Self-rearranging DNA vectors

Abstract

Disclosed are replicatable viral DNA vectors encoding a site-specific DNA-altering enzyme and a DNA target recognized by the enzyme, the enzyme selectively converting, in a cell expressing the enzyme, the DNA vector to a rearranged form. The invention further relates to methods for assembling recombinant adenoviral DNAs. These methods include the steps of: (a) providing a first linearized DNA vector including a restriction site and a cos site and a second linearized DNA vector including the restriction site, an adenoviral nucleic acid molecule, and a cos site; and (b) ligating the first and second linearized DNA vectors, the ligation assembling a recombinant adenoviral DNA.

Description

BACKGROUND OF THE INVENTION

[0002] The invention relates to DNA vectors.

[0003] Mammalian cell expression vectors based on DNA viruses have been widely discussed as gene delivery vehicles for genetic therapy. Among the different DNA viruses proposed for this purpose have been adenoviruses, baculovirus, Epstein Barr virus, and herpes simplex virus. In addition other smaller viruses that have an intranuclear phase in which the viral genome is present as a double stranded DNA, such as retroviruses and parvoviruses, have been proposed as gene delivery vehicles.

[0004] Adenoviral vectors (AdV), for example, have a recognized potential for gene delivery, founded in their broad host range, robust growth in culture, and capacity to infect mitotically quiescent cells (Graham and Prevec, Manipulation of adenovirus vectors, p. 109-128, In E. J. Murray (ed.), Methods in Molecular Biology, vol. 7, Humana, Clifton, N.J., 1991; Trapnell and Gorziglia, Curr. Opin. Biotechnol. 5:617-625, 1994). AdV can be propagated in a helper cell line, 293, a human embryonic kidney cell line transformed by adenovirus type 5 (Graham et al., J. Gen. Virol. 36:59-72, 1994). 293 cells express the viral E1 gene products (E1a and E1b) that are the master regulatory proteins for subsequent viral gene expression. E1 deleted viruses can propagate in 293 cells, but not in other cells. Although it would be expected that E1 deleted viruses lack the machinery to express viral genes, several studies have demonstrated that cellular E1-like components can stimulate viral gene expression (Imperiale et al., Mol. Cell. Biol. 4:867-74, 1984; Onclercq et al., J. Virol. 62:4533-7,1988; Spergel et al., J. Virol. 66:1021-30, 1992). The expression of these viral genes results in the relatively rapid elimination of transduced cells in vivo as a result of cytotoxic T cell responses (Yang et al., Immunity 1:433-42, 1994; Yang et al., Gene Ther. 3:137-44, 1996; Yang et al., J. Virol. 69:2004-15, 1995).

[0005] Thus attention has been focused on eliminating the remaining vestiges of viral expression. Viral genes that have been deleted for this purpose include the gene for E4 proteins (Armentano et al., Hum. Gene Ther. 6:1343-53, 1995; Kochanek et al., Proc. Natl. Acad. Sci. USA 93:5731-6, 1996; and Yeh et al., J. Virol. 70:559-565, 1996), DNA binding protein (Engelhardt et al., Proc. Natl. Acad. Sci. USA 21:6196-6200, 1994; and Gorziglia et al., J. Virol. 70:4173-8, 1996), DNA polymerase (Amalfitano et al., J. Virol. 72:926-33, 1998), and the preterminal protein (Schaack et al., Proc. Natl. Acad. Sci. USA 93:14686-91, 1996). The most aggressive approach has been the creation of helper virus-dependent vectors that lack all viral genes (Hardy et al., J. Virol. 71:1842-9, 1997; Kochaneketal., Proc. Natl. Acad. Sci. USA 93:5731-6, 1996; Lieber et al., J. Virol. 70:8944-60, 1996; Mitani et al., Proc. Natl. Acad. Sci. USA 92:3854-8, 1995; and Parks et al., Proc. Natl. Acad. Sci. USA 93:13565-13570, 1996). These vectors have high capacity, evoke reduced cellular immune responses and show prolonged expression in vivo (Morsy et al., Proc. Natl. Acad. Sci. USA 95:7866-71, 1998). However to deploy these viruses on the scale required for human clinical application presents major challenges because a cesium chloride (CsCl) gradient is needed to remove the helper virus.

SUMMARY OF THE INVENTION

[0006] In one aspect, the invention features a replicatable viral DNA vector encoding a site-specific DNA-altering enzyme and a DNA target recognized by the enzyme, the enzyme selectively converting, in a cell expressing the enzyme, the DNA vector to a rearranged form.

[0007] In preferred embodiments, the rearranged form includes an autonomously replicating episome and a linear DNA product. In other preferred embodiments, the vector comprises adenoviral DNA.

[0008] In yet other preferred embodiments, the vector includes a genetically-engineered recombination site (such as a target of Cre or FLP). Preferably, such a recombination site includes a recognition sequence of a site-specific DNA altering enzyme.

[0009] In another preferred embodiment, the site-specific DNA altering enzyme is a recombinase (such as Cre or FLP) or an integrase. Preferably, such an enzyme is functional in a mammalian cell. Preferred embodiments of the vector also include an origin of replication that functions in a mammalian cell (such as an Epstein Barr Virus replicon). Moreover, the vector typically includes a gene of interest (such as a therapeutic gene that encodes a protein or polypeptide or an RNA product).

[0010] In another aspect, the invention features a method for assembling a recombinant adenoviral DNA. The method, in general, includes the steps of: (a) providing a first linearized DNA vector comprising a restriction site and a cos site and a second linearized DNA vector comprising the restriction site, an adenoviral nucleic acid molecule, and a cos site; and (b) ligating the first and second linearized DNA vectors, the ligation assembling a recombinant adenoviral DNA.

[0011] In preferred embodiments, the first linearized DNA vector comprises a selectable marker (such as a gene encoding a polypeptide that confers, on a host cell expressing such a polypeptide, resistance to an antibiotic). In other preferred embodiments, the first linearized DNA vector includes an adenoviral left-end inverted terminal repeat, a gene of interest, or both. In still other preferred embodiments, the second linearized DNA vector includes a selectable marker. Preferably, the second linearized DNA vector includes an adenoviral right-end inverted terminal repeat.

[0012] The method further includes packaging the assembled adenoviral DNA into a phage and infecting a host cell. Typically the first and second linearized DNAs include cosmid vector DNA. In addition, such adenoviral DNA is typically flanked by cleavage sites (such as intron endonuclease cleavage sites).

[0013] In another aspect, the invention features an adenovirus producer cell having a nucleic acid molecule that expresses a dominant negative site-specific DNA-altering enzyme. In preferred embodiments, the site-specific DNA altering enzyme is a dominant negative recombinase (for example, a Cre recombinase such as CreY324C or a Flp recombinase). Exemplary adenovirus producer cells include, without limitation, 293 human embryonic kidney cells, per.C6 cells, and N52 cells.

[0014] In yet another aspect, the invention features a vector comprising, in the 5′ to 3′ direction, a first genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; a gene of interest; a lineage-specific gene promoter; a second genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; and a nucleic acid molecule encoding a site-specific DNA altering enzyme.

[0015] In still another aspect, the invention features a vector including, in the 5′ to 3′ direction, a first genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; a gene of interest; a bi-directional promoter, comprising a second genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; and a nucleic acid molecule encoding a site-specific DNA altering enzyme.

[0016] In related aspects, the invention features a method of gene therapy including the administration to a patient in need of gene therapy a therapeutically effective amount of the vector of the invention, which is expressed in the patient. The invention further relates to a population of cells transfected with the vector of the invention.

[0017] Accordingly, the invention further relates to the use of a recombinant viral vector or use of a recombinant viral particle for gene therapy. Such vectors and viral particles may be introduced either in vitro into a host cell removed from the patient, or directly in vivo, into the body to be treated, according to standard methods known in the art.

[0018] The invention also relates to a pharmaceutical composition that includes a therapeutically effective amount of a recombinant viral vector or viral particle prepared according to the methods disclosed herein, in combination with a vehicle that is acceptable from a pharmaceutical standpoint. Such a pharmaceutical composition may be prepared according to the techniques commonly employed and administered by any known administration route, for example systemically (in particular, by intravenous, intratracheal, intraperitoneal, intramuscular, subcutaneous, intratumoral, or intracranial routes) or by aerosolization or intrapulmonary administration.

[0019] One skilled in the art will appreciate that suitable methods of administering a vector (particularly an adenoviral vector) of the present invention to an animal for purposes of gene therapy, chemotherapy, and vaccination are available, and, although more than one route can be used for administration, one particular route may provide a more immediate and more effective reaction than another. Pharmaceutically acceptable excipients also are well known to those who are skilled in the art, and are readily available. The choice of excipient will be determined, in part, by the particular method used to administer the recombinant vector or particle. Accordingly, there are a wide variety of suitable formulations for use in the context of the present invention.

