The present invention provides an adenovirus serotype 30 (Ad30) fiber amino acid sequence. The present invention also provides polynucleotides and expression vectors encoding an Ad30 fiber and viral particles and cells containing such expression vectors. The present invention further provides methods of treating genetic diseases or cancers in a mammal using the polynucleotides, polypeptides, expression vectors, viral particles and cells of the present invention.

Description of the Invention

SUMMARY OF THE INVENTION

The present invention provides adenovirus serotype 30 (Ad30) fiber proteins, such as the polypeptide encoded by SEQ ID NO:1. The present invention also provides a polynucleotide encoding such Ad30 fiber protein, such as the polynucleotide encoded by SEQ ID NO:12. As used herein, the term "fiber protein" includes variants or biologically active or inactive fragments of this polypeptide. A "variant" of the polypeptide is a fiber protein that is not completely identical to a native fiber protein. A variant fiber protein can be obtained by altering the amino acid sequence by insertion, deletion or substitution of one or more amino acid. The amino acid sequence of the protein is modified, for example by substitution, to create a polypeptide having substantially the same or improved qualities as compared to the native polypeptide. The substitution may be a conserved substitution. A "conserved substitution" is a substitution of an amino acid with another amino acid having a similar side chain. A conserved substitution would be a substitution with an amino acid that makes the smallest change possible in the charge of the amino acid or size of the side chain of the amino acid (alternatively, in the size, charge or kind of chemical group within the side chain) such that the overall peptide retains its spacial conformation but has altered biological activity. For example, common conserved changes might be Asp to Glu, Asn or Gln; His to Lys, Arg or Phe; Asn to Gln, Asp or Glu and Ser to Cys, Thr or Gly. Alanine is commonly used to substitute for other amino acids. The 20 essential amino acids can be grouped as follows: alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan and methionine having nonpolar side chains; glycine, serine, threonine, cystine, tyrosine, asparagine and glutamine having uncharged polar side chains; aspartate and glutamate having acidic side chains; and lysine, arginine, and histidine having basic side chains. Stryer, L. Biochemistry (2d edition) W. H. Freeman and Co. San Francisco (1981), p. 14-15; Lehninger, A. Biochemistry (2d ed., 1975), p. 73-75.

It is known that variant polypeptides can be obtained based on substituting certain amino acids for other amino acids in the polypeptide structure in order to modify or improve biological activity. For example, through substitution of alternative amino acids, small conformational changes may be conferred upon a polypeptide that result in increased bioactivity. Alternatively, amino acid substitutions in certain polypeptides may be used to provide residues that may then be linked to other molecules to provide peptide-molecule conjugates that retain sufficient properties of the starting polypeptide to be useful for other purposes.

One can use the hydropathic index of amino acids in conferring interactive biological function on a polypeptide, wherein it is found that certain amino acids may be substituted for other amino acids having similar hydropathic indices and still retain a similar biological activity. Alternatively, substitution of like amino acids may be made on the basis of hydrophilicity, particularly where the biological function desired in the polypeptide to be generated in intended for use in immunological embodiments. The greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity. U.S. Pat. No. 4,554,101. Accordingly, it is noted that substitutions can be made based on the hydrophilicity assigned to each amino acid. In using either the hydrophilicity index or hydropathic index, which assigns values to each amino acid, it is preferred to conduct substitutions of amino acids where these values are .+-.2, with .+-.1 being particularly preferred, and those with in .+-.0.5 being the most preferred substitutions.

The variant amino acid molecule of the present invention has at least 50%, at least about 80%, or even at least about 90% but less than 100%, contiguous amino acid sequence homology or identity to the amino acid sequence of a corresponding native nucleic acid molecule or polypeptide.

The amino acid sequence of the variant fiber protein corresponds essentially to the native fiber protein's amino acid sequence. As used herein "corresponds essentially to" refers to a polypeptide sequence that will elicit a biological response substantially the same as the response generated by native fiber protein. Such a response may be at least 60% of the level generated by native fiber protein, and may even be at least 80% of the level generated by native fiber protein.

A variant of the invention may include amino acid residues not present in the corresponding native fiber protein, or may include deletions relative to the corresponding native fiber protein. A variant may also be a truncated "fragment" as compared to the corresponding native fiber protein, i.e., only a portion of a full-length protein. For, example, the polypeptide of the present invention may contain one or more of the three regions of an Ad30 fiber, i.e., a tail region (such as amino acids 1-45 of SEQ ID NO:1), a shaft region (such as amino acids 46-188 of SEQ ID NO:1) or a knob region (such as amino acids 189-371 of SEQ ID NO:1). Fiber protein variants also include peptides having at least one D-amino acid.

The variant fiber protein of the present invention may be expressed from an isolated DNA sequence encoding the variant fiber protein. The amino acid changes from the native to the variant fiber protein are achieved by changing the codons of the corresponding nucleic acid sequence. "Recombinant" is defined as a peptide or nucleic acid produced by the processes of genetic engineering. It should be noted that it is well-known in the art that, due to the redundancy in the genetic code, individual nucleotides can be readily exchanged in a codon, and still result in an identical amino acid sequence. The terms "protein," "peptide" and "polypeptide" are used interchangeably herein.

The Ad30 fiber protein as described above may be operably linked to an amino acid sequence for a therapeutic agent. An amino acid or nucleic acid is "operably linked" when it is placed into a functional relationship with another amino acid or nucleic acid sequence. For example, DNA a pre-sequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a pre-protein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, "operably linked" means that the amino acid or nucleic acid sequences being linked are contiguous, and, in the case of a secretory leader in DNA, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.

