The present invention provides a cell line capable producing infectious hepatitis C virus 1a (HCV 1a) particles in culture. Disclosed are compositions and methods for an HCV 1a (clone H77) transfected immortal human hepatocyte (IHH) capable of generating infectious HCV 1a virus particles in culture. Also disclosed are methods of using the cell line, or HCV 1a virus particles derived from said cell line, to screen for potential therapeutic agents which interfere with HCV 1a virus propagation to treat hepatic disease.

Description of the Invention

BACKGROUND OF THE INVENTION

1. Field of the Invention

This invention relates generally to compositions and methods of propagating hepatitis C viral genomes and infectious particles. Specifically, the invention is directed to an immortalized human hepatic cell line comprising the hepatitis C viral 1a genome, (IHH/HCV 1a) which is capable of replicating the hepatitis C viral 1a (HCV 1a) genotype and producing fully infectious HCV 1a virus particles.

2. Description of the Related Art

According to the American Liver Foundation, over 300,000 Americans are hospitalized each year for cirrhosis of the liver. The primary causes of cirrhosis are alcohol abuse and chronic hepatitis C(HCV). To date, approximately 3.9 million Americans suffer from hepatitis C. The most important feature of HCV infection is the development of chronic hepatitis in a significant number of infected individuals and the potential for disease progression to cirrhosis and hepatocellular carcinoma (6, 7, 11, 27). At present, the only approved therapy for chronic HCV infection is interferon (IFN)-.alpha. with or without ribavirin (9, 21), but this therapy fails to clear HCV from a significant number of patients (22). A number of HCV genomes have been cloned, and sequence divergence indicates several genotypes as well as a series of subtypes for this virus (28). In the United States, HCV genotypes 1a and 1b are predominant in patients with chronic hepatitis C (31). Progress in the understanding HCV biology has been hampered due to the lack of an efficient cell culture system for virus growth. The establishment of self-replicating HCV full-length genomic replicons from genotypes 1a and 1b in human hepatoma (Huh-7) cells has provided an important tool for the study of HCV replication mechanisms (3, 10, 23). Although some groups have reported the generation of infectious virus from transfection of genomic RNA of HCV genotype 2a into Huh-7 (5, 15, 29, 32), the generation of infectious HCV genotype 1a has not been successful to date, and therefore a long felt need exists.

The inventors and others have previously shown that HCV core protein transcriptionally regulates a number of cellular genes (26). The inventors have also previously described the generation of immortalized human hepatocytes (IHH) by transfection of the HCV core genomic region from genotype 1a (2, 25). IHH exhibit a weak level of HCV core protein expression, albumin secretion, glucose phosphatase activity, and absence of smooth muscle actin. IHH also displayed focal cytoplasmic and membrane staining for carcinoembryonic antigen (CEA), biliary glycoprotein (BGP1/CEACAM1) and nonspecific cross-reacting antigen (NCA/CEACAM6), and expression of hepato-biliary transport marker genes (MRP, LST1 and NTCP). Together, these results suggested that IHH are well differentiated. HCV core protein selectively degrades STAT1, reduces phosphorylated STAT1 (P-STAT1) accumulation in the nucleus in a proteasome-dependent manner, and impairs IFN-.alpha.-induced signal transduction via suppressor of cytokine signaling-3 expression (1, 4, 16). HCV core protein is competent to partially rescue growth of a genetically engineered influenza A virus lacking its own IFN antagonist (4). The core protein can modulate interferon regulatory factor (IRF), Jak-STAT and inducible nitric oxide synthetase (iNOS) pathways, and suggest mechanisms by which core could affect HCV persistence and pathogenesis (20). Since HCV core protein transcriptionally regulates several cellular genes involved in cell growth, apoptosis and defense mechanism, the inventors hypothesize that IHH may set the stage for HCV genome replication and assembly.

The inventors have sought to address the long felt need of providing a cell line permissible for HCV 1a replication and generation of infections virus particles. A cell line with this capability will be invaluable to researchers not only by providing easy access to HCV 1a infectious virus particles, but to identify HCV mediators and their pathways. In addition, it will be invaluable as a tool to screen new therapeutic strategies or potential pharmacological agents which interfere with the propagation of HCV and resulting diseases caused by the virus.