[0020] By “recombinant DNA vector” is meant a DNA sequence containing a desired sequence (such as a gene of interest) and an appropriate regulatory element(s) necessary for the expression of the operably linked sequence in a particular host organism (such as a mammal).

[0021] By “operably linked” is meant that a gene and a regulatory element(s) are connected to permit gene expression when the appropriate molecules (for example, transcriptional activator proteins) are bound to the regulatory sequence(s).

[0022] By “regulatory element” is meant a genetic element that controls some aspect of the expression of a nucleic acid sequence. For example, a promoter is a regulatory element that facilitates the initiation of transcription of an operably linked coding region. Other genetic regulatory elements include, without limitation, splicing signals, polyadenylation signals, and termination signals. For example, transcriptional regulatory elements in eukaryotes include promoter and enhancer elements. Promoters and enhancers include arrays of DNA sequences that interact directly or indirectly with cellular proteins involved in transcription. Promoter and enhancer elements have been isolated from a variety of eukaryotic sources including genes in mammalian cells and viruses.

[0023] By “transfection” is meant the introduction of foreign DNA into eukaryotic cells. Transfection is typically accomplished by a variety of means known in the art including, without limitation, calcium phosphate-DNA co-precipitation, DEAE-dextran-mediated transfection, electroporation, microinjection, liposome fusion, lipofection, protoplast fusion, and biolistics.

[0024] By “stably transfected” is meant the introduction of foreign DNA into the genome of the transfected cell. In general, transfer and expression of transgenes in mammalian cells are now routine practices to those skilled in the art, and have become major tools to carry out gene expression studies and to generate vectors useful in gene therapy.

[0025] By “gene of interest” is meant a gene inserted into a vector whose expression is desired in a host cell. Genes of interest include, without limitation, genes having therapeutic value, as well as reporter genes. A variety of such genes are useful in the invention, including genes of interest encoding a protein, which provides a therapeutic function. In addition, the gene of interest, if a therapeutic gene, can render its effect at the level of RNA, for instance, by encoding an antisense message or ribozyme, a protein which affects splicing or 3′ processing (e.g., polyadenylation), or it can encode a protein which acts by affecting the level of expression of another gene within the cell (i.e., where gene expression is broadly considered to include all steps from initiation of transcription through production of a processed protein), for example, by mediating an altered rate of mRNA accumulation, an alteration of mRNA transport, and/or a change in post-transcriptional regulation.

[0026] By “reporter gene” is meant a gene sequence that encodes a reporter molecule (including an enzyme). A “reporter molecule” is detectable in any detection system, including, but not limited to, enzyme (e.g., ELISA, as well as enzyme-based histochemical assays), fluorescent, radioactive, and luminescent systems. Exemplary reporter gene systems include the E. coli beta-galactosidase or glucuronidase genes, green fluorescent protein (GFP), blue fluorescent protein (BFP), the human placental alkaline phosphatase gene, and the chloramphenicol acetyltransferase (CAT) gene; other reporter genes are known in the art and may be employed as desired.

[0027] By “transgene” is meant any piece of DNA that is inserted by artifice into a cell, and becomes part of the genome of the organism that develops from that cell. Such a transgene may include a gene that is partly or entirely heterologous (i.e., foreign) to the transgenic organism, or may represent a gene homologous to an endogenous gene of the organism.

[0028] By “transgenic” is meant any cell that includes a DNA sequence that is inserted by artifice into a cell, and becomes part of the genome of the organism that develops from that cell.

[0029] By “polypeptide” is meant any chain of amino acids, regardless of length or post-translational modification (for example, glycosylation or phosphorylation).

[0030] By “derived from” is meant isolated from or having the sequence of a naturally occurring sequence (e.g., a cDNA, genomic DNA, synthetic, or combination thereof).

[0031] By “nucleic acid” is meant a polynucleotide (DNA or RNA).

[0032] By “gene” is meant any nucleic acid sequence coding for a protein or an RNA molecule.

[0033] By “gene product” is meant either an untranslated RNA molecule transcribed from a given gene or coding sequence (such as mRNA or antisense RNA) or the polypeptide chain translated from the mRNA molecule transcribed from the given gene or coding sequence. Nucleic acids according to the invention can be wholly or partially synthetically made, can comprise genomic or complementary DNA (cDNA) sequences, or can be provided in the form of either DNA or RNA.

[0034] The presently claimed invention affords a number of advantages. For example, applicants' gene therapy vehicles, particularly those based on recombinant adenoviruses, minimize the propensity of the vectors to activate host immune surveillance, and thereby maximize the persistence for the DNA transduced. The invention therefore facilitates the development of gene delivery vectors designed to enhance persistence of virally delivered genes and evade the cellular immune response by severing the connection between the sole adenoviral enhancer and the sequences encoding potentially antigenic viral proteins.

[0035] As described in more detail below, the mechanism by which this is accomplished differs significantly from any other previous approaches. For example, to reduce the immunogenicity of vectors it is widely acknowledged that some intervention, such as the removal of key genes, or the prevention of their expression in the cells targeted for therapy, is important; however, many related approaches are directed at the host and have generally focused on the selective induction of tolerance to adenoviral antigens, or similar strategies directed at inducing a temporally restricted or antigen-specific compromise of the immune system.

[0036] In addition, the poor persistence of transduced DNA appears to be due in part to immunological rejection of transduced cells and to the inability of the viral DNA to replicate, a feature generally inherent in the design of adenoviral vectors, but one which is not associated with applicants' claimed gene therapy vehicles.

[0037] Moreover, some contemporary adenoviral vectors are designed to propagate in specific host cells which provide essential replication factors in trans. These vectors are typically based on cell lines which express the master regulatory proteins of the E1 complex, which are required for induction of adenoviral DNA replication. In cells expressing E1 genes, the best studied of which is a human embryonic kidney cell line transformed by DNA from human adenovirus 5 (called HEK293, or simply 293), viruses lacking E1 genes propagate well. Such viruses do not propagate on cell lines which do not express E1, and do not generally propagate well in the target cells to which the therapeutic gene is to be delivered. Cells transduced with E1-deleted adenovirus vectors also do not express high levels of viral genes in the absence of E1. However, the weak residual expression that remains in such vectors appears to be sufficient to induce cellular immune responses that contribute to the destruction of the transduced cells.

[0038] In addition, the gene therapy vectors claimed herein are hybrid vectors capable of self-rearrangement to form circular and linear DNA products. The linear DNA has a compromised ability to express adenoviral genes, and therefore has a lower immunological profile. And the circular DNA behaves like a mammalian plasmid, encoding the gene of interest and persisting by autonomous replication in the nucleus.

[0039] For example, the circularization of an adenoviral vector via the action of Cre recombinase beneficially places a gene of interest (for example, a therapeutic gene) on a self-replicating episome. Vector circularization occurs in a tissue-targeted manner, for example, as a result of the activation of a synthetic liver-specific promoter upstream of the recombinase Cre. Once circularized, the EBV replicon in the episome confers improved persistence on the therapeutic gene as detected by reporter gene expression and direct assay for the presence of vector DNA sequences.

[0040] Furthermore, the invention eliminates the requirement for a helper virus, thus avoiding two potential limitations of that system. First, the continuous expression of Cre recombinase may lead to toxicity in host cells, either as a direct consequence of the protein's activity or via its immunogenicity. Second, the Cre helper virus may itself produce antigenic viral proteins that contribute to the immunologic elimination of infected host cells. In contrast, the self-resolving adenovirus/EBV vector system disclosed herein advantageously provides no alternative source of viral proteins, and Cre expression is terminated upon rearrangement.

[0041] In addition, the invention described herein provides tools for analyzing the roles of the enhancer in viral gene regulation and virus growth.

[0042] The invention also provides a convenient general system for creating recombinant adenoviruses, which increase their attractiveness as gene transduction tools for basic research. The system, for example, employs two conventional plasmid vectors and a γ phage packaging step. The entire recombinant AdV genome is assembled into a single cosmid that is easily amplified in E. coli. The use of intron endonuclease recognition sequences flanking the ITRs enhances virus production while simplifying insertion of therapeutic gene sequences into the pLEP shuttle plasmid. The convenience of this vector system has facilitated the construction of over two hundred recombinant viruses to date.

[0043] Other embodiments and advantages of the invention will be apparent from the detailed description thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0044] The application file contains drawings executed in color (FIGS. 7A, 7B, 7C, 10C, 11, 15A, 17, and 21). Copies of this patent or patent application with color drawings will be provided by the U.S. Patent and Trademark Office upon request and payment of the necessary fee.