As used herein, the term "therapeutic agent" refers to any agent or material that has a beneficial effect on the mammalian recipient. Thus, "therapeutic agent" embraces both therapeutic and prophylactic molecules having nucleic acid or protein components. The mammalian recipient may have a condition that is amenable to gene replacement therapy. As used herein, "gene replacement therapy" refers to administration to the recipient of exogenous genetic material encoding a therapeutic agent and subsequent expression of the administered genetic material in situ. Thus, the phrase "condition amenable to gene replacement therapy" embraces conditions such as genetic diseases (i.e., a disease condition that is attributable to one or more gene defects), acquired pathologies (i.e., a pathological condition that is not attributable to an inborn defect), cancers and prophylactic processes (i.e., prevention of a disease or of an undesired medical condition).

According to one embodiment, the mammalian recipient has a genetic disease and the exogenous genetic material comprises a heterologous gene encoding a therapeutic agent for treating the disease. In yet another embodiment, the mammalian recipient has an acquired pathology and the exogenous genetic material comprises a heterologous gene encoding a therapeutic agent for treating the pathology. According to another embodiment, the patient has a cancer and the exogenous genetic material comprises a heterologous gene encoding an anti-neoplastic agent. In yet another embodiment the patient has an undesired medical condition and the exogenous genetic material comprises a heterologous gene encoding a therapeutic agent for treating the condition.

The present invention also provides expression vectors containing an Ad backbone nucleic acid sequence and polynucleotide encoding a chimeric Ad fiber polypeptide comprising a tail region, a shaft region and a knob region, wherein at least one of these regions comprises an Ad30 tail region, an Ad30 shaft region or an Ad30 knob region. The expression vector may also contain a nucleotide sequence encoding a therapeutic agent.

The present invention also provides viral particles and mammalian cells containing the expression vector described above. The cell may be human, and may be from prostate, brain, breast, lung, spleen, kidney, heart, or liver. Alternatively, the cell may be a neuroprgenitor or stem cell.

The present invention also provides a method of transducing cells lacking CAR comprising contacting the cells with an expression vector or virus particle containing Ad backbone nucleic acid sequence and polynucleotide encoding a chimeric Ad fiber polypeptide comprising a tail region, a shaft region and a knob region, wherein at least one of these regions comprises an Ad30 tail region, an Ad30 shaft region or an Ad30 knob region. The cell may be a neuronal or epithelial cell, such as a human umbilical vein epithelial cell (HUVEC), or may be a tumor cell.

The present invention further provides a method of treating a genetic disease or cancer in a mammal by administering a polynucleotide, polypeptide, expression vector, or cell described above. The genetic disease or cancer may be one of the diseases listed in Tables 1-3 (see Original Patent).

In general, the invention relates to polypeptides that can be used as a therapeutic agent, and polynucleotides, expression vectors, virus particles and genetically engineered cells, and the use of them, for expressing the therapeutic agent. In particular, the invention may be used as a method for gene therapy that is capable of both localized and systemic delivery of a therapeutically effective dose of the therapeutic agent.

According to one aspect of the invention, a cell expression system for expressing a therapeutic agent in a mammalian recipient is provided. The expression system (also referred to herein as a "genetically modified cell") comprises a cell and an expression vector for expressing the therapeutic agent. The expression vector further includes a promoter for controlling transcription of the heterologous gene. The promoter may be an inducible promoter. The expression system is suitable for administration to the mammalian recipient. The expression system may comprises a plurality of non-immortalized genetically modified cells, each cell containing at least one recombinant gene encoding at least one therapeutic agent.

The cell expression system can be formed ex vivo or in vivo. To form the expression system ex vivo, one or more isolated cells are transduced with a virus or transfected with a nucleic acid or plasmid in vitro. The transduced or transfected cells are thereafter expanded in culture and thereafter administered to the mammalian recipient for delivery of the therapeutic agent in situ. The genetically modified cell may be an autologous cell, i.e., the cell is isolated from the mammalian recipient. The genetically modified cell(s) are administered to the recipient by, for example, implanting the cell(s) or a graft (or capsule) including a plurality of the cells into a cell-compatible site of the recipient.

According to yet another aspect of the invention, a method for treating a mammalian recipient in vivo is provided. The method includes introducing an expression vector for expressing a heterologous gene product into a cell of the patient in situ. To form the expression system in vivo, an expression vector for expressing the therapeutic agent is introduced in vivo into target location of the mammalian recipient by, for example, intraperitoneal injection.

The expression vector for expressing the heterologous gene may include an inducible promoter for controlling transcription of the heterologous gene product. Accordingly, delivery of the therapeutic agent in situ is controlled by exposing the cell in situ to conditions that induce transcription of the heterologous gene.

According to yet another embodiment, a pharmaceutical composition is disclosed. The pharmaceutical composition comprises a plurality of the above-described genetically modified cells or polypeptides and a pharmaceutically acceptable carrier. The pharmaceutical composition may be for treating a condition amenable to gene replacement therapy and the exogenous genetic material comprises a heterologous gene encoding a therapeutic agent for treating the condition. The pharmaceutical composition may contain an amount of genetically modified cells or polypeptides sufficient to deliver a therapeutically effective dose of the therapeutic agent to the patient. Exemplary conditions amenable to gene replacement therapy are described below.

According to another aspect of the invention, a method for forming the above-described pharmaceutical composition is provided. The method includes introducing an expression vector for expressing a heterologous gene product into a cell to form a genetically modified cell and placing the genetically modified cell in a pharmaceutically acceptable carrier.

According to still another aspect of the invention, a cell graft is disclosed. The graft comprises a plurality of genetically modified cells attached to a support that is suitable for implantation into the mammalian recipient. The support may be formed of a natural or synthetic material.

According to still another aspect of the invention, an encapsulated cell expression system is disclosed. The encapsulated expression system comprises a plurality of genetically modified cells contained within a capsule that is suitable for implantation into the mammalian recipient. The capsule may be formed of a natural or synthetic material.

DETAILED DESCRIPTION OF THE INVENTION

Adenovirus has been shown to transduce a large number of cells including lung epithelial cells, muscle cell, endothelial cell, fibroblasts and neuronal cells. However, the efficiency is variable due to the different levels of CAR expression. Inefficient gene delivery into skeletal muscles, vascular smooth muscle, some endothelial cells and certain tumorogenic cells is a result of low expression of CAR.

