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Journal of Virology, February 2006, p. 1405-1413, Vol. 80, No. 3
0022-538X/06/$08.00+0 doi:10.1128/JVI.80.3.1405-1413.2006
Zhensheng Zhang,
Jin Woo Kim,
Ying Huang, and
T. Jake Liang*
Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
Received 2 September 2005/ Accepted 8 November 2005
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We have previously demonstrated that the proteasome complex is a cellular target of HBX (16, 17) and that this interaction is functionally important in the pleiotropic effect of HBX (37, 38). Two subunits of the 26S proteasome complex, PSMA7 and PSMC1, were identified as putative targets of HBX by using a yeast two-hybrid system. This interaction is specific using an in vitro binding assay, comigration in sucrose gradient, and coimmunoprecipitation (16, 37). Functional assay showed that HBX could lead to the inhibition of peptidase and proteinase activities of the proteasome complex in tissue culture (16). The transactivating activity of HBX was specifically inhibited by proteasome-specific inhibitors, such as MG132 and lactacystin, in a dose-dependent manner, whereas calpain protease inhibitor ALLM has no effect. Because proteasome plays a crucial role in diverse cellular functions ranging from cell differentiation, cell cycle control, signal transduction, stress response, transcriptional activation, DNA repair, apoptosis, and antigen presentation, the interaction between HBX and the proteasome complex may represent an important pathway for the biological functions of HBX.
In the woodchuck model, we demonstrated that X-deficient mutants of woodchuck hepatitis virus (WHV) are not completely defective, behaving like attenuated viruses (38). Our experiments also suggested that the function of HBX in HBV replication may be medicated through a proteasome-dependent pathway (36). In cells infected with either the recombinant adenovirus-HBV or baculovirus-WHV, the replication of the wild-type virus was not affected, while the replication of X-minus virus of either HBV or WHV was enhanced and restored to the wild-type level by proteasome inhibitors.
To further understand the role of HBX in the viral life cycle and the pathogenesis of HBV, we studied the effects of HBX on proteasome activities in vivo and the global gene expression profiles by microarray analysis in a transgenic mouse model expressing the HBX gene. In this model, the HBX expression is developmentally regulated by the mouse major urinary protein (MUP) promoter in the liver (15). We here demonstrate that the proteasome activities were inhibited in the HBX mice and an unrelated cellular protease complex, the Tricon protease, was activated at the same time, suggesting a compensatory mechanism of the cellular proteolysis pathways. Microarray analysis revealed that that a broad spectrum of genes was altered in the HBX mouse livers. Functional clustering showed that a number of transcription factors, cell growth regulators, proteolysis components, and detoxification enzymes were significantly affected in HBX mice.
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Reagents and proteasome inhibitors. Proteasome peptidase substrates Sue-Leu-Leu-Val-Tyr-amino-4-methylcoumarin (AMC) (LLVY), Boc-Leu-Arg-Arg-AMC (LRR), and Z-Leu-Leu-Glu-ßNa (LLE) were obtained from BACHEM Bioscience Inc. (Torrance, CA). Proteasome-specific inhibitors MG132 and lactacystin were obtained from BIOMOL Research Laboratoroies (Plymouth Meeting, PA). Tricorn protease peptide substrate H-Ala-Ala-Phe-AMC (AAF) was purchased from BACHEM Bioscience Inc. (Torrance, CA).
RNA preparations and Northern blot analysis. Total RNA from the liver of the transgenic mouse was prepared by the guanidium isothiocyanate-acid-phenol method (ULTRASPEC RNA Isolation Kit; BIOTECX Laboratories, Houston, TX), partially purified by two ethanol precipitation, and stored precipitated at 80°C until use. For Northern blot analysis, total RNA was analyzed by 1% formaldehyde agarose gel electrophoresis and hybridized with a 32P-labeled HBV-specific probe.
Analysis of proteasome and Tricorn protease activities. The proteasome complexes from livers of both transgenic mice and wild-type controls were extracted and purified as previously described (16). The peptidase activities of the proteasome complex were measured using three kinds of fluorogenic peptide substrates as described previously (16). In brief, 3 µg of the proteasome preparation was incubated with 0.1 mM LLVY, LRR, or LLE in a 50-µl total volume of reaction buffer (20 mM Tris-HCl [pH 7.5], 5 mM MgCl2, 1 mM dithiothreitol, 1 mM ATP) at 37°C for 20 min. The reactions were stopped by adding 1 ml of 1% sodium dodecyl sulfate. The resulting fluorescence was measured with a spectrofluorometer (Packard Instruments, Downers Grove, IL). The Tricorn protease activity was determined using synthesized AAF as a substrate (13). For activity gel analysis, partially purified proteasome was electrophoresed on a 4% native acrylamide gel in 90 mM Tris-borate-5 mM MgCl2-1 mM ATP-0.5 mM dithiothreitol-0.1 mM EDTA. After electrophoresis, the gel was incubated with 0.2 mM LLVY at 37°C for 15 min and visualized with a UV transilluminator. The bands representing 26S and 20S proteasomes were photographed and quantitated by using ImageQuant software (Molecular Dynamics).