[0045] FIG. 1A is a schematic diagram of the structure of an adenoviral type A vector and its fate in a target cell. “enh” refers to the Ad2 enhancer; “GFP” refers to the marker gene green fluorescent protein; “EBV” refers to the Epstein Barr Virus replicon; “TetO7” refers to a heptamer of Tet operator; “TetR” refers to the Tet repressor; “VP 16” refers to the viral protein 16 of Herpes simplex virus, SD refers to the splice donor site; and SA refers to the splice acceptor site.

[0046] FIG. 1B is a schematic diagram of the structure of an adenoviral type B vector and its fate in a target cell. enh refers to the Ad2 enhancer; GFP refers to the marker gene green fluorescent protein; EBV refers to the Epstein Barr Virus replicon; SD refers to the splice donor site; and SA refers to the splice acceptor site.

[0047] FIG. 2A shows a schematic diagram of the pLEP cosmid polylinker region and its position relative to the adenoviral left ITR. The adenovirus enhancer/packaging sequence (ψ) is boxed.

[0048] FIG. 2B is a schematic diagram showing the generation of a single cosmid encoding the AdV genome by the direct ligation of two smaller plasmids. A gene expression unit, CMVGFP, was inserted into the pLEP cosmid at the polylinker region. pLEP and pREP cosmids were digested with an intron endonuclease (PI-PspI), ligated, and packaged in vitro to generate pAd2CMVGFP. This DNA was then digested with another intron endonuclease (1-CeuI) to expose the ITRs at both ends of the viral genome. Finally, cosmid digestion mixtures were transfected into 293 cells. Plaques generated by recombinant viruses are detected in 7-10 days.

[0049] FIG. 3A shows the restriction analysis of cosmids carrying the full length AdV DNA showing uniform generation of the desired vector DNA. 2 μg DNA samples from four pAd2-7CMVGFP colonies were digested with Bgl II, resolved on a 1% agarose gel and stained with ethidium bromide. The predicted sizes of the DNA fragments are: 13261, 7684, 5228, 5088, 2284, 1757, 1549, 1270, 351, and 275 base pairs (bp). The 5228 and 5088 fragments appear as a doublet, and the 351 and 275 bp fragments are too small to be seen on the gel.

[0050] FIG. 3B shows the release of the recombinant Ad DNA from cosmids by I-CeuI digestion. 2 μg of pAd2-7CMV DNA from two clones was digested with I-CeuI. The position of the released recombinant AdV DNA and the vector fragments of approximately 35 kb and 5 kb, respectively, are indicated.

[0051] FIG. 4A shows the appearance of plaques in 293 cells transfected with 10 μg of pIAdGFPB with no ITR exposed (undigested), one ITR exposed (BsaBI or I-CeuI), or both ITRs exposed (BsaBI plus I-CeuI). Values represent the mean plaque counts per dish and the time required for plaque development in 293 cells from three separate experiments. “I” designates I-CeuI; and “B” designates Bsa BI.

[0052] FIG. 4B shows the viral titers obtained from plaques that were allowed to grow over 10 days after transfection. Viruses were harvested and the titer of each virus stock was determined by a GFP based semi-quantitative titration procedure described herein. Values represent the mean±SE of three independent determinations.

[0053] FIG. 5 is a schematic diagram showing a linear AdV that resolves into a circular episome. The elements involved in the self-directed rearrangement of the vector are shown schematically in pLEP1BHCRGFP/EBV and in the corresponding AdV. Starting from the left ITR, the elements are shown as following sequence: left ITR, 147 bp; first 34 bp loxP site; 185 bp enhancer/packaging signal; 64 bp splicing acceptor (SA) from EF1α gene first intron; 720 bp GFP cDNA; 230 bp SV40 poly(A); 1.7 kb TK-EBNA-1/OriP; 970 bp HCR12 promoter; 1 kb EF1α gene first intron containing splicing donor (SD) and acceptor (SA) sites with the second loxP site inserted at 64 bp upstream of the 3′end; 1.2 kb Cre gene tagged with AU1 and a nuclear localization signal; ˜120 bp poly(A) signal and PI-PspI site. After infection of liver cells, the HCR12 promoter drives the expression of Cre which results in the cleavage of the two loxP sites. This results in the circularization of the fragment containing the EBV replicon. The excision severs the connection between the enhancer/packaging signals and the remainder of the AdV genome. The Cre gene becomes promoterless and is left on the AdV genome fragment. After excision, the HCR12 promoter drives the expression of the GFP reporter gene. The EBV replicon maintains the excised circle as an episome in host cells.

[0054] FIG. 6A is a schematic representation of the loxP sites and EBNA-1 locations in the AdV genome. The relevant Bgl II site is also shown.

[0055] FIG. 6B shows the time course of rearrangement in HepG2 and Hela cells at an equal multiplicity of infection (moi) of 1,000 particles per cell. Cells were infected with Ad2HCRGFP/EBV viruses for 2 hours at 37° C. Hirt DNA samples were extracted from the cells. ˜5 μg of Hirt DNA samples were digested with Bgl II, fractionated on a 1% agarose gel, and analyzed by Southern blot techniques using a 32P-labeled EBNA-1 fragment as the hybridization probe.

[0056] FIG. 6C shows the DNA blot results obtained from Hela cells infected at a moi of 10,000; and HepG2 at 1,000. The upper bands (4915 bp) represent the circularized DNA fragments whereas the lower bands (3162 bp) represent the non-circularized AdV.

[0057] FIG. 7A shows green fluorescent protein (GFP) expression in liver and non-liver cells infected with the Ad2HCRGFP/EBV viruses. Cells were cultured in 35 mm dishes and infected with the Ad2HCRGFP/EBV virus at desired moi. HepG2 cells were infected with 1,000 particles per cell, whereas Hela cells were infected with a moi of 10,000. GFP expression was examined at the indicated time points after infection. Fluorescent cells were photographed using an Olympus SC35 mm camera mounted on an Olympus IX70 fluorescent microscope, at 200× magnification, using a filter with peak excitation and emission wavelengths of 450 nm and 510 nm, respectively.

[0058] FIG. 7B shows the expression of GFP in HepG2, Hela, A431, and HT29 cells. Cells were seeded in 35 mm dishes and infected with the Ad2HCRGFP/EBV virus at a moi of 10,000 particles per cell. GFP expression was examined at 72 hours after infection.

[0059] FIG. 7C shows the expression of GFP in human primary hepatocytes. These cells were photographed under bright field (left) and fluorescent conditions (right).

[0060] FIG. 8A shows the results of RT-PCR that was performed to detect the tripartite leader sequence (upper panel) for virus late gene expression; and PCR was performed in the DNA samples for detection of the AdV genomes. The specific target sequences are described in detail infra. PCR analyses of adenovirus late gene expression in cells infected with the first generation AdVs or the self-resolving Ad2HCRGFP/EBV was analyzed. HepG2 cells were cultured in 35 mm dishes and infected with increasing moi (0, 10, 100, 1000, 10,000, and 100,000) of adenoviral vectors. RNA and DNA were isolated in parallel from the cells at 72 hours after infection.

[0061] FIG. 8B shows a summary of quantitative RT-PCR and PCR results. Each determinant was the average of three experiments.

[0062] FIG. 9A is a schematic diagram depicting the deletion analysis of the OriP and EBNA-1 regions of the EBV replicon. Structures of the deletions in EBNA-1 and OriP are schematically represented. Elements considered important for episomal maintenance are indicated. “FR” refers to the family of repeats; “DS” designates the region of dyad symmetry; “LR1” refers to the so-called linker region 1; “GA” refers to gly-ala repeats; “LR2” refers to linker region 2; and “Dimerization” designates the dimerization domain.

[0063] FIG. 9B is a graph depicting fractions of GFP positive cells carrying the EBV replicons represented in FIG. 9A.

[0064] FIG. 10A shows the positions and identities of Cre mutants tested for their dominant negative Cre activities.

[0065] FIG. 10B is a schematic diagram of the substrate Cre plasmid (ad2239) used to test dominant negative functions of Cre mutants.

[0066] FIG. 10C shows GFP expression in cells cotransfected with the substrate Cre plasmid (ad2239) and the indicated Cre mutants.

[0067] FIGS. 10D and 10E show Cre mutants tested for their ability to inhibit rearrangement. Only those showing the strongest inhibitory activities were retested in FIG. 10E. GFP intensity was normalized to that of cells in the absence of inhibition.