Adenovirus tropism is the result of specific binding of the virus to the cell to be infected, by means of a cellular receptor. The viral C-terminal portion of fiber or "knob" is responsible for specificity of receptor recognition by the virus. Human coxsackievirus and adenovirus receptor (CAR) interacts with the fiber knob of several adenoviral serotypes (2, 4, 5, 9, 12, 15, 17, 19, 31, 41) (Bergelson, et al., (1997) Science 275:1320-1323; Roelvink, et al., (1998) J. Virol. 72:7909-7915; Freimuth, etal., (1999) J. Virol. 73(2):1392-1398; Wang, et al., (1999) J. Virol 73(3):2559-2562; Zabner, et al., (1999) J. Virol 73(10):8689-8695), indicating that CAR is the likely cellular receptor for the serotypes mentioned. The mouse homologue of CAR (mCAR) has also been isolated and shows an ability to mediate adenoviral infection (Tomko, et al., (1997) Proc.Natl.Acad.Sci. U.S.A. 94:3352-3356; Bergelson, et al., (1997) J. Virol. 72:415-419). The majority of adenoviral serotypes have been shown to interact with CAR; however, there are some exceptions namely, Ad3 (Stevenson, et al., (1995). J. Virol. 69:2850-2857) and Ad35 (Shayakhmetov, et al., (2000) J. Virol. 74(6):2567-2583) that do not. It has been demonstrated that some D-serotype viruses utilize CAR 2. Ad30 was not among the serotypes tested.

In order to improve the utility of recombinant adenoviral vectors by increasing the therapeutic index, a capsid exhibiting a higher efficiency of transduction was sought. Such a capsid could then be used in conjunction with a gutted adenoviral genome to promote long term transgene expression with minimal immune response.

In an effort to find a capsid exhibiting a higher efficiency of transduction, numerous adenoviral serotypes were screened for infection efficiency of primary fetal rat CNS cultures and human umbilical vein epithelial cells (HUVECs) (Chillon, et al., (1999) J. Virol. 73(3):2537-2540). It was determined that Subgroup D viruses exhibit enhanced gene transfer to both culture types. It was thought that this increase in efficiency when compared to Ad5 was due to differences between the viruses in their fiber protein amino acid sequence or length. Ad30 fibers are approximately one-third shorter than those of Ad5. The importance of this difference could be attributed to the two-step process of adenoviral infection. The shorter length of the Ad30 fibers may allow higher affinity interactions with cellular a.sub.v integrins to occur. It was reasoned that such tropism could be passed to another adenovirus by replacement of its endogenous fiber sequence with that of the Ad30 fiber sequence. In order to demonstrate that the Ad30 fiber protein was responsible for the increase in CNS and HUVEC tropism, it was decided to replace the endogenous fiber sequence of Ad5 with that of Ad30. The ability of the Ad5 genome to tolerate such changes has been demonstrated by several groups (Shayakhmetov, et al., (2000) J. Virol. 74(6):2567-2583; Crompton, et al., (1994) J. Gen. Virol. 75:133-139; Gall, et al., (1996) J. Virol. 70:2116-2123; Gonzalez, et al., (1999) Gene Ther. 6(3):314-320; Krasnykh, et al., (1996) J. Virol. 70(10):6839-6846; Krasnykh, et al., (1998) J. Virol. 72:1844-1852; Legrand, et al., (1999) J. Virol. 73(2):907-919; Michael, et al., (1995) Gene Ther. 2:660-668; Miyazawa, et al., (1999) J. Virol. 73(7):6056-6065; Stevenson, et al., (1997) J. Virol. 71:4782-4790; Wickham, et al., (1995) Gene Ther. 2:750-756.).

Almost no information was available on Ad30 prior to the present work. There was no sequence data to be obtained and it was unknown if Ad30 like other adenoviral serotypes (2, 4, 5, 9, 12, 15, 17, 19, 31, 37?, 41) (Bergelson, et al., (1997) Science 275:1320-1323; Roelvink, et al., (1998) J. Virol. 72:7909-7915; 10 Freimuth, et al., (1999) J. Virol. 73(2):1392-1398; Wang, et al., (1999) J. Virol. 73(3):2559-2562; Zabner, et al., (1999) J. Virol. 73(10):8689-8695) could bind CAR. Ad30 was propagated and viral particles were purified. Once purified particles were available, genomic DNA could be isolated and sequence data generated.

The fiber gene was sequenced using degenerate primers based on other D-serotype fiber sequences followed by specific primers as the Ad30 sequence data was generated. It was then possible to create a chimeric fiber protein consisting of AdS tail and Ad30 shaft/knob by overlapping PCR. This chimeric fiber protein was cloned into the Ad5 backbone replacing the endogenous Ad5 fiber by means of homologous recombination in E coli. A chimeric virus was thus developed that also expressed the reporter gene eGFP. Once propagated this virus was compared to normal Ad5 expressing eGFP in infection studies of cultured cells. It was found that the chimeric virus was less efficient in transduction of CAR positive cells but more efficient in transducing HUVECs.

The Ad30 Fiber Gene

To further the study of adenoviral serotypes tropic for CNS cells (Chillon, et al., (1999) J. Virol. 73(3):2537-2540), the Ad30 fiber gene needed to be cloned.

Ad30 genomic DNA was isolated and the fiber gene was amplified by means of degenerate primers based on known D serotype fiber sequences. As sequence data was acquired further specific primers were designed and employed until the entire nucleic acid sequence of the Ad30 fiber gene was known (SEQ ID NO:12). The amino acid sequence of Ad30 (SEQ ID NO:1) is shown in FIG. 1 (see Original Patent).

