KB, 2004. Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3, 673–683. [DOI] [PubMed] [Google Scholar]
  2. Bouchard J, Walker MC, Leclerc JM, Lapointe N, Beaulieu R, Thibodeau L, 1990. 5-azacytidine and 5-azadeoxycytidine inhibit human immunodeficiency virus type 1 replication in vitro. Antimicrob Agents Chemother 34, 206–209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Choi E, Mallareddy JR, Lu D, Kolluru S, 2018. Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 4, FSO338. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Clouser CL, Bonnac L, Mansky LM, Patterson SE, 2014. Characterization of permeability, stability and anti-HIV-1 activity of decitabine and gemcitabine divalerate prodrugs. Antivir Chem Chemother 23, 223–230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Clouser CL, Chauhan J, Bess MA, van Oploo JL, Zhou D, Dimick-Gray S, Mansky LM, Patterson SE, 2012. Anti-HIV-1 activity of resveratrol derivatives and synergistic inhibition of HIV-1 by the combination of resveratrol and decitabine. Bioorg Med Chem Lett 22, 6642–6646. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Clouser CL, Holtz CM, Mullett M, Crankshaw DL, Briggs JE, Chauhan J, VanHoutan IM, Patterson SE, Mansky LM, 2011. Analysis of the ex vivo and in vivo antiretroviral activity of gemcitabine. PLoS One 6, e15840. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Clouser CL, Patterson SE, Mansky LM, 2010. Exploiting drug repositioning for discovery of a novel HIV combination therapy. J Virol 84, 9301–9309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dapp MJ, Clouser CL, Patterson S, Mansky LM, 2009. 5-Azacytidine can induce lethal mutagenesis in human immunodeficiency virus type 1. J Virol 83, 11950–11958. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. de Avila AI, Gallego I, Soria ME, Gregori J, Quer J, Esteban JI, Rice CM, Domingo E, Perales C, 2016. Lethal Mutagenesis of Hepatitis C Virus Induced by Favipiravir. PLoS One 11, e0164691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. de Sousa Cavalcante L, Monteiro G, 2014. Gemcitabine: metabolism and molecular mechanisms of action, sensitivity and chemoresistance in pancreatic cancer. Eur J Pharmacol 741, 8–16. [DOI] [PubMed] [Google Scholar]
  11. Domingo E, Sheldon J, Perales C, 2012. Viral quasispecies evolution. Microbiol Mol Biol Rev 76, 159–216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Graci JD, Harki DA, Korneeva VS, Edathil JP, Too K, Franco D, Smidansky ED, Paul AV, Peterson BR, Brown DM, Loakes D, Cameron CE, 2007. Lethal mutagenesis of poliovirus mediated by a mutagenic pyrimidine analogue. J Virol 81, 11256–11266. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Greggs WM 3rd, Clouser CL, Patterson SE, Mansky LM, 2012. Discovery of drugs that possess activity against feline leukemia virus. J Gen Virol 93, 900–905. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Guo H, Jiang D, Zhou T, Cuconati A, Block TM, Guo JT, 2007. Characterization of the intracellular deproteinized relaxed circular DNA of hepatitis B virus: an intermediate of covalently closed circular DNA formation. J Virol 81, 12472–12484. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hutin Y, Nasrullah M, Easterbrook P, Dongmo Nguimfack B, Burrone E, Averhoff F, Bulterys M, 2018. Access to treatment for hepatitis B virus infection-Worldwide, 2016. Am J Transplant 18, 2595–2598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Jiang YC, Feng H, Lin YC, Guo XR, 2016. New strategies against drug resistance to herpes simplex virus. Int J Oral Sci 8, 1–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ladner SK, Otto MJ, Barker CS, Zaifert K, Wang GH, Guo JT, Seeger C, King RW, 1997. Inducible expression of human hepatitis B virus (HBV) in stably transfected hepatoblastoma cells: a novel system for screening potential inhibitors of HBV replication. Antimicrob Agents Chemother 41, 1715–1720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Long Q, Yan R, Hu J, Cai D, Mitra B, Kim ES, Marchetti A, Zhang H, Wang S, Liu Y, Huang A, Guo H, 2017. The role of host DNA ligases in hepadnavirus covalently closed circular DNA formation. PLoS Pathog 13, e1006784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lucifora J, Protzer U, 2016. Attacking hepatitis B virus cccDNA--The holy grail to hepatitis B cure. J Hepatol 64, S41–S48. [DOI] [PubMed] [Google Scholar]
  20. Moreno H, Tejero H, de la Torre JC, Domingo E, Martin V, 2012. Mutagenesis-mediated virus extinction: virus-dependent effect of viral load on sensitivity to lethal defection. PLoS One 7, e32550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ni Y, Lempp FA, Mehrle S, Nkongolo S, Kaufman C, Falth M, Stindt J, Koniger C, Nassal M, Kubitz R, Sultmann H, Urban S, 2014. Hepatitis B and D viruses exploit sodium taurocholate co-transporting polypeptide for species-specific entry into hepatocytes. Gastroenterology 146, 1070–1083. [DOI] [PubMed] [Google Scholar]
  22. Nishitsuji H, Ujino S, Shimizu Y, Harada K, Zhang J, Sugiyama M, Mizokami M, Shimotohno K, 2015. Novel reporter system to monitor early stages of the hepatitis B virus life cycle. Cancer Sci 106, 1616–1624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pas SD, Fries E, De Man RA, Osterhaus AD, Niesters HG, 2000. Development of a quantitative real-time detection assay for hepatitis B virus DNA and comparison with two commercial assays. J Clin Microbiol 38, 2897–2901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Prichard MN, Shipman C Jr., 1990. A three-dimensional model to analyze drug-drug interactions. Antiviral research 14, 181–205. [DOI] [PubMed] [Google Scholar]
  25. Qi Y, Gao Z, Xu G, Peng B, Liu C, Yan H, Yao Q, Sun G, Liu Y, Tang D, Song Z, He W, Sun Y, Guo JT, Li W, 2016. DNA Polymerase kappa Is a Key Cellular Factor for the Formation of Covalently Closed Circular DNA of Hepatitis B Virus. PLoS Pathog 12, e1005893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Rawson JM, Daly MB, Xie J, Clouser CL, Landman SR, Reilly CS, Bonnac L, Kim B, Patterson SE, Mansky LM, 2016. 5-Azacytidine Enhances the Mutagenesis of HIV-1 by Reduction to 5-Aza-2’-Deoxycytidine. Antimicrob Agents Chemother 60, 2318–2325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Rawson JM, Heineman RH, Beach LB, Martin JL, Schnettler EK, Dapp MJ, Patterson SE, Mansky LM, 2013. 5,6-Dihydro-5-aza-2’-deoxycytidine potentiates the anti-HIV-1 activity of ribonucleotide reductase inhibitors. Bioorg Med Chem 21, 7222–7228. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Rawson JM, Landman SR, Reilly CS, Bonnac L, Patterson SE, Mansky LM, 2015. Lack of mutational hot spots during decitabine-mediated HIV-1 mutagenesis. Antimicrob Agents Chemother 59, 6834–6843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Reina J, Reina N, 2017. [Favipiravir, a new concept of antiviral drug against influenza viruses]. Rev Esp Quimioter 30, 79–83. [PubMed] [Google Scholar]
  30. Tang L, Zhao Q, Wu S, Cheng J, Chang J, Guo JT, 2017. The current status and future directions of hepatitis B antiviral drug discovery. Expert Opin Drug Discov 12, 5–15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Todt D, Walter S, Brown RJ, Steinmann E, 2016. Mutagenic Effects of Ribavirin on Hepatitis E Virus-Viral Extinction versus Selection of Fitness-Enhancing Mutations. Viruses 8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Yan R, Zhang Y, Cai D, Liu Y, Cuconati A, Guo H, 2015. Spinoculation Enhances HBV Infection in NTCP-Reconstituted Hepatocytes. PLoS One 10, e0129889. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplemental Figure 1