[0068] FIG. 11 shows GFP expression in 293 TetON cells and #17 cells transfected with ad2239. The ability of #17 cells to inhibit Cre activity is demonstrated by the weak GFP signal in cells treated with 2 μM doxycycline.

[0069] FIG. 12 is a schematic diagram depicting the tetracycline mediated auto-regulatory circuit.

[0070] FIGS. 13A and 13B show the effects of different basal elements on synthetic TetO promoter activity. FIG. 13A shows a schematic diagram of the components of various auto-regulatory synthetic TetO promoters. FIG. 13B shows a comparison of the strength of auto-regulatory synthetic TetO promoters bearing different basal elements, in the presence and absence of tetracycline, using GFP as a marker in HepG2 cells.

[0071] FIG. 14 shows the structure of a Cre substrate plasmid (ad2265). The promoter, Ef1α, and the gene, BFP, are interrupted by two loxP sites, which can be joined by Cre-mediated recombination. “PA” stands for poly A; “BFP” for blue fluorescent protein.

[0072] FIGS. 15A and 15B show the estrogen regulation of Cre recombinase activity. 293 cells infected with type B virus, AD121.5, in which the Cre enzyme is fused with estrogen ligand binding domain at both the N- and C-termini were cultured in the presence or absence of 1 μM estrogen. Cre-mediated rearrangement in the presence of estrogen is shown in FIG. 15A, whereas blot analysis of extrachromosomal DNA from the same cells is shown in FIG. 15B. “L” represents the position corresponding to the unrearranged adenoviral DNA; and “C” represents the position corresponding to the circular form of DNA.

[0073] FIG. 16 shows the rearrangement of adenoviral sequences in vivo. Extrachromosomal DNA from the livers of Rag-2 mice sacrificed 2.5 hours post injection of type A adenovirus, AD102.7, was analyzed by DNA blot. “L” represents the size corresponding to linear adenoviral DNA; and “C” represents the size corresponding to rearranged circular DNA.

[0074] FIG. 17 is a photomicrograph depicting high level GFP expression in Rag2 mouse hepatic tissues 48 hours post type A adenovirus (AD102.7) injection.

[0075] FIGS. 18A and 18B show schematic diagrams of the structures of adenoviral vectors and their fates in target cells. “enh” refers to Ad2 enhancer; “GFP” refers to green fluorescent protein; “EBV” refers to Epstein Barr Virus replicon; “TetO7” refers to heptamer of Tet operator; “TetR” refers to Tet repressor; “VP16” refers to transcriptional activator domain from HSV protein 16; “SD” refers to splice donor site; and “SA” refers to splice acceptor site.

[0076] FIG. 19A shows the structure of a FLP substrate plasmid, ad2879. The promoter, Ef1α, and the gene, GFP, are interrupted by 2 FRT sites, which can be joined by the FLP-mediated recombination. “PA” stands for poly A; “BFP” for blue fluorescent protein.

[0077] FIG. 19B shows the structure of a cre substrate plasmid, ad2204.

[0078] FIG. 20 shows the structures of several FLPe anti-sense plasmids.

[0079] FIG. 21 is a panel of photomicrographs showing inhibition of FLP enzyme activity by anti-sense FLP. 293 cells were transfected with FLP substrate (FIG. 12) and plasmids indicated in each photo. High GFP intensity indicate the higher expression of FLP and less inhibition by the anti-sense expressed.

[0080] FIG. 22 shows a schematic diagram of FRT/Cre and loxP/FLP adenovirus.

DETAILED DESCRIPTION

[0081] Described herein are systems for the regulated self-rearrangement of DNA vectors, for example, gene therapy vectors. Such regulated self-rearrangement has the potential to prevent unwanted expression of vector genes not required for a therapeutic effect, and to allow the stable association of the therapeutic gene with the target cell.

[0082] The essential elements of the regulated DNA rearrangement system are a gene that encodes one or more proteins that induce DNA rearrangement, a method for regulating the activity of those proteins or their abundance, and a target DNA sequence on which those proteins act. Particularly desirable are methods for regulating the activity of the proteins or their abundance which can be easily carried out on an intact organism, such as administration or withdrawal of a drug, hormone, or environmental stimulus such as heat or irradiation, which induces the activity or abundance of the proteins which cause DNA rearrangement.

[0083] Especially desirable are regulated DNA rearrangement systems in which all of the components can be delivered in a single vector. An example of this is a virus that bears both the cis-acting sequences for DNA rearrangement as well as the protein or proteins that act on those sequences, and the regulatory apparatus which controls the activity or abundance of those proteins. However, it is not necessary that the different elements be encoded in a single nucleic acid.

[0084] The important elements of this strategy are: the compromise of vector gene function by regulated rearrangement of DNA topology, the generation of plasmid circles from vector DNA in a regulated manner, and the removal of enhancer or promoter elements from the vector DNA by regulated excision. It is also important that the circular DNA generated by site-specific recombination possesses a mechanism for stable association with the host genome in some form, here conferred by the EBV replicon. In other embodiments, the circular DNA might possess the ability to direct its integration into the host chromosomes by a site-specific integration. Site-specific integration into the host chromosomes may also be generated by the action of a regulated site-specific recombinase on a linear template without passing through a circular intermediate.

[0085] Also described herein is one particular self-rearranging vector that begins as a hybrid adenovirus vector which is capable of converting itself into two unlinked molecules, a circular and a linear DNA. After this event the linear DNA product is deleted for two important cis-acting sequences: the packaging signals, which are required for insertion of the viral DNA into the viral capsid, and the enhancer, which increases the expression of other promoters encoded in the viral DNA. The remaining linear DNA is thereby compromised in its ability to express adenoviral genes, endowing the vector with a lower immunological profile. The circular DNA generated by the excision event is a mammalian cell plasmid which has the capacity to persist by autonomous replication in the nucleus. This capacity is encoded in genetic elements derived from the Epstein Barr virus (EBV). A schematic diagram of such a vector is illustrated in FIG. 5.

[0086] Epstein Barr virus is a human herpes virus which is the etiologic agent of infectious mononucleosis and which has been implicated in the genesis of Burkitt's lymphoma, a B cell neoplasm, and is thought to be a predisposing factor for some forms of nasopharyngeal carcinoma. Approximately 85% of the adult Western population has a persistent population of B cells which contain a circular latent form of the viral-genome, maintained in cells by the action of Epstein Barr Nuclear Antigen 1 (EBNA1), a DNA replication protein that acts on the viral latent phase origin of replication, OriP. EBNA1 in and of itself is not thought to promote neoplasia; current thinking places greater weight on the actions of the EBNA2 proteins and LMP, latent membrane protein, in the inception of EBV-associated neoplasm.

[0087] Mammalian cell plasmids have been created which bear the EBNA1 gene and OriP. In nonrodent cells, these plasmids persist by replication with each transit of the cell cycle. Multiple transcription units can be borne by these plasmids, allowing regulated expression of diverse gene products.

[0088] Preferred adenoviral vectors, shown in FIGS. 1A and 1B, are linear forms of an EBV plasmid flanked by loxP sites, cis-acting sequences required for site-specific recombination directed by the bacteriophage P1 cre protein. To prepare an adenovirus bearing both the cre protein and loxP sites, it is necessary to insure that the cre protein is not expressed while the vector is being propagated in 293 cells. To lower the immunological profile of the vector, it is also desirable that the cre protein not be expressed after the vector delivered its payload to the target cell and the cre protein performed its function.

[0089] To accomplish these objectives, two general approaches have been developed for the production of adenoviral chromosomes that circularize following the regulated expression of site-specific recombinases. In each case, the vector is engineered to allow for the production of viruses in 293 cells, and to provide transitory expression of recombinase that induces rearrangement in target tissues. The major difference between the two strategies lies in the way the deinduction of recombinase is achieved.

[0090] In the first approach, adenoviral vectors are engineered to turn an activating transcription factor into a repressor upon chromosomal rearrangement. Vectors employing this approach are referred to herein as type A vectors (FIG. 1A). In the second approach, the recombinase promoter is redirected following chromosomal rearrangement. Vectors utilizing the second approach are referred to as type B vectors (FIG. 1B). In both cases a linear chromosome is converted to its circular episomal form and a resulting deleted linear form. The circular DNA contains an Epstein Barr virus (EBV) replicon, which allows synchronous replication of the episome with the host mitotic cycle (Reisman et al., Mol. Cell Biol. 8: 1822-32, 1985; Yates et al., Nature 313: 812-15, 1985). The linear DNA is deleted for the enhancer and E1 genes.