Once the sequence was available it become possible to compare its amino acid sequence with that of other sequenced fibers. Ad30 fiber is quite similar to Ad9 (SEQ ID NO:2) and Ad17 (SEQ ID NO:3), is less similar to Ad3 (SEQ ID NO:4), and is the least similar to Ad5 (SEQ ID NO:5), as shown in FIG. 1. This comparison was important in light of recent discoveries regarding the amino acid residues present in the Ad5 knob that are important for binding to CAR (Roelvink, et al., (1999) Science 286:1568-1571; Kirby, et al., (2000) J. Virol. 74(6):2804-2813).

It was found that Ad30 shares 25% overall identity of amino acid residues with Ad5 in the fiber protein. When analyzed according to regions within the fiber protein 59%, 11% and 48% identity is seen in the regions of tail, shaft and knob respectively. The 11% identity in the shaft region is due primarily to the difference in shaft length between the two fibers. Ad30 shaft is less than one-half the length of that of Ad5. Of those residues that have been shown to be critical for CAR binding two out of four are conserved in Ad30 fiber. Of those amino acid residues that have an effect on CAR binding none are conserved. These differences are illustrated in FIG. 2 (see Original Patent).

Chimeric Fiber

It was previously demonstrated that wild-type Ad30 exhibited improved tropism for vascular (endothelial) and neuronal cells, when compared to recombinant Ad5-based vectors. To show that Ad30 fiber could be responsible for this difference, a chimeric virus, Ad5RSVeGFPf30, was generated by means of homologous recombination in BJ5183 cells (Anderson, et al., (2000) Gene Ther. 7(12):1034-1038).

A chimeric fiber gene was created by overlapping PCR. The Ad5 tail was amplified, as were the A30 shaft and knob. These products were then combined in the second round of PCR amplification to yield a chimeric fiber gene. This gene was cloned into the Ad5 backbone in place of the endogenous Ad5 fiber as depicted in FIG. 3 (see Original Patent). The plasmid containing the chimeric Ad5f30 genome was subjected to sequence analysis to be certain that the chimeric fiber gene was correctly cloned. Western blot analysis of both viruses indicated that Ad5f30 indeed had a shorter fiber corresponding to the appropriate size (FIG. 4 (see Original Patent)). This plasmid was then linearized by restriction digest and transfected into HEK293 cells to generate virus as previously described (Anderson, et al., (2000) Gene Ther. 7(12):1034-1038).

Ad5f30 generated CPE much slower than AdS (45 hrs. vs. 30 hrs.) and the total particles isolated for Ad5f30 was .about.3 fold less than that for Ad5. To compare the number of infectious units of the two viruses two experiments were undertaken. First, plaque assay on HEK293 cells infected with either virus and incubated over several days was performed. Using this method the titer of Ad5f30 was 2.5' 10.sup.9 pfu/ml and Ad5 was 2' 10.sup.9 pfu/ml. To circumvent fiber-dependent titers, titers were performed with viral-CaPi co-precipitants.

To test if the delayed growth properties of Ad30 and Ad5f30 could be attributed to reduced infection efficiency, the two viruses were compared in A549 and HeLa cells. Both cell types were infected with equal particle numbers of the two viruses. It was found that Ad5 was more efficient in infecting A549 and HeLa cells than the chimeric vector, Ad5f30. A549 cells and HeLa cells were incubated in the presence of 5000 particles per cell of each virus for 1 hour at 37.degree. C. Viral particles were then removed, the cells were washed and then incubated an additional 24 hrs. at 37.degree. C. FACS analysis indicated that Ad5RSVeGFP infected 93% and 95% of A549 and HeLa cells respectively (FIG. 5a. (see Original Patent)). Ad5RSVeGFPf30 infected only 33% and 29% of A549 and HeLa cells respectively (FIG. 5a.).

To be certain that fiber was responsible for the differences in infection efficiencies observed and not a difference in viral particle infectivity, both adenoviral vectors were precipitated with calcium phosphate (CaPi) (Fasbender, et al., (1998) J. Clin.Invest. 102(1):184-193). Such precipitation of adenoviral vectors has been shown to ameliorate fiber dependent cell entry (Fasbender, et al., (1998) J. Clin.Invest. 102(1):184-193). After A549 and HeLa cells were incubated with Ad5:CaPi and Ad5f30:CaPi coprecipitates for 30 min at 37.degree., Ad5 infected 95% of A549 and HeLa cells (FIG. 5b. (see Original Patent)). Ad5f30 infected 85% and 88% of A549 and HeLa cells respectively (FIG. 5b.). These results demonstrate that the chimeric fiber of Ad5f30 is responsible for the difference in tropism initially seen between Ad5 and Ad5f30 as both viruses were shown to be nearly equal in infectivity once the requirement for the Ad5 fiber was removed. The difference in infection efficiencies without CaPi precipitation of the two viruses for A549 and HeLa cells suggested that Ad5f30 infected via a different pathway than that used by Ad5.

Ad5 has been shown to infect cells via CAR (Bergelson, et al., (1997) Science 275:1320-1323; Roelvink, et al., (1998) J. Virol. 72:7909-7915; Freimuth, et al., (1999) J. Virol. 73(2):1392-1398; Wang, et al., (1999) J. Virol. 73(3):2559-2562; Zabner, et al., (1999) J. Virol. 73(10):8689-8695). To assess the potential use of the CAR receptor by both viruses, 3T3 and CHO cells were used, as both cell types have been shown to express little if any CAR (Tomko, et al., (1997) Proc.Natl.Acad.Sci.U.S.A. 94:3352-3356; Shayakhmetov, et al., (2000) J. Virol. 74(6):2567-2583). Both cell types were incubated with 500 particles per cell of both viruses for 30 min. Ad5 infected 3% and 0% of 3T3 and CHO cells respectively (FIG. 6. (see Original Patent)). Ad5f30 infected 1% of 3T3 and 0% of CHO cells (FIG. 6.). To assess infection with the addition of CAR, 3T3 cells and CHO cells were incubated with an Ad5CMVhCAR:CaPi co-precipitant for 30 min at 37.degree. C. It was found that after gene transfer 3T3 and CHO cells were 92% and 96% positive for CAR expression as determined by FACs (FIG. 6. (see Original Patent)). CAR expression dramatically increased Ad5 infection (21% for 3T3 and 57% for CHO cells). However, introduction of CAR had no significant impact on infection efficiency of Ad5f30 (1% and 2% for 3T3 and CHO cells) (FIG. 6.).