Supplemental Figure 1. Location of mutations in the pol/s of rcDNA in the presence of 5-aza-dC treatment. HepAD38 cells (1.0 × 105 cells per well) were plated in a 24-well plate 24 h prior to induction of virus production. Five days following removal of tetracycline from cultured HepAD38 cells and cell treatment with 50 μM 5-aza-dC, HBV rcDNA was purified from cell culture supernatants. A portion of the pol/s gene (HBV sequence 87-800) was analyzed by DNA sequence by amplifying a 714 bp product by PCR, ligating to a pGEM-T vector, and transforming E. coli. Recombinant plasmid DNAs were purified and sequenced, with alignments being done by using the SeqMan assembler of the Lasergene 7 software package (DNAStar; Madison, WI). Sequencing results are from 3 independent experiments. Mutations are shown above the sequence. Individual mutations are represented as colored dots, as indicated.

NIHMS1695728-supplement-Supplemental_Figure_1.pdf (36.4KB, pdf)
Supplemental Table 1

Supplemental Table 1. Significant increase in HBV rcDNA mutation frequency in the presence of either 5-aza-dC or 5-aza-C.

NIHMS1695728-supplement-Supplemental_Table_1.pdf (82.2KB, pdf)
Supplemental Figure 1 legend
NIHMS1695728-supplement-Supplemental_Figure_1_legend.pdf (54.6KB, pdf)

RESOURCES