[0091] One self-regulated gene switch, employing the type A vector strategy, was designed based on the bacterial transposon Tn10 tetracycline repressor (tetR) gene. In its natural context, the tetR protein binds to specific sequences (tet operator sequences) upstream of a tetracycline resistance gene, preventing transcription of the gene unless tetracycline is present. To adapt this protein for eukaryotic gene regulation, a gene fusion is created between tetR and an active portion of a strong eukaryotic transcriptional activator, the herpes simplex virus VP16 protein. The fusion protein exerts its action on a synthetic promoter created by the insertion of multiple tet operator sequences upstream of a basal promoter element. This configuration allows high-level gene expression whenever the tetR-VP16 fusion protein binds to its cognate operator sequences. Because the tetR protein normally does not bind to its operator in the presence of tetracycline, the activity of this synthetic promoter is high in the absence of tetracycline and low in its presence.

[0092] One example of a type A vector is shown in FIG. 1A. This self-regulated gene expression cassette, present in a hybrid adenovirus, consists of a bi-directional promoter element in which central tetR binding sites are flanked by divergently oriented basal promoter elements. In one direction the promoter directs the formation of a transcript encoding the cre protein; in the other direction, the promoter directs the formation of a tetR-VP16 fusion protein. The latter differs from the conventional version in bearing a loxP site between the tetR component and the VP16 component. When tetracycline is present this gene switch is silent. As shown in FIG. 1A, upon introduction into a target cell in the absence of tetracycline, the tetR-loxP-VP16 fusion protein is produced, stimulating further production of the fusion protein, and the cre protein. The cre protein then acts to promote site specific recombination between the loxP site in the tetR-loxP-VP16 coding sequences, and a distant loxP site. As a result of this recombination, the fusion protein coding sequence is disrupted so that the promoter no longer directs the formation of a tetR-loxP-VP16 fusion protein, but gives rise to an inert tetR-loxP-VP16 fusion protein for binding to the promoter upstream elements, thereby extinguishing promoter activity.

[0093] As shown in FIG. 1A, the excised circular DNA element contains at least two transcription units. In addition, other transcription units or internal ribosome entry site elements may be used to allow the coexpression of gene products which are useful for extending the persistence of the delivered DNA, regulating expression of the gene of interest, or providing for ablation of the transduced cells once their presence is no longer desirable. In addition, the linear DNA remaining after excision of the circular gene expression plasmid lacks both viral packaging sequences and the cis-acting enhancer. Within this linear DNA, additional loxP sites may be placed to provide for the rearrangement of the remaining vector DNA in the target cell, disrupting the normal topology of the genes, and further thwarting expression.

[0094] Using the type B vector design strategy, described in greater detail below, a recombinant adenoviral gene delivery system that is capable of undergoing growth phase-dependent site-specific recombination has also been constructed.

[0095] The following examples are presented for the purpose of illustrating, not limiting, the invention.

Type B Vectors—Experimental Results

[0096] Several experimental examples for constructing type B vectors and for carrying out the general approaches of the invention are now described below.

[0097] Two-Cosmid System for Efficient Construction of Recombinant AdV

[0098] To simplify and facilitate the generation of recombinant AdV, a system was established to assemble the desired AdV genome in a single plasmid by ligation (shown in FIGS. 2A and 2B). The system consists of two component vectors, a left end plasmid, pLEP, and a right end plasmid, pREP. The left end Ad sequences (nt 1-376) in pLEP include the viral inverted terminal repeat, the cis-acting packaging sequences, and the viral enhancer. Nucleotide (nt) positions described herein refer to the wild type Ad2 sequence in GenBank (J019017). The Ad sequences are followed by the gene expression unit intended for delivery and an intron endonuclease (PI-PspI) cleavage site. The right end plasmid contains a PI-PspI site followed by the Ad2 genome from the end of the E1 locus rightward (nt 3527-35937).

[0099] pLEP is a small tractable vector for cloning, whereas pREP is much larger and contains less frequently manipulated genes. Both pLEP and pREP contain a bacteriophage γ cos site, oriented to generate a single cosmid of appropriate length for in vitro packaging following ligation of the two plasmids at the PI-PspI cleavage site. pLEP is tetracycline resistant (Tetr) and pREP is ampicillin (Ampr) resistant, allowing the recombinants to be selectively isolated by co-selection for both markers. In the resulting assembled cosmid, the adenoviral sequences are closely flanked by cleavage sites for the intron endonuclease I-CeuI. Digestion with I-CeuI liberates the entire recombinant AdV genome from the parent cosmid (see FIG. 2B).

[0100] Three classes of pREP have been constructed to allow the preparation of AdVs bearing E1 (pREP7; SEQ ID NO.: 2), E1 and E3 (pREP8; SEQ ID NO.: 3), or E1, E3, and E4 (pREP12; SEQ ID NO.: 4) deletions. pREP7 (SEQ ID NO.: 2) contains nt 3527-35937 of the Ad2 genome, and pREP8 (SEQ ID NO.: 3) carries an additional deletion in the E3 region (Δ nt 27901-30841). pREP12 (SEQ ID NO.: 4) has deleted open reading frames (ORF) 1-4 of the E4 region (Δ nt 34121-35469, 1348 bp). AdV generated with these cosmids should be able to accommodate 5, 8, and 10 kb inserts, respectively.

[0101] These aforementioned vectors were constructed as follows. The EcoRI to BsaI fragment that spans the ampicillin resistance gene in pBR322 was deleted and replaced by a synthetic adapter, and the bacteriophage γ cos site was inserted between the unique StyI and BsmI sites. A PCR amplified Ad2 fragment containing the left end ITR (L.ITR), enhancer elements, and the encapsidation signal (nt 1-376) was created and inserted into the adapter (FIGS. 2A, 2B) to yield the tetracycline-resistant left-end plasmid pLEP. The right end of Ad2 from the AflII site to the right end (nt 3527-35937) was assembled into an ampicillin resistant cosmid vector, pACKrr3 (SEQ ID NO.: 1), by multiple steps of PCR amplification and fragment interchange. The resultant cosmid was termed pREP7 (SEQ ID NO.: 2). To expand vector capacity, two deletions were incorporated into the pREP7 (SEQ ID NO.: 2) cosmid, an E3 gene deletion (nt 27901-30841, 2840 bp); cosmid pREP8 (SEQ ID NO.: 3) and a 1.3 kb deletion (nt 34121-35469) in the E4 region of the Ad2 region; pREP12 (SEQ ID NO.: 4) An example of the construction of an AdV carrying a CMV-GFP expression unit is outlined in FIG. 2. pLEPCMVGFP (Tetr) was digested with PI-PspI and ligated to the pREP7 (SEQ ID NO.: 2; ΔE 1, Ampr) digested with the same enzyme. The ligation mixture was packaged with γ phage extracts (MaxPlax lambda packaging extracts, Epicentre Technologies) and a fraction of the packaged phage was used to infect a recombination-deficient E. coli host, with selection for the assembled plasmid on Amp/Tet plates. Transductants containing pLEP fused to pREP were selected on agar containing 25 μg/ml ampicillin and 12.5 μg/ml tetracycline (Amp/Tet). Colonies were selected and DNA isolated (Qiagen). DNA was used either for restriction analysis or for tranfection of 293 cells as described herein.

[0102] FIG. 3A shows typical results for the Bgl II digestion pattern of a pLEP3CMVGFP/pREP7 hybrid cosmid, pAd2-7CMVGFP DNA. Because of the size minimum (˜40 kbp) for γ phage in vitro packaging and the double antibiotic selection, most of the colonies growing on Amp/Tet plates were the desired hybrid cosmids, and undesired rearrangements were rarely seen. In the present example, all four pAd2-7CMVGFP clones exhibited the digestion pattern predicted from the inferred sequence. The entire recombinant AdV genome was then released from the cosmid by I-CeuI digestion (FIG. 3B). I-CeuI digestion leaves ten nucleotides to the left of the left ITR and eight nucleotides to the right of the right ITR. Short flanking sequences have been reported to be eliminated during replication of recombinant viruses after transfecting the DNA into 293 (human embryonic kidney) cells (Hanahan et al., Mol. Cell. Biol. 4:302-309, 1984).

[0103] The digestion reaction can be transfected into 293 cells without purification as follows. 293 cells, obtained from Microbix Bisosystems (Ontario, Canada), were cultured in 10 cm dishes in complete Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% FBS, 2 mM glutamine and penicillin/streptomycin (Gibco BRL), and maintained at 37° C. and 5% CO2 atmosphere in an incubator. Cells were grown to ˜50% confluence on the day of transfection. Ten fig of cosmid DNA were digested with I-CeuI in a volume of 50 μl. The reaction mixture was transfected into 293 cells by calcium phosphate precipitation (Graham and Prevec, Manipulation of adenovirus vectors, p. 109-128, In E. J. Murray (ed.), Methods in Molecular Biology, vol. 7, Humana, Clifton, N.J., 1991) without purification. After transfection, cells were cultured and examined daily for the appearance of cytopathic effects (CPE). Virus propagation, purification, plaque assay, and viral DNA isolation were performed using established protocols (Graham and Prevec, supra). At day six post-transfection, 5-30 viral plaques/10 cm dish/10 ug DNA were usually apparent, which compared favorably with the 30-50 plaques/10 cm dish/10 μg DNA found for 293 cells transfected with purified wild type Ad2 DNA.