The inventors previously demonstrated that Ad30 infected of HUVECs more efficiently than Ad5 (Chillon, et al., (1999) J. Virol. 73(3):2537-2540). To determine if the fiber gene was responsible, confluent HUVECs were infected with Ad5 or Ad5f30 (5000 particles per cell) for one hour and quantified the number of eGFP positive cells three days later. A two-fold increase in eGFP positive cells from Ad5f30 was seen as compared to Ad5 (FIG. 7a (see Original Patent)). The results showed 72% positive cells with Ad5f30 and 36% for Ad5. A similar increase was seen with an incubation time of 15 or 30 min. To be certain that these results did not indicate a difference in titer between the two viruses, both viruses were precipitated with CaPi and the virus:CaPi co-precipitant was used to infect HUVECs. After CaPi precipitation, over 90% of the cells were eGFP positive with either virus (FIG. 7b).

Thus, the present inventors obtained, amplified and purified Ad30 wild-type particles. Genomic DNA from these particles was isolated and used to obtain the sequence of the Ad30 fiber protein by means of degenerate primers. When the Ad30 fiber sequence was compared to that of Ad5 fiber significant differences were evident. The shaft of the Ad30 fiber is less than half the length of the Ad5 fiber. Of note also, is the fact that of the seven amino acids shown to be important for CAR binding Ad30 lacks all but two. Those amino acids, conserved between Ad5 and Ad30 fibers, are in the hinge region between shaft and knob and are well conserved among most adenoviral serotypes. These results indicate that Ad30 most likely does not use CAR as its primary receptor.

Both viruses were used to infect a number of cell types. Ad5f30 was less efficient in infecting A549 and HeLa cells. A coprecipitant of Ad5f30 and CaPi, however, was very nearly equal in infection efficiency to a coprecipitant of Ad5:CaPi. These results indicated that the chimeric virus was viable and that the differences in infection efficiency were due to the different fibers present on the viral capsids. Both viruses were also tested in 3T3 and CHO cells in the presence or absence of CAR. It is evident from those experiments that the presence of CAR may not play a role in the infection efficiency of Ad5f30.

Both viruses were also tested in primary cultures. It was found that the infection efficiency of Ad5f30 was two-fold that of Ad5 at all time-points and particle concentrations when the HUVECs are confluent. As confluence of the HUVECs decreases so does the infection efficiency of Ad5f30 relative to that of Ad5. It is possible that in context of the shorter Ad30 fiber the Ad5 penton is better able to mediate viral entry. It is also possible that Ad5f30 uses another receptor present on the cell surface of the HUVEC.

It is evident from these studies that the fiber protein is responsible for the tropism and infection efficiency exhibited by a virus. Replacement of an endogenous fiber with that of a different serotype alters its infection profile. These fiber proteins are useful for various research and clinical applications.

Methods of Generating Adenoviral Vectors

Recombinant adenoviruses are useful vectors for basic research and for clinical applications. When used in delineating protein function, vectors that contain a given transgene with mutations or alterations to the coding sequence are compared at the same time. Adenoviruses can be made by standard transfection of a shuttle plasmid and viral DNA backbone into HEK 293 cells. Homologous recombination occurs in vivo, and recombinant virus can be isolated and propagated. The major drawback of this technique is that the starting viral DNA backbone, restricted of E1 containing sequences, must be 100% free of full-length Ad DNA. Otherwise, varying amounts of wild-type virus are also propagated. Alternatively, adenoviruses can be made via the streamlined method set forth in U.S. patent application Ser. No. 09/521,524 and in Anderson, et al., (2000) Gene Ther. 7(12):1034-1038.

Methods of Treating Genetic Disease or Cancer

The present invention provides methods of treating a genetic disease or cancer in a mammal by administering a polynucleotide, polypeptide, expression vector, viral particle or cell. For the gene therapy methods, a person having ordinary skill in the art of molecular biology and gene therapy would be able to determine, without undue experimentation, the appropriate dosages and routes of administration of the a polynucleotide, polypeptide, expression vector, viral particle or cell used in the novel methods of the present invention.

The instant invention provides a cell expression system for expressing exogenous genetic material in a mammalian recipient. The expression system, also referred to as a "genetically modified cell," comprises a cell and an expression vector for expressing the exogenous genetic material. The genetically modified cells are suitable for administration to a mammalian recipient, where they replace the endogenous cells of the recipient. Thus, the preferred genetically modified cells are non-immortalized and are non-tumorogenic.

According to one embodiment, the cells are transformed or otherwise genetically modified ex vivo. The cells are isolated from a mammal (such as a human), transformed (i.e., transduced or transfected in vitro) with a vector for expressing a heterologous (e.g., recombinant) gene encoding the therapeutic agent, and then administered to a mammalian recipient for delivery of the therapeutic agent in situ. The mammalian recipient may be a human and the cells to be modified are autologous cells, i.e., the cells are isolated from the mammalian recipient.

According to another embodiment, the cells are transformed or otherwise genetically modified in vivo. The cells from the mammalian recipient, are transformed (i.e., transduced or transfected) in vivo with a vector containing exogenous genetic material for expressing a heterologous (e.g., recombinant) gene encoding a therapeutic agent and the therapeutic agent is delivered in situ.