SUMMARY OF THE INVENTION

Progress in the understanding hepatitis C virus (HCV) biology has remained challenging due to the lack of an efficient cell culture system for virus growth. Therefore, the inventors examined HCV core protein mediated immortalized human hepatocytes (IHH) for support of HCV 1a genomic replication, infectious particle generation, and propagation. In vitro transcribed HCV full-length RNA from genotype 1a (clone H77) was electroporated into IHH. Viral RNA replication was evident by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of cellular RNA isolated from the HCV 1a genome-transfected IHH (IHH/HCV 1a). HCV full-length genome transfected IHH also displayed viral protein expression as indicated by indirect immunofluorescence. In contrast, cells transfected with polymerase-defective HCV (H77/GND) RNA as a negative control did not exhibit expression of viral genome. Immunogold labeling and transmission electronic microscopy demonstrated localization of the viral E1 protein in the rough endoplasmic reticulum of RNA transfected IHH. Virus-like particles of .about.50 nm in the cytoplasm were also observed. Naive IHH, inoculated with culture medium from HCV full-length genome transfected cells, displayed NS5a protein expression in a dilution dependent manner, which was reduced upon prior incubation of the inoculums with HCV infected patient serum. Based on NS5a positive immunofluorescence, the inventors determined .about.4.5.times.10.sup.4-1.times.10.sup.5 fluorescent focus units (ffu)/ml of cell culture medium, removed from cultures of IHH transfected with H77 full-length RNA. A similar level of virus growth was observed by transfection of RNA from HCV genotype 2a (JFH1) into IHH. Taken together, our results suggest that IHH support HCV genome replication and virus assembly.

Therefore, an object of this invention is an immortal human hepatocyte comprising a full length HCV 1a genome (IHH/HCV 1a) capable of sustaining HCV 1a replication and generation of infectious HCV 1a virus particles.

In another embodiment, an object of this invention is an infectious HCV 1a virus particle produced by IHH/HCV 1a in culture.

In another embodiment, an object of this invention is a method of using IHH/HCV 1a to study HCV 1a biology and to screen for potential therapeutic agents which interfere with any stage of HCV propagation.

In another embodiment, IHH/HCV 1a derived HCV 1a virus particles may be used to study infectivity and screen therapeutic agents which may interfere with HCV 1a infection.

It is envisioned that the instant IHH/HCV 1a will be propagated in vitro, frozen for convenient storage, and typically manipulated as a conventional cell line.

It is also envisioned that IHH/HCV 1a, its prodigy, or derivatives, in whole or in part, maybe be used separately, or combined with other biological systems to screen for therapeutic agents which interfere with pathways of viral replication, assembly, and infection, for development of pharmaceutical compositions for the treatment of hepatic disease.

DETAILED DESCRIPTION OF THE INVENTION

HCV replication is believed to proceed as follows. HCV RNA is translated directly to a precursor viral polypeptide. This precursor polypeptide is then proteolytically cleaved to form individual proteins. A replicase complex amplifies viral RNA genome via a minus strand intermediate. Plus strand RNA progeny are then packaged into virus particles which acquire their envelope by budding into the lumen of the endoplasmic reticulum. HCV particles are exported via the constitutive secretory pathway. Based on this working principle, the inventors have shown that IHH support HCV genome replication and protein expression from genotype 1a.

Transmission electron microscopy and immunogold labeling, using a monoclonal antibody directed against HCV E1 glycoprotein, demonstrated the localization of this antigen to the rough endoplasmic reticulum, and also the formation of virus-like particles. The inventors transferred culture medium, previously in contact with IHH/HCV 1a, to naive IHH cultures and subsequently detected HCV infection in these cells by RT-PCR and indirect immunofluorescence.

The inventors observed JFH1 replication and virus assembly in IHH. The infectious unit of JFH1 replicated in IHH similarly to JFH1 grown in Huh-7 cells or its derivatives. The inventors also observed similar levels of genomic copy of H77 or JFH1, in transfected IHH culture supernatant, and in fluorescence focus units. The inventors did not purify virus particles for negative staining due to the relatively low infectious units present in the culture medium.

Three different groups of investigators have reported different densities of HCV 2a particles. Zhong et al. (32) observed peak infectivity from an apparent density of 1.105 gm/ml, Wakita et al. (29) observed peak infectivity at a density of .about.1.15 gm/ml, and Lidenbach et al. (15) observed a broad distribution of virus infectivity over a range of 1.01 to 1.12 gm/ml. A similar finding suggesting a variation of buoyant density of cell culture grown HCV 2a between 1.06 and 1.16 gm/ml was reported by Cai et al. (5). HCV is known to associate with serum immunoglobulin and lipoproteins (24). The inventors found HCV infectivity within a density range of 1.09 to 1.12 sucrose gradient, which did not correlate with the highest copy number of virus genomic RNA (data not shown).

Recently, HCV production was reported from a HCV-ribozyme construct of genotype 1a (clone H77) in Huh-7 cells, although infectivity of virus was not demonstrated (8). Virus genome replication and assembly are multi-step processes, and are influenced by the intracellular milieu. Inhibition of host cell growth and induction of cytokines, such as interferons, may have an impact on prevention of virus replication (3). The inventors provide evidence for HCV replication and assembly of infectious genotype 1a in IHH. Others have not been successful in generating infectious HCV 1a from cells in culture.