[0104] To compare the efficiency of recombinant virus production, similar viruses were also generated by homologous recombination. 20 μg of pREP7 (SEQ ID NO.: 2) was co-transfected into 293 cells with 10 μg of a plasmid encoding the left end of the adenoviral genome and a green fluorescent reporter gene (pLITREF1αGFP). pLITREF1αGFP contained the Ad2 left end nt 1-376, an EF1α promoter/GFP expression unit and Ad2 sequence (from 3525-8120) that overlaps with the same sequence in pREP7 (SEQ ID NO.: 2). This overlap fragment served as the region for homologous recombination. Each co-transfection was performed in duplicate. Initial plaques took longer to appear (14 days post transfection) and were less abundant (0-3 plaques per plate).

[0105] Data in the literature suggest that exposed ITR ends favor efficient virus production (Hanahan et al., supra). To assess the importance of this effect, an AdV cosmid, pIAdEF1αGFPB, in which the AdV ITRs were flanked with a different restriction site at each end was constructed. pIAdEF1αGFPB DNA was digested with BsaBI to expose the right ITR, I-CeuI to expose the left ITR, or the two enzymes were used together to expose both ends. Digested cosmid DNA samples were transfected into 293 cells and plaques were allowed to develop. Virus propagation, purification, plaque assay, and viral DNA isolation were performed using established protocols described in Graham and Prevec. (Manipulation of adenovirus vectors, In E. J. Murray (ed.), Methods in Molecular Biology, vol. 7. Humana, Clifton, N.J., pp. 109-128, 1991).

[0106] Ten days after transfection the viruses were harvested and viral titers were determined. The average titer for the viral stocks (FIGS. 4A and 4B) was 1.3×104 pfu (plaque forming unit)/ml from transfection with undigested DNA; 2.4×105 pfu/ml from BsaBI linearized DNA (free right ITR); 1.1×105 pfu/ml from I-CeuI linearized DNA (free left ITR); and 2.7×106 pfu/ml for the BsaBI/I-CeuI double digested DNA (both ITRs free). Thus liberation of each end resulted in an approximate increase in the efficiency of generating virus by a factor of ten (FIGS. 4A and 4B).

[0107] Construction of an AdV Capable of Self-Rearrangement

[0108] One approach to attenuating adenoviral gene expression and improving transgene persistence is the creation of viruses capable of undergoing internal, self-directed rearrangement upon delivery to the target tissue. In principle, this objective can be achieved through the regulated expression of site-specific recombinases in vectors that contain the cis-acting target of recombinase action. To allow such vectors to be created, the recombinase activity must be suppressed during propagation in the packaging cell line. As described in more detail below, the use of a lineage-specific promoter to control recombinase expression has been successfully employed to achieve this end.

[0109] An example of this is shown in FIG. 5. The expression of Cre recombinase was controlled by a liver-specific promoter constructed as follows. The human hepatic control region 1 and 2 (HCR1 and 2) of the ApoE/C gene locus (Allan et al., J. Biol. Chem. 270:26278-81, 1995; and Dang et al., J. Biol. Chem. 270:22577-85, 1995) were amplified by PCR using 293 cell genomic DNA as the template. The following primers were used to amplify both HCR1 and HCR2 fragment: HCRtop-5′gcggaattcggcttggtgacttagagaacagag 3′ (SEQ ID NO.:5); HCRbot-5′ gcgggatccttgaacccggaccctctcacacta 3′ (SEQ ID NO.:6). The amplified PCR fragments (˜0.39 kb) were cloned into pUC19. The HCR1 and HCR2 sequences were confirmed by dideoxy DNA sequencing. The two fragments were assembled in a head to tail orientation, fused with a synthetic basal TATA element and cloned in a parental pLEP vector containing a GFP reporter gene. The resultant plasmid was named pLEPHCR12GFP. The synthetic liver-specific, as demonstrated below, provided a means to control Cre recombinase expression during propagation of the vector in 293 cells, and allowed for testing the consequences of abstracting the enhancer from the linear vector DNA upon delivery of the DNA to the target cells.

[0110] In 293 cells, this promoter is silent, allowing the viral chromosome to be propagated with minimal rearrangement. Any rearranged viruses that are formed lack packaging signals and so disappear from the pool of propagating vectors. In liver cells the Cre recombinase is induced by the action of the tissue-specific promoter. The resulting Cre-induced recombination excises a circular episome and redirects the transcriptional output of the liver-specific promoter so that it directs the synthesis of the transgene of interest. The remaining linear fragment consists of an adenoviral genome lacking the enhancer and packaging signals and a Cre expression unit devoid of promoter sequences.

[0111] In the form discussed here, one loxP site is located at nucleotide 147 of the Ad2 genome, between the left ITR and the enhancer/packaging sequences, and the second loxP site is placed inside an intron a few bases upstream of the splice acceptor sequence. Hence the loxP site does not appear in the resulting mature transcript. The Cre coding sequence that remains on the right end linear fragment after rearrangement lies downstream from a splice acceptor that lacks a splice donor or upstream promoter sequences. This effectively terminates the expression of Cre following excision.

[0112] Prior to recombination, the Cre recombinase gene is under the control of a synthetic promoter (referred to as HCR12), consisting of hepatic locus control elements from the human ApoE/C locus fused to the first intron of the human EF1α gene. After cyclization the HCR12 promoter lies upstream of the transgene (in this case GFP) and the distal segment of the intron (beyond the loxP site) contains the adenoviral enhancer. To facilitate manipulation of the plasmids in E. coli, the human IgG 1 hinge-CH2 intron (118 bp) was inserted in the Cre coding sequence at nucleotide 237, suppressing Cre expression in bacteria. The circularized episome contains the latent origin of replication (OriP) and trans-acting DNA replication protein (EBNA-1) of Epstein Barr virus, and hence is capable of autonomous replication in synchrony with the host mitotic cycle (Yates et al., Nature 313:812-815, 1985).

[0113] Using the two cosmid system described above, the pLEP plasmid containing the self-resolving components, pLEP1BHCR12, was ligated with pREP8 (SEQ ID NO.: 3; ΔE1ΔE3) to create pAdVHCRGFP/EBV. The latter was digested with I-CeuI and transfected into 293 cells. Appearance of plaques from AdVHCRGFP/EBV was retarded (by 8 days) compared to non-rearranging viruses, perhaps as a result of basal expression of the liver-specific promoter in 293 cells. However high titer viral stocks of 1012 nominal (absorbance-determined) particles/ml was achieved.

[0114] Rearrangement in Target and Nontarget Cells

[0115] To test excision efficiency, HepG2 (hepatocellular carcinoma) and Hela (cervical carcinoma) cells, obtained from ATCC, were infected with virus at a multiplicity of infection (moi) of 1,000 nominal particles/cell. This titer corresponds to approximately 10 plaque forming units per cell. For these experiments, HepG2 and Hela cells were seeded in 35 mm dishes and cultured to approximately 80% confluence in DMEM/FBS as described herein. Cells were infected with the desired multiplicity of virus in a volume of 1 ml at 37° C. for 2 hours. At the end of the incubation, cells were washed with PBS twice and cultured in 2 ml of medium. Cells were collected in parallel at desired points for low molecular weight DNA and RNA extraction. Cells were examined for GFP expression by fluorescence microscopy (Olympus, IX70) or microtiter plate reader (PerSeptive Biosystem, CytoFluor II) before extraction of DNA for analysis of chromosomal rearrangement.

[0116] DNA analysis of chromosomal rearrangement was performed as follows. 5 μg of Hirt DNA was digested with Bgl II and analyzed by DNA blot techniques using a labeled EBNA-1 gene fragment as probe (FIG. 6). The Bgl II fragment from the non-circularized AdV is 3162 bp, generated from the 5 ′end of the AdV to the first BglII site in the AdV. The circularized fragment created from the two loxP sites has a size of 4915 bp (FIG. 6A). Densitometry revealed that at 72 hours post infection, 95% or more of the input genomes had undergone circularization in HepG2 cells. In contrast, low but detectable levels of circularized fragment was visualized in Hela cells infected at the same time and at the same multiplicity of infection used for the HepG2 cells (FIG. 6B).