As used herein, "exogenous genetic material" refers to a nucleic acid or an oligonucleotide, either natural or synthetic, that is not naturally found in the cells; or if it is naturally found in the cells, it is not transcribed or expressed at biologically significant levels by the cells. Thus, "exogenous genetic material" includes, for example, a non-naturally occurring nucleic acid that can be transcribed into anti-sense RNA, as well as a "heterologous sequence" (i.e., a sequence encoding a protein that is not expressed or is expressed at biologically insignificant levels in a naturally-occurring cell of the same type). To illustrate, a synthetic or natural sequence encoding human erythropoietin (EPO) would be considered "exogenous genetic material" with respect to human peritoneal mesothelial cells since the latter cells do not naturally express EPO; similarly, a human interleukin-1 gene inserted into a peritoneal mesothelial cell would also be an exogenous gene to that cell since peritoneal mesothelial cells do not naturally express interleukin-1 at biologically significant levels. Still another example of "exogenous genetic material" is the introduction of only part of a genetic sequence to create a recombinant sequence, such as combining an inducible promoter with an endogenous coding sequence via homologous recombination.

In the certain embodiments, the mammalian recipient has a condition that is amenable to gene replacement therapy. As used herein, "gene replacement therapy" refers to administration to the recipient of exogenous genetic material encoding a therapeutic agent and subsequent expression of the administered genetic material in situ. Thus, the phrase "condition amenable to gene replacement therapy" embraces conditions such as genetic diseases (i.e., a disease condition that is attributable to one or more gene defects), acquired pathologies (i.e., a pathological condition that is not attributable to an inborn defect), cancers and prophylactic processes (i.e., prevention of a disease or of an undesired medical condition). Accordingly, as used herein, the term "therapeutic agent" refers to any agent or material that has a beneficial effect on the mammalian recipient. Thus, "therapeutic agent" embraces both therapeutic and prophylactic molecules having nucleic acid (e.g., antisense RNA) and/or protein components.

A number of diseases caused by single-gene defects have been identified (Roemer, K. and Friedmann, T., Eur J. Biochem. 208:211-225 (1992); Miller, A. D., Nature 357:455-460 (1992); Larrick, J. W. and Burck, K. L. Gene Therapy. Application of Molecular Biology, Elsevier, N.Y., (1991) and references contained therein). Examples of these diseases, and the therapeutic agents for treating the exemplary diseases, are provided in Table 1 (see Original Patent).

As used herein, "acquired pathology" refers to a disease or syndrome manifested by an abnormal physiological, biochemical, cellular, structural, or molecular biological state. Exemplary acquired pathologies, and the therapeutic agents for treating the exemplary pathologies, are provided in Table 2 (see Original Patent).

The condition amenable to gene replacement therapy alternatively can be a genetic disorder or an acquired pathology that is manifested by abnormal cell proliferation, e.g., cancers. According to this embodiment, the instant invention is useful for delivering a therapeutic agent having anti-neoplastic activity (i.e., the ability to prevent or inhibit the development, maturation or spread of abnormally growing cells), to primary or metastasized tumors, (e.g., ovarian carcinoma, mesothelioma, colon carcinoma). Therapeutic agents for treating these and other cancers include, for example, the anti-neoplastic agents provided in Table 3 (see Original Patent).

Delivery of a therapeutic agent by a genetically modified cell is not limited to delivery to a particular location in the body in which the genetically modified cells would normally reside. For example, it is possible that a therapeutic agent secreted by a genetically modified cell within a coelomic cavity could reach the lymphatic network draining that coelomic cavity. Accordingly, the genetically modified cells of the invention are useful for delivering a therapeutic agent, such as an anti-neoplastic agent, to various parts of the body.

Alternatively, the condition amenable to gene replacement therapy is a prophylactic process, i.e., a process for preventing disease or an undesired medical condition. Thus, the instant invention embraces a cell expression system for delivering a therapeutic agent that has a prophylactic function (i.e., a prophylactic agent) to the mammalian recipient. Such therapeutic agents (with the disease or undesired medical condition they prevent appearing in parentheses) include: estrogen/progesterone (pregnancy); thyroxine (hypothyroidsm); and agents that stimulate, e.g., gamma-interferon, or supplement, e.g., antibodies, the immune system response (diseases associated with deficiencies of the immune system).

In summary, the term "therapeutic agent" includes, but is not limited to, the agents listed in Tables 1-3 (see Original Patent), as well as their variants or functional equivalents. As used herein, the term "functional equivalent" refers to a molecule (e.g., a peptide or protein) that has the same or an improved beneficial effect on the mammalian recipient as the therapeutic agent of which is it deemed a functional equivalent. Accordingly, the instant invention embraces therapeutic agents encoded by naturally-occurring DNAs, as well as by non-naturally-occurring DNAs that encode the same protein as encoded by the naturally-occurring DNA.

The above-disclosed therapeutic agents and conditions amenable to gene replacement therapy are merely illustrative and are not intended to limit the scope of the instant invention. The selection of a suitable therapeutic agent for treating a known condition is deemed to be within the scope of one of ordinary skill of the art without undue experimentation.

Methods for Introducing Genetic Material into Cells

The exogenous genetic material (e.g. a cDNA encoding one or more therapeutic proteins) is introduced into the cell ex vivo or in vivo by genetic transfer methods, such as transfection or transduction, to provide a genetically modified cell. Various expression vectors (i.e., vehicles for facilitating delivery of exogenous genetic material into a target cell) are known to one of ordinary skill in the art.

As used herein, "transfection of cells" refers to the acquisition by a cell of new genetic material by incorporation of added DNA. Thus, transfection refers to the insertion of nucleic acid into a cell using physical or chemical methods. Several transfection techniques are known to those of ordinary skill in the art including: calcium phosphate DNA co-precipitation (Methods in Molecular Biology, Vol. 7, Gene Transfer and Expression Protocols, Ed. E. J. Murray, Humana Press (1991)); DEAE-dextran (supra); electroporation (supra); cationic liposome-mediated transfection (supra); and tungsten particle-faciliated microparticle bombardment (Johnston, S. A., Nature 346:776-777 (1990)). Strontium phosphate DNA co-precipitation (Brash D. E. et al. Molec. Cell. Biol. 7:2031-2034 (1987) is an alternative transfection method.