cDNA microarray hybridization and data processing. The indirect labeling method was used for labeling the cDNA with fluorescence dye Cy3 or Cy5 in the experiment. Briefly, 25 µg of total RNA was reverse transcribed to cDNA, which was then used as the template for coupling with fluorescence dyes. RNA from six wild-type mice was pooled as one sample and labeled with Cy3, whereas RNA from HBX mice was labeled individually with Cy5. Then, Cy5-labeled sample was mixed with age-matched Cy3-labeled pooled control sample and purified for cDNA microarray hybridization. Five or six HBX transgenic mice from each time point were used in the experiment. As an internal control for the microarray analysis, RNA from control mice at each time point was labeled with Cy3 or Cy5 and then combined as a probe for hybridization.
cDNA microarrays were purchased from the National Cancer Institute microarray facility (Frederick, MD). It contains 9,800 cDNA clones. The chips were hybridized with the above-labeled probes at 60°C overnight and washed in graded SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) buffers. Then, the chips were scanned with a GenePix 4000 microarray scanner (Axon Instruments, Union City, CA). Each spot was converted to a numerical ratio of Cy5 to Cy3 based on the intensity of the fluorescence. Using Genepix 4.0 software, a TIFF file (image of the hybridized cDNA spots on the chip) and a GPR file (Genepix analysis of the relative intensity of each spot) were created and uploaded to our database maintained by the Center for Information Technology at NIH for further analysis.
Data analysis and statistics. In our experiment, we have observed that variations of the ratios of Cy5/Cy3 intensity in the self-hybridized internal controls, which represent the intrinsic errors of the hybridization, could influence the final results of analysis if not corrected. This raised the question that using a cutoff ratio without a normalization against the internal control could potentially eliminate the genes of interest and include those of little value (19, 20). To address this issue, we adopted a computational system that would allow us to dissect the changes in a statistical manner, namely, by comparing the average ratios of each spot from a number of samples with that of its corresponding control. The BRB ArrayTools (version 3.01) developed by G. Simon and A. Lam (Biometric Research Branch, National Cancer Institute, NIH) was used for the analysis. The class comparison tool used the F test to examine the number of genes that were differentially expressed in the livers of HBX transgenic and wild-type mice. The analysis was done on all the genes on the chips that survived the basic screening. Average ratios of Cy5 over Cy3 intensity from five or six mice at each time point were compared with those of the paired internal controls. To further reduce the variability, only genes within ratios between 0.8 and 1.25 in internal control chips and with a P of <0.001 between the HBX transgenic and wild-type mice were deemed significant and used for further analysis. Genes that passed the above test in the HBX mice were then grouped together based on their functional characteristics and plotted with the hierarchical clustering tool embedded in the software.
Quantitative real-time PCR analysis. To validate the results of microarray analysis, a few genes that showed significant changes, including insulin-like growth factor-binding protein 1 (IGFBP-1), interferon consensus binding protein 1, and serine protease inhibitor 1, were selected for further real-time reverse transcription (RT)-PCR TaqMan analysis using the ABI Prism 7700 Sequence Detector System (PE Applied Biosystems, Foster City, CA). Briefly, cDNA was generated using 200 ng total RNA in a 20-µl linear RT reaction with the First-Strand cDNA Synthesis System for Quantitative RT-PCR Kit (Marligen Biosciences, Ljamsville, MD) as templates. TaqMan probes and primers for the genes of interest were purchased from PE Applied Biosystems, and the manufacturer's manual was followed. Standard curves for each individual target amplicon were constructed using a common mouse cDNA. All PCR assays were performed in duplicate, and results are represented by the mean values for five or six mice. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a housekeeping gene against which all samples were normalized. All three genes analyzed were consistent with the changes of microarray results.