[0117] At the time of infection (t=0, FIG. 6B), the amount of input viral DNA detected by DNA blot was higher for HepG2 cells than for Hela cells when similar virus multiplicities were applied (moi of 1,000). This may reflect differences in AdV adsorption or infection efficiency between the two cell types, possibly as a result of the lower levels of coxsackievirus-adenovirus receptor on the Hela cells surface. To achieve similar viral genome input into HepG2 and Hela cells, Hela cells were infected with ten-fold more virus (moi of ˜10,000) than HepG2 cells (moi of 1,000). Episomal DNA samples were extracted and analyzed by blotting. The results (FIG. 6C) indicated that when comparable amounts of viral genome are present in the nucleus, the cyclization rate in both cell types was similar. Because the level of subsequent GFP expression is much higher in HepG2 cells than in HeLa cells (FIG. 7A), it is likely that very small amounts of Cre recombinase suffice to promote rearrangement, and that recombinase expression is not limiting for rearrangement in either HepG2 or HeLa cells.

[0118] GFP expression cannot be detected until rearrangement has taken place, so the measurement of the fraction of GFP positive cells provided a simple alternate method for assessing the degree of productive rearrangement. FIG. 7A shows that GFP expression developed quickly in transduced HepG2 cells, but that only a few GFP positive cells can be detected in Hela cells infected with a ten fold higher moi, conditions that allow circularization to a comparable extent to that seen in HepG2 cells (FIG. 6C).

[0119] The HCR12 promoter specificity was also tested by infecting two additional non-hepatic cell lines, A431 (human epidermoid carcinoma) and HT29 (human colon adenocarcinoma), with the Ad2HCRGFP/EBV vector. Both cell lines were obtained from ATCC and cultured using DMEM/FBS as described herein. A few cells, with weak GFP signal, were detected at 72 hours after infection in these cells (FIG. 7B). In contrast, these non-hepatic cells could be infected efficiently with a first generation AdV, Ad2CMVGFP virus (data not shown), indicating that the low GFP signal was not due to the low infectivity of these cells by AdV.

[0120] To further assess the utility of the AdV genome rearrangement, primary human hepatocytes were infected with the Ad2HCRGFP/EBV vector. For these experiments, primary human hepatocytes, generously provided by Dr. Albert Edge (Diacrin, Inc., Charlestown, Mass.) were isolated and cultured as described by Gunsalus et al. (Nat. Med. 3:48-53, 1997), infected with adenovirus, and GFP expression was analyzed. As shown in FIG. 7C, GFP expression was readily detected 72 hours after infection.

[0121] Diminished Viral Gene Expression in Rearranged AdV

[0122] After excision, the adenovirus major enhancer/packaging signal segregates with the episomal DNA, yielding a linear fragment containing the remainder of the AdV genome without this important cis-element (FIG. 5). To assess the impact of enhancer deletion, PCR amplification and quantitative RT-PCR measurement of late viral gene expression was performed as follows.

[0123] Four μg of total RNA was reverse transcribed into cDNA using M-MLV RT by a standard protocol (Promega). 1 μl of the cDNA from each sample was used in subsequent PCR reactions. PCR primers were designed to amplify the tripartite leader sequence of the adenovirus late genes: TPL1-5′ act ctc ttc cgc atc gct gt 3′ (SEQ ID NO.: 7) and TPL2-5′ ctt gcg act gtg act ggt tag 3′ (SEQ ID NO.:8). For detection of the AdV genome in the Hirt DNA samples, 1 μg DNA was employed in the PCR amplification using the following primers which are specific for the adenovirus DNA in the fiber gene: Fiber1-5′ ccg cac cca cta tct tca ta 3′ (SEQ ID NO.: 9) and Fiber2-5′ ggt gtc caa agg ttc gga ga 3′ (SEQ ID NO.: 10). PCR reactions were performed as 95° C. 30 seconds; 54° C. 30 seconds; 72° C. 30 seconds for 30 cycles. All amplified products were analyzed on a 2% agarose gel.

[0124] For quantitative PCR, a molecular beacon based universal amplification and detection system was used (Intergen). A common leading sequence (Z sequence, 5′ act gaa cct gac cgt aca 3′) was added to the TPL1 and Fiber1 primers. The TPL2 and Fiber2 primers, described above, were used in the quantitative PCR reactions. 1 μl of the cDNA and one μg of Hirt DNA from each sample were used in the assay. The PCR were carried out in a 96-well spectrofluorometric thermal cycler (Applied Biosystems Prism 7700). The number of template molecules in the PCR reaction was calculated from the standard curve using linearized plasmid as templates.

[0125] As most late adenoviral genes transcripts share a common ˜200 bp tripartite leader sequence (TPL) (Akusjarvi and Persson, Nature 292:420-6, 1981), the TPL sequence was chosen as a marker of viral gene expression. HepG2 cells were infected with the first generation vectors Ad2CMVGFP and Ad2HCRGFP, or the self-resolving vector, Ad2HCRGFP/EBV, using increasing multiplicities of infection. Total cellular RNA and low molecular weight DNA were isolated in parallel as described by Hirt (J. Mol. Biol. 26:365-9, 1967) and total RNA was prepared using RNAzol solution (Te1-Test. Inc.). RT-PCR was performed to quantitate the amount of RNA encoding the TPL in the cDNA samples. PCR amplification of a 201 bp fiber gene fragment from the AdV genome was used to detect the amount of viral genome in the DNA samples. A representative result of three experiments is shown in FIG. 8A. TPL sequences were detected, 72 hours post-infection, with either 100 or 1000 viruses infected per cell, using both of the first generation adenoviruses (upper panel).

[0126] In contrast, no TPL signal was detected in the self-resolving Ad2HCRGFP/EBV infected cells, even at a moi of 100,000/cell. PCR amplification of the AdV fiber gene revealed comparable levels of AdV genomic DNA in cells infected at comparable moi's. (FIG. 8A, lower panel). The cDNA samples in which the TPL signals were detected were further analyzed by real-time fluorescence PCR. The corresponding genomic DNA samples were also analyzed to determine the number of AdV genomes present in each sample. The results are summarized in FIG. 8B. There were approximately 1×104 TPL per 1×106 AdV genomes detected in the Ad2HCRGFP infected cells, but no detectable TPL in the self-resolving Ad2HCRGFP/EBV infected cells. These results indicate that adenoviral gene expression was dramatically reduced by the separation of the viral enhancer sequences occasioned by the re-arrangement of the self-resolving vector.

Type A And Type B Vectors—Experimental Results

[0127] Additional experimental examples now follow that further illustrate the general approaches of the invention relating to using and constructing type A and type B vectors. For generating such adenoviral vectors, DNA sequences important for gene expression in the target tissue were placed between two loxP sites. The first loxP site was inserted between the Ad2 left-end inverted terminal repeat (ITR) and the enhancer sequence, replacing a BspLU11I and BstZ17 fragment of Ad2. A target gene expression cassette, comprising a promoter, a gene of interest, polyadenylation signals, the EBV replicon, and site specific recombinase expression unit were inserted in place of the E1 locus.

[0128] In type A adenoviral vectors, the second loxP site is placed between TetR and VP16, preserving the coding frame of both (FIG. 1A). A bidirectional promoter in which a central heptamer of tetracycline operator sites (TetO) (Gossen and Bujard, Proc. Natl. Acad. Sci. USA 89:5547-5551, 1992) was flanked by two divergently oriented basal elements, directs the expression of TetR loxP VP 16 from a synthetic TATA element, whereas Cre recombinase is controlled by the same heptamer of operator upstream of the HIV LTR basal element.

[0129] In the case of type B viruses (FIG. 1B), the second loxP site was inserted in the first intron of the Ef1α gene, which contains the transcription stimulating sequences described herein. In addition, a splice acceptor sequence was added to the 5′ end of the coding sequence of the gene of interest. To avoid rearrangement during plasmid construction in bacteria, the Cre recombinase coding sequence was interrupted by the addition of the human IgG1 hinge-CH2 intron (between amino acids Q78 and A79), as described herein.

[0130] Designing a Compact EBV Replicon

[0131] Most plasmids employing the EBV latent origin of replication exceed 10 kb in length. To provide a means for increasing the capacity of the recombinant adenoviral type A or type B vectors to accommodate a therapeutic gene, a compact EBV replicon having episomal stability was designed. To this end, deletions were generated in both the cis-acting origin of replication, OriP, and the sequences encoding the trans-acting replication protein, Epstein Barr virus nuclear antigen-1 (EBNA-1) (FIG. 9A). Episomal persistence was assessed with a green fluorescent protein (GFP)-bearing test plasmid by determining the fraction of cells retaining green fluorescence as a function of time, assuming that the half-life of GFP, in daughter cells that have not received an episome as a result of segregation failure, is approximately 1.4 days (Fukumura et al., Cell 94:715-725, 1998).