In contrast, "transduction of cells" refers to the process of transferring nucleic acid into a cell using virus. A cell that has been transduced with a chimeric DNA virus (e.g., an adenovirus carrying a cDNA encoding a therapeutic agent), will not have the exogenous genetic material incorporated into its genome but will be capable of expressing the exogenous genetic material that is retained extrachromosomally within the cell.

Typically, the exogenous genetic material includes the heterologous gene (usually in the form of a cDNA comprising the exons coding for the therapeutic protein) together with a promoter to control transcription of the new gene. The promoter characteristically has a specific nucleotide sequence necessary to initiate transcription. Optionally, the exogenous genetic material further includes additional sequences (i.e., enhancers) required to obtain the desired gene transcription activity. For the purpose of this discussion an "enhancer" is simply any non-translated DNA sequence that works contiguous with the coding sequence (in cis) to change the basal transcription level dictated by the promoter. The exogenous genetic material may introduced into the cell genome immediately downstream from the promoter so that the promoter and coding sequence are operatively linked so as to permit transcription of the coding sequence. An expression vector may include an exogenous promoter element to control transcription of the inserted exogenous gene. Such exogenous promoters include both constitutive and inducible promoters.

Naturally-occurring constitutive promoters control the expression of essential cell functions. As a result, a gene under the control of a constitutive promoter is expressed under all conditions of cell growth. Exemplary constitutive promoters include the promoters for the following genes that encode certain constitutive or "housekeeping" functions: hypoxanthine phosphoribosyl transferase (HPRT), dihydrofolate reductase (DHFR) (Scharfnann et al., Proc. Natl. Acad. Sci. USA 88: 4626-4630 (1991)), adenosine deaminase, phosphoglycerol kinase (PGK), pyruvate kinase, phosphoglycerol mutase, the .beta.-actin promoter (Lai et al., Proc. Natl. Acad. Sci. USA 86: 10006-10010 (1989)), and other constitutive promoters known to those of skill in the art. In addition, many viral promoters function constitutively in eucaryotic cells. These include the early and late promoters of SV40, the long terminal repeats (LTRs) of Moloney Leukemia Virus and other retroviruses, and the thymidine kinase promoter of Herpes Simplex Virus, among many others. Accordingly, any of the above-referenced constitutive promoters can be used to control transcription of a heterologous gene insert.

Genes that are under the control of inducible promoters are expressed only or to a greater degree, in the presence of an inducing agent, (e.g., transcription under control of the metallothionein promoter is greatly increased in presence of certain metal ions). Inducible promoters include responsive elements (REs) that stimulate transcription when their inducing factors are bound. For example, there are REs for serum factors, steroid hormones, retinoic acid and cyclic AMP. Promoters containing a particular RE can be chosen in order to obtain an inducible response and in some cases, the RE itself may be attached to a different promoter, thereby conferring inducibility to the recombinant gene. Thus, by selecting the appropriate promoter (constitutive versus inducible; strong versus weak), it is possible to control both the existence and level of expression of a therapeutic agent in the genetically modified cell. If the gene encoding the therapeutic agent is under the control of an inducible promoter, delivery of the therapeutic agent in situ is triggered by exposing the genetically modified cell in situ to conditions for permitting transcription of the therapeutic agent, e.g., by intraperitoneal injection of specific inducers of the inducible promoters that control transcription of the agent. For example, in situ expression by genetically modified cells of a therapeutic agent encoded by a gene under the control of the metallothionein promoter, is enhanced by contacting the genetically modified cells with a solution containing the appropriate (i.e., inducing) metal ions in situ.

Accordingly, the amount of therapeutic agent that is delivered in situ is regulated by controlling such factors as: (1) the nature of the promoter used to direct transcription of the inserted gene, (i.e., whether the promoter is constitutive or inducible, strong or weak); (2) the number of copies of the exogenous gene that are inserted into the cell; (3) the number of transduced/transfected cells that are administered (e.g., implanted) to the patient; (4) the size of the implant (e.g., graft or encapsulated expression system); (5) the number of implants; (6) the length of time the transduced/transfected cells or implants are left in place; and (7) the production rate of the therapeutic agent by the genetically modified cell. Selection and optimization of these factors for delivery of a therapeutically effective dose of a particular therapeutic agent is deemed to be within the scope of one of ordinary skill in the art without undue experimentation, taking into account the above-disclosed factors and the clinical profile of the patient.

In addition to at least one promoter and at least one heterologous nucleic acid encoding the therapeutic agent, the expression vector may also include a selection gene, for example, a neomycin resistance gene, for facilitating selection of cells that have been transfected or transduced with the expression vector. Alternatively, the cells are transfected with two or more expression vectors, at least one vector containing the gene(s) encoding the therapeutic agent(s), the other vector containing a selection gene. The selection of a suitable promoter, enhancer, selection gene and/or signal sequence (described below) is deemed to be within the scope of one of ordinary skill in the art without undue experimentation.

The therapeutic agent can be targeted for delivery to an extracellular, intracellular or membrane location. If it is desirable for the gene product to be secreted from the cells, the expression vector is designed to include an appropriate secretion "signal" sequence for secreting the therapeutic gene product from the cell to the extracellular milieu. If it is desirable for the gene product to be retained within the cell, this secretion signal sequence is omitted. In a similar manner, the expression vector can be constructed to include "retention" signal sequences for anchoring the therapeutic agent within the cell plasma membrane. For example, all membrane proteins have hydrophobic transmembrane regions that stop translocation of the protein in the membrane and do not allow the protein to be secreted. The construction of an expression vector including signal sequences for targeting a gene product to a particular location is deemed to be within the scope of one of ordinary skill in the art without the need for undue experimentation.