The inventors speculate that the cellular defense mechanism against HCV infection is attenuated or compromised in IHH. The inventors realize the importance of determining these factors including mechanisms for growth of HCV in IHH, as well as identification of critical control points in the HCV life-cycle. The inventors currently have studies in progress to determine cellular and viral factors influencing virus growth, such as serial passage requirements for adaptation in IHH, mutations at specific sites of the HCV genome, and selection of cell populations for attenuation protective mechanisms. The inventors realize the importance of further characterizing biophysical properties of cell culture grown HCV 1a, including infectivity in appropriate animal models.

Therefore, the invention is drawn to (1) an immortal human hepatocyte cell line comprising a full length HCV 1a genome, capable of producing infectious HCV 1a virus particles, (2) methods of producing said cell line (3) methods of producing infectious HCV 1a virus particles, (4) methods of using said cell line for evaluating potential therapeutic agents for the prevention of HCV 1a propagation, (5) methods of using cell culture derived HCV 1a for evaluating potential therapeutic agents for the prevention infection.

Sequence identity or percent identity is intended to mean the percentage of same residues between two sequences. The reference sequence is Hepatitis C Viral Genome 1a accession number NC.sub.--004102 which is derived from AF009606. In all of the sequence comparisons, the two sequences being compared are aligned using the Clustal method (Higgins et al, Cabios 8:189-191, 1992) of multiple sequence alignment in the Lasergene biocomputing software (DNASTAR, INC, Madison, Wis.). In this method, multiple alignments are carried out in a progressive manner, in which larger and larger alignment groups are assembled using similarity scores calculated from a series of pairwise alignments. Optimal sequence alignments are obtained by finding the maximum alignment score, which is the average of all scores between the separate residues in the alignment, determined from a residue weight table representing the probability of a given amino acid change occurring in two related proteins over a given evolutionary interval. Penalties for opening and lengthening gaps in the alignment contribute to the score. The default parameters used with this program are as follows: gap penalty for multiple alignment=10; gap length penalty for multiple alignment=10; k-tuple value in pairwise alignment=1; gap penalty in pairwise alignment=3; window value in pairwise alignment=5; diagonals saved in pairwise alignment=5. The residue weight table used for the alignment program is PAM250 (Dayhoff et al., in Atlas of Protein Sequence and Structure, Dayhoff, Ed., NBRF, Washington, Vol. 5, suppl. 3, p. 345, 1978).

Table 1 (see Original Patent) shows the calculations of identity for comparisons of HCV derived from H77.

Preferred embodiments of the invention are described in the following examples. Other embodiments within the scope of the claims herein will be apparent to one skilled in the art from consideration of the specification or practice of the invention as disclosed herein. It is intended that the specification, together with the examples, be considered exemplary only, with the scope and spirit of the invention being indicated by the claims, which follow the examples.

EXAMPLE 1

Replication of HCV Genome and Virus Protein Expression

The object of the invention is a cell line to provide HCV 1a genotype replication and generation of infectious virus particles. The inventors have previously described the generation of immortalized human hepatocytes (IHH) by transfection of HCV core genomic region from genotype 1a, as well as the conditions and requirements for maintaining IHH in culture (2, 25) which are herein incorporated by reference. Full-length RNAs from HCV genotype 1a (clone H77, GenBank Accession number NC.sub.--004102, SEQ ID NO:1) has also previously described (3, 13, 14) and are herein incorporated by reference. Restriction enzyme Xba I and T7 RNA polymerase were obtained from Invitrogen and Promega, (Madison, Wis.) respectively and used according to the supplier's protocol. The individual elements of the inventors' methodology is generally well known and described in detail in numerous laboratory protocols, one of which is Molecular Cloning 2.sup.nd edition, (1989) Sambrook, J., Fritsch, E. F. and Maniatis, J., Cold Spring Harbor.

Clone H77 contains a 5' untranslated region (5' UTR) coding sequence and 3' UTR, which is suggested to be necessary for replication (14, 30). In vitro transcribed full-length HCV 1a RNA from clone H77 was used for transfection of IHH which was performed by electroporation. Polymerase defective H77/GND RNA was similarly used as a negative control. H77 cDNA was first linearized by digestion with Xba I, and the linearized product purified by agarose gel electrophoresis. Purified H77 cDNA was then transcribed in vitro using T7 RNA polymerase. In vitro transcribed RNA (1-2 .mu.g) was introduced into 5.times.10.sup.6 IHH by electroporation (950 .mu.F and 270 V) using a BioRad Gene pulse Xcell system (Hercules, Calif.). The transfected cells were plated on collagen coated plastic dishes, and maintained using standard cell culture techniques to allow for HCV replication.