For TaqMan real-time PCR analysis of IGFBP-1 in the woodchuck liver, IGFBP-1 primers and probe were custom designed and synthesized as described above. Since the sequence of the woodchuck IGFBP-1 gene is not available from the data bank, primer and probe sequences were selected from the conserved regions of both human and mouse IGFBP-1 cDNA and examined with API Primer Express software for validity in TaqMan PCR. RT-PCR of woodchuck liver RNA showed a correctly amplified woodchuck IGFBP-1 cDNA fragment. The respective of sequences were as follows: forward primer, 5'-TACCTGCCAAACTGCAACAAG; reverse primer, 5'-GGTAGACGCACCAGCAGAGT; probe, 5'-TTATCACAGCAGACAGTGTGA.
The expression of insulin-like growth factor 1 (IGF-1) was quantified by real-time PCR in both the mouse and woodchuck livers as described above. Mouse IGF-1 primers and probe purchased from PE Applied Biosystems worked well in both the mouse and woodchuck samples.
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FIG. 1. HBX expression in the livers of transgenic mice. Total RNAs were isolated from livers of HBX transgenic mice at various ages as indicated and subjected to Northern blot analysis (10 µg total RNA per lane). The blot was then stripped and reprobed with GAPDH as an internal loading control.
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FIG. 2. Inhibition of hepatic proteasome activities in HBX transgenic mice. For determination of the peptidase activities of the hepatic proteasomes, three peptidase substrates (LLVY, LRR, and LLE) were used to determine the proteasome activities from the livers of both transgenic mice and the wild-type controls (WT). A total of 3 µg of purified proteasome complexes was used for each reaction. Data shown are the mean values of triplicate determinations based on the percentage of the activity in the transgenic animal over that of age-matched wild-type controls. Standard errors of the mean (SEM) are shown as error bars. To determine the Tricorn protease activities, 3 µg of purified cell lysate from the livers of both transgenic mice and wild-type controls was assayed with the AAF substrate. The results are the means of three independent determinations with the SEM. Asterisks indicate differences with statistical significance (*, P < 0.05; **, P < 0.01) between the HBX and WT mice by using Student's t test.
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FIG. 3. Analysis of proteasome activity by activity gel assay. For the activity gel assay, 10 µg of a partially purified proteasome complex from the livers of both transgenic mice and wild-type controls (WT) was separated on a 4.0% native polyacrylamide electrophoresis gel. After electrophoresis, the gels were incubated with LLVY for 15 min at 37°C. Representative gels are shown at the top, and the means of the relative intensities of three independent experiments are shown at the bottom with standard errors of the mean. Asterisks indicate differences with statistical significance (*, P < 0.05) between the HBX and WT mice by using Student's t test.
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FIG. 4. Enzymatic analysis of the proteasome complex. To analyze the kinetics of the protease activities of the proteasome complex, the activities of the proteasome complex from the livers of both transgenic mice and wild-type controls (WT) were tested at various doses of peptidase substrates. Data shown are representative of those from the livers of mice at the age of week 1. Three peptidase substrates (LLVY, LRR, and LLE) were analyzed, and only LLVY was shown. Results are representative of three independent experiments.
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FIG. 5. Global gene expression in the livers of HBX transgenic mice. (A) The number of genes that changed significantly (P < 0.001 compared with control) in HBX transgenic mice increased with age after birth. There were 97 genes at week 1, which increased to 236 at week 3 and 424 at week 8 after birth. The majority of these genes overlapped with earlier time points. (B) Hierarchical clustering of the 424 significantly changed genes selected from the 8-week-old mice. Genes were divided into two subgroups as up- or down-regulation. The figure shows a clear trend of gradual change in the direction of up- or down-regulated genes during the course of development. The time after birth is indicated as week 1, 3, and 8, with 0 as the control. Each row represents a single gene, and each column represents one sample. Green, down-regulation; red, up-regulation. The scale is plotted from 1/4 to 4.
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FIG. 6. Hierarchical clustering of gene expression in HBX transgenic mouse livers. (A) Changes of transcriptional factors in HBX transgenic mouse livers. A total of 30 genes that were significantly altered at 8 weeks after birth belong to this group. (B) Genes related to protein degradation. A total of 14 genes that were significantly altered fall into this group, with 11 genes up-regulated and 3 genes down-regulated. The genes are presented in the same way as in Fig. 5.
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In SAGE-based analysis of the transcriptional profiles on normal primary human hepatocytes expressing HBX protein by transient transfection, Wu et al. observed that the up-regulated genes fell into three categories, including genes encoding ribosomal protein, transcription factors with the zinc finger motif, multiple proteasome subunits, ubiquitin, and ubiquitin-associated proteins (33). Some of these changes showed a pattern similar to that found in our transgenic mouse model expressing the HBX protein, although the genes with significant changes are different. This difference is probably a result of disparate experimental systems (33, 34). Our model is probably more physiologically relevant because it is an in vivo model. The changes in these gene groups relevant to HBX functions provide a valuable clue to understanding the complicated functions of this elusive viral protein.