The following discussion is directed to various utilities of the instant invention. For example, the instant invention has utility as an expression system suitable for detoxifying intra- and/or extracellular toxins in situ. By attaching or omitting the appropriate signal sequence to a gene encoding a therapeutic agent capable of detoxifying a toxin, the therapeutic agent can be targeted for delivery to the extracellular milieu, to the cell plasma membrane or to an intracellular location. In one embodiment, the exogenous genetic material containing a gene encoding an intracellular detoxifying therapeutic agent, further includes sequences encoding surface receptors for facilitating transport of extracellular toxins into the cell where they can be detoxified intracellularly by the therapeutic agent. Alternatively, the cells can be genetically modified to express the detoxifying therapeutic agent anchored within the cell plasma membrane such that the active portion extends into the extracellular milieu. The active portion of the membrane-bound therapeutic agent detoxifies toxins that are present in the extracellular milieu.

In addition to the above-described therapeutic agents, some of which are targeted for intracellular retention, the instant invention also embraces agents intended for delivery to the extracellular milieu and/or agents intended to be anchored in the cell plasma membrane.

The selection and optimization of a particular expression vector for expressing a specific gene product in an isolated cell is accomplished by obtaining the coding sequence, such as with one or more appropriate control regions (e.g., promoter, insertion sequence); preparing a vector construct comprising the vector into which is inserted the coding sequence; transfecting or transducing cultured cells in vitro with the vector construct; and determining whether the gene product is present in the cultured cells.

In the present invention the adenovirus is used as an expression vector for transformation of cells. The adenovirus is frequently responsible for respiratory tract infections in humans and thus appears to have an avidity for the epithelium of the respiratory tract (Straus, S., The Adenovirus, H. S. Ginsberg, Editor, Plenum Press, New York, P. 451-496 (1984)). Moreover, the adenovirus is infective in a wide range of cell types, including, for example, muscle and endothelial cells (Larrick, J. W. and Burck, K. L., Gene Therapy. Application of Molecular Biology, Elsevier Science Publishing Co., Inc., New York, p. 71-104 (1991)). The adenovirus also has been used as an expression vector in muscle cells in vivo (Quantin, B., et al., Proc. Natl. Acad. Sci. USA 89:2581-2584 (1992)).

The adenovirus genome is adaptable for use as an expression vector for gene therapy, i.e., by removing the genetic information that controls production of the virus itself (Rosenfeld, M. A., et al., Science 252:431434 (1991)). Because the adenovirus functions in an extrachromosomal fashion, the recombinant adenovirus does not have the theoretical problem of insertional mutagenesis.

The instant invention also provides various methods for making and using the above-described genetically-modified cells. In particular, the invention provides a method for genetically modifying cell(s) of a mammalian recipient ex vivo and administering the genetically modified cells to the mammalian recipient. In one embodiment for ex vivo gene therapy, the cells are autologous cells, i.e., cells isolated from the mammalian recipient. As used herein, the term "isolated" means a cell or a plurality of cells that have been removed from their naturally-occurring in vivo location. Methods for removing cells from a patient, as well as methods for maintaining the isolated cells in culture are known to those of ordinary skill in the art.

The instant invention also provides methods for genetically modifying cells of a mammalian recipient in vivo. According to one embodiment, the method comprises introducing an expression vector for expressing a heterologous gene product into cells of the mammalian recipient in situ by, for example, injecting the vector into the recipient.

In one embodiment, the preparation of genetically modified cells contains an amount of cells sufficient to deliver a therapeutically effective dose of the therapeutic agent to the recipient in situ. The determination of a therapeutically effective dose of a specific therapeutic agent for a known condition is within the scope of one of ordinary skill in the art without the need for undue experimentation. Thus, in determining the effective dose, one of ordinary skill would consider the condition of the patient, the severity of the condition, as well as the results of clinical studies of the specific therapeutic agent being administered.

If the genetically modified cells are not already present in a pharmaceutically acceptable carrier they are placed in such a carrier prior to administration to the recipient. Such pharmaceutically acceptable carriers include, for example, isotonic saline and other buffers as appropriate to the patient and therapy.

The genetically modified cells are administered by, for example, intraperitoneal injecting or implanting the cells or a graft or capsule containing the cells in a target cell-compatible site of the recipient. As used herein, "target cell-compatible site" refers to a structure, cavity or fluid of the recipient into which the genetically modified cell(s), cell graft, or encapsulated cell expression system can be implanted, without triggering adverse physiological consequences. More than one recombinant gene can be introduced into each genetically modified cell on the same or different vectors, thereby allowing the expression of multiple therapeutic agents by a single cell.

The instant invention further embraces a cell graft. The graft comprises a plurality of the above-described genetically modified cells attached to a support that is suitable for implantation into a mammalian recipient. The support can be formed of a natural or synthetic material.

According to another aspect of the invention, an encapsulated cell expression system is provided. The encapsulated system includes a capsule suitable for implantation into a mammalian recipient and a plurality of the above-described genetically modified cells contained therein. The capsule can be formed of a synthetic or naturally-occurring material. The formulation of such capsules is known to one of ordinary skill in the art. In contrast to the cells that are directly implanted into the mammalian recipient (i.e., implanted in a manner such that the genetically modified cells are in direct physical contact with the cell-compatible site), the encapsulated cells remain isolated (i.e., not in direct physical contact with the site) following implantation. Thus, the encapsulated system is not limited to a capsule including genetically-modified non-immortalized cells, but may contain genetically modified immortalized cells.
 

Claim 1 of 17 Claims

1. A method of transducing a cell lacking coxsackievirus and adenovirus receptor (CAR) comprising contacting the cell with an expression vector comprising an Ad backbone nucleic acid sequence and polynucleotide encoding a chimeric adenovirus (Ad) fiber polypeptide comprising at least one of the following: a tail region, a shaft region and a knob region, wherein the polynucleotide encoding a chimeric Ad fiber polypeptide encodes SEQ ID NO:1, encodes amino acids 46-188 of SEQ ID NO:1, encodes amino acids 189-371 of SEQ ID NO:1, or wherein the polynucleotide comprises SEQ ID NO:12, comprises nucleotides 1-564 of SEQ ID NO:12, comprises nucleotides 1-135 of SEQ ID NO:12, or comprises nucleotides 136-564 of SEQ ID NO:12.

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