Total cellular RNA was extracted 5 days post transfection. For detection of HCV genome, total cellular RNA and random hexamer were used for cDNA synthesis with a SuperScript III first-strand synthesis system (Invitrogen), according to the supplier's protocol. PCR amplification was performed with cDNA as a template, using sense (5'-ACCCGCTGAATTCCTGGAGA-3') (SEQ ID NO:2) and antisense (5'-CACGGTCTTCTAGACCTCCC-3') (SEQ ID NO:3) primers from 5' UTR, at 94.degree. C. for 30s, annealing at 55.degree. C. for 60s, and extension at 72.degree. C. for 90s. GPDH was used as an internal control, with specific primers (17). RT-PCR analyses suggested amplification of 120 bp sequence from the 5' UTR (FIG. 1, panel A, see Original Patent). In contrast, cells transfected with H77/GND RNA did not exhibit the presence of HCV genomic sequence. To rule out the integration of H77 plasmid DNA into IHH, the genomic DNA from cell lines were isolated and examined for HCV genome by PCR. These results suggested the absence of HCV sequence, indicating HCV genomic RNA replication in the cytoplasm of IHH (data not shown). Filtered culture supernatant was also treated with RNaseA prior to isolation of viral RNA. RT-PCR was performed for NS5A region (17) and the inventors have observed amplification of specific RNA sequence.

Western blot analysis was performed to analyze the expression of core and NS3 proteins in control and experimental cells using specific antibodies. An equal amount of proteins from whole cell lysates in sample buffer were separated by SDS-PAGE. Proteins were transferred onto nitrocellulose, incubated with specific antibodies, and detected by chemiluminescence (Amersham, Piscataway, N.J.). HCV core protein was detected by a specific rabbit antiserum, and NS3 was detected by a specific mouse monoclonal antibody (Virogen, Watertown, Mass.). Blots were stripped and re-probed using a mouse monoclonal antibody to actin (Oncogene Science, Cambridge, Mass.). IHH supporting HCV genome replication displayed the presence of core (.about.21 kDa) and NS3 (.about.63 kDa) proteins (FIG. 1, panels B and C, see Original Patent). On the other hand, IHH transfected with H77/GND RNA did not show a detectable level of core or NS3 proteins. A weak level of core protein was detected in this set of IHH for immortalization by HCV core protein (FIG. 1, panel B, see Original Patent). IHH transfected with HCV full-length RNA were passaged at 4 or 5 day intervals. HCV RNA and protein expression were detected up to 12 days of cell culture, and discontinued for the lack of growth after 2 weeks.

To further examine intracellular expression of HCV protein, IHH transfected with H77 RNA were fixed with 3.7% formaldehyde and incubated at room temperature for 1 h with monoclonal antibodies to NS5a (Biogenesis, Kingstone, N.H.). Cells were washed three times with PBS and stained with anti-mouse Ig conjugated with Alexa 568 (Molecular Probes, Eugene, Oreg.), and mounted for fluorescence microscopy. Primary antibodies and secondary antibody-fluorochrome conjugates were titrated for use of optimum dilutions where there was no background fluorescence. The inventors have observed cytoplasmic expression of NS5a (FIG. 2, panel A, see Original Patent) in 60% IHH after 5 days of transfection. HCV genotype 2a (clone JFH1) has been shown to grow in Huh-7 cells or its derivatives (5, 15, 29, 32). In vitro transcribed RNA from clone JFH1 was used for transfection of IHH to determine if the immortalized hepatocyte cell line supports HCV growth. Intracellular localization of NS3 protein from JFH1 RNA transfected IHH was detected by immunofluorescence (FIG. 2, panel C, see Original Patent). The inventors have also used Huh-7.5 cells transfected with JFH1 RNA as a positive control (29) and observed NS3 expression by indirect immunofluorescence (data not shown). On the other hand, IHH similarly transfected with RNA from H77/GND or JFH1/GND clone did not display virus protein expression by immunofluorescence (FIG. 2, panels B and D, see Original Patent).

Claim 1 of 7 Claims

1. A cultured cell comprising, a) a human hepatocyte comprising HCV 1a cDNA, b) whereby the HCV 1a cDNA consists of HCV 1a cDNA encoding the HCV 1a core protein, c) whereby the cell is immortal, d) further comprising a full length hepatitis C virus 1a genome, e) whereby the full length hepatitis C virus 1a genome consists of RNA, f) whereby the cell is permissive for replication of the RNA genome and generation of infective hepatitis C virus 1a virus particles.

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