HBX protein has been implicated in the hepatocarcinogenesis of both the HBX transgenic mouse model and human livers with chronic hepatitis B virus infection, but the mechanism has not been fully elucidated. In our microarray analysis, we identified a significant down-regulation of IGFBP-1 in the livers of HBX transgenic mice. The change was further validated by quantitative TaqMan real-time PCR analysis in two HBX transgenic mouse models (Fig. 7A). IGFBP-1 is produced mainly in the liver and regulates the biological functions of the IGF (1). It has been demonstrated that IGF plays an important role in liver cancer development by enhancing cell growth and tumor transformation (1). This evidence indicates that IGFBP-1 may function as a negative modulator by neutralizing the effect of IGF in tumorigenesis. It was found that the overexpression of IGFBP-1 in transgenic mice inhibits hepatic neoplasia (22). Reduced expression of IGFBP-1 was also detected in various human cancers such as hepatocelluar carcinoma and prostate cancer (14, 21, 29). Therefore, the down-regulation of IGFBP-1 in HBX transgenic mouse livers may contribute to the carcinogenic potential of HBX.
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FIG. 7. Quantitative real-time PCR analysis of IGFBP-1 (A) and IGF-1 (B) expression in HBX transgenic livers. Gene expression levels of IGFBP-1 and IGF-1 were quantified by TaqMan RT-PCR. Liver samples from 1- and 8-week-old FVB/n mice (background for the MUP-HBX transgenic mice) and 8-week-old Cd1 mice (background for the second line of HBX transgenic mice) were analyzed as controls. HBX transgenic mice samples were compared with the corresponding control mice with the same background. Five or six mice were analyzed in each group, and the values are averaged from the individual mice. The data (means ± standard deviations) are displayed as fold changes of transgenic over control mice. Asterisks indicate differences with statistical significance (**, P < 0.01) between the HBX and wild-type (wt) mice by using Student's t test.
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To further study the biological relevance of IGFBP-1 down-regulation by HBX in HBV infection, we examined the expression of IGFBP-1 during the acute phase of WHV infection in a woodchuck model. As shown in Fig. 8, the level of IGFBP-1 expression decreased significantly following WHV infection and was maintained at a low level until week 16, when WHV DNA became undetectable, and then rebounded to a higher level above the basal level. Similar to the MUP-HBX transgenic mice, the hepatic expression of IGF-1 also demonstrated an increase during the acute infection (Fig. 8C). However, this increase appeared to occur later than the decrease of IGFBP-1, suggesting a secondary change in the response to reduced IGFBP-1 expression. All three animals tested exhibited a similar trend. The correlation of IGFBP-1 down-regulation with WHV infection further supports the effect of HBX on IGFBP-1 expression in the context of viral infection and suggests an important role of IGFBP-1 in the pathogenesis of HBV infection.
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FIG. 8. Expression of IGFBP-1 and IGF-1 in woodchuck liver infected with WHV. Naïve adult woodchucks were infected with WHV as described previously (38). Blood and liver biopsy samples were collected at various time points before and after the virus inoculation. A representative course of WHV infection with serologic markers and liver function tests is shown (arrow indicates time of infection) (A). Quantitative real-time PCR analysis of the expression for IGFBP-1 (B) and IGF-1 (C) was performed using total RNA isolated from the liver biopsy samples of three separates woodchucks (numbered as 6032, 6044, and 6062) at various time points during acute WHV infection as indicated in the figure. The values of IGFBP-1 and IGF-1 expression were normalized to the level of GAPDH.
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Our study provided evidence for the inhibitory effect of HBX on the proteasome activities in vivo, which may be one of the mechanisms that lead to the profound changes in the global gene expression patterns of hepatocytes. These perturbations occur in a manner that is consistent with the pleiotropic functions of HBX and render a potential molecular mechanism for the biological role of HBX in HBV infection and hepatocellular carcinoma development.
This work was supported in part by the Intramural Research Program of the NIH, National Institute of Diabetes and Digestive and Kidney Diseases.
Both Z.H. and Z.Z. made equal contributions to the manuscript. ![]()
Present address: Department of Surgery, University of Pittsburgh, BST W1502, 200 Lothrop Street, Pittsburgh, PA 15213. ![]()
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B via oxidative stress. Mol. Cell. Biol. 21:7721-7730.
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