[0132] EBNA-1 contains a central repeated structure that consists entirely of Gly and Ala residues, termed the GA repeats (FIG. 9A). Although deletion of this structure has been reported to have little consequence, a deletion mutant consisting of both a short OriP and a short EBNA-1 (SoriP +SEBNA1) was generated and found not to support plasmid maintenance effectively (approximately 40% loss per cell division). A version of this mutant, reconstructed with 40 GA repeats, in which the short OriP was paired with a short EBNA-1 provided significantly better plasmid stability (20% loss per cell division vs. 10% per cell division for the wild type) (FIG. 9B). Since most target tissues are relatively quiescent mitotically, this level of segregation fidelity provides reasonable stability in a compact replicon.

[0133] Producing Cell Lines that Express Cre- or FLP-Dominant Negative Mutants

[0134] As discussed herein, one obstacle to creating adenovirus carrying both recombinase and target sites has been the difficulty of controlling recombinase activity during virus propagation. Since efficient recombinase activity is needed in target cells, recombinase activity is best tempered in the production cell line.

[0135] Vector-independent methods to suppress recombinase activity during the production phase are attractive because they allow vector design objectives to be pursued with fewer constraints. In principle, dominant negative recombinase mutants provide the desired antagonism of recombinase activity. Cell lines expressing such recombinase dominant negative mutants were produced as follows.

[0136] Dominant negative Cre mutants were selected from known point mutants (Wierzbicki et al., J. Mol. Biol. 195:785-794, 1987) that are defective in recombination function but are likely to retain dimerization function FIGS. 10A-E. Several mutants were screened for their abilities to inhibit Cre activity of a type B vector construct (ad2239 in FIG. 10B) in a transient cotransfection assay. Under these conditions, Cre activity is detected by the expression of GFP that occurs upon rearrangement. FIGS. 10D and 10E show the point mutants that were assessed and their relative activities in the transient cotransfection assay. Dilution studies, in which increasing amounts of substrate/Cre plasmid were cotransfected with the mutant forms, were conducted and based on its favorable profile, one mutant recombinase, designated CreY324C, was chosen for further development (FIG. 10D).

[0137] Strong constitutive expression of CreY324C, under control of the Ef1α promoter failed to yield stable cell lines. Stable clones were obtained when the Ef1α promoter was replaced with a tetracycline regulated promoter (Gossen et al., Science 268:1766-1769, 1995). Clones were then tested for the ability to inhibit Cre enzymatic activities, and one clone, designated cell line #17, was selected for additional experiments. When a plasmid bearing Cre and capable of undergoing Cre-directed rearrangement to create a GFP transcription unit (ad2239) was transfected into #17 cells or parental 2930N cells, GFP expression in the #17 cells in the presence of 2 μM doxycycline was significantly lower than those of controls (FIG. 11), showing that Cre enzyme activity can be inhibited in #17 cells.

[0138] In addition to dominant negative Cre mutants, dominant negative FLP mutants may also be identified. FLP belongs to the same family of site-specific recombinases as Cre recombinase. A number of FLP mutations that show defects in either cleavage or ligation of FRT sites have been identified. Mutant FLP defective in cleaving FRT site (for example, H309L, L315P, G328R, G28E, N329D, S336Y, S336F, A339D, Y343F, and H345L) are generated using standard methods. Mutants that inhibit the wild type enzyme are then identified for generating stable cell lines according to the methods described above. These and the other cell lines (described herein) are then used for producing FRT/FLP containing virus.

[0139] As mentioned above, difficulties creating stable cell lines expressing Cre dominant negative mutants were occasionally encountered. This difficulty was not limited to Cre mutants, but was also observed with the wild-type Cre enzyme. In contrast, 293 cell lines stably expressing a thermostable FLP, referred to as FLPe (Buckholz et al., Nat. Biotechnol. 16:657-662, 1998), were created, suggesting that FLPe might not be as cytostatic as Cre protein. To demonstrate this, 293 cells were transfected with plasmids expressing either Cre or FLPe, and puromycin resistant colonies were selected. To generate stable cell lines expressing Cre or FLP mutants, 293 TetON cells were transfected with linearized plasmid expressing Cre or FLP mutants and puromycin acetyltransferase and selected with 1 μg/ml of puromycin. Puromycin resistant colonies were characterized further for their ability to inhibit Cre recombinase using the cre (ad2239) or flp (ad2879) substrate plasmids. Table 1 shows that there are more puromycin resistant colonies selected from FLPe transfected cells than from Cre transfected cells. From this result, it is expected that stable cell lines expressing a reasonably high level of dominant negative FLP may be readily created.

TABLE 1
Puromycin Resistant Colonies Formed When Cre
Expressing or FLPe Expressing Plasmid was
Used to Transfect 293 Cells
Expression Plasmid Number of colonies (2 μg/ml puromycin)
Control            236
Cre                92
FLPe               127

[0140] Cre or Cre dominant negative mutants were also found to inhibit FLP activity (Table 2). Accordingly, cell lines, such as cell line #17, that stably express a Cre dominant negative mutant (for example, CreY324C), are useful for producing FLP/FRT carrying adenovirus.

TABLE 2
Cre Inhibition of FLP Activity in trans
Plasmids                         Arbitrary GFP intensity
Ef1α FLP + FLP substrate + vector control 4.9
Ef1α FLP + FLP substrate + Ef1α Cre 0.78
Ef1α FLP + FLP substrate + Ef1α Cre R173C 2.23
FLP enzyme activity was measured by the GFP intensity by cotransfecting with a FLP substrate plasmid, ad2879 (FIG. 19A). GFP intensity was quantified using IP lab software.

[0141] Transcriptional Regulation of Cre or FLP Recombinases

[0142] It has been relatively difficult to achieve high-level promoter inducibility in a replicating adenovirus. The challenge is similar to that of achieving faithful control of transcription in a transient expression setting. One approach to increase the induction ratio in a transient setting is the use of auto-regulatory (feed-forward) circuits. One such system, based on tetracycline dependent activation, is shown in FIG. 12. A central heptamer of tetracycline promoter operator sites (TetO sites) was placed between two divergently oriented basal TATA elements. The leftward TATA controls the expression of the TetR-VP16 fusion protein, in which a loxP (or FRT) site has been placed between the TetR DNA binding domain and the VP16 transcriptional activator. The rightward TATA box directs the synthesis of recombinase, either Cre or the yeast FLP enzyme. In the presence of tetracycline, the promoter has reduced activity in both directions. Upon removal of tetracycline, the synthesis of both TetR-VP16 and recombinase are induced (FIG. 1A). The induced recombinase then disjoins the TetR DNA binding element from the transcriptional activation contributed by VP16. Any existing TetR-VP16 fusions thereafter promote transcription of TetR, which competes with TetR-VP16 for TetO, resulting in deinduction of recombinase transcription.

[0143] When a model target cell line, HepG2, was tested with this type of adenovirus, the efficiency of circularization was low relative to that seen in 293 cells (data not shown), indicating a cell dependence of the bidirectional TetO promoter. To correct this, the TATA element of the TetO synthetic promoter (derived from the CMV immediate early promoter) was replaced with that of the HIV LTR. Constructs bearing differing components of the HIV basal promoter were analyzed for strength and regulation in 293 and HepG2 cells (FIG. 13A). Among the constructs tested, one version bearing the HIV LTR TATA and Sp1 elements (D in FIG. 13A) showed the least basal expression in 293 cells (data not shown) and the greatest induction in HepG2 cells (FIG. 13B).

[0144] Using this promoter, a construct (ad3400) containing the auto-regulatory structure D as shown in FIG. 13A was engineered, and Cre activities in the presence and in the absence of tetracycline were assayed. Plasmid ad2265 (FIG. 14) in which a blue fluorescent protein (BFP) expression unit is interrupted by two loxP sites and transcription termination sequences was used as a substrate for Cre. Cre-mediated recombination joins BFP to the promoter resulting in BFP expression. As shown in Table 3, no difference was found in the intensity of BFP expression, either in the presence or absence of tetracycline. One possible explanation for this is that very little Cre protein is required for activity. Consistent with this idea, standard imunohistochemical techniques failed to reveal the presence of Cre enzyme in cells that were fully induced (data not shown).

TABLE 3
Cre Recombinase Activity Regulation in Type A Constructs
Construct	Cre Form	+tet −tam	−tet −tam	+tet +tam	−tet +tam
ad3400	Cre	2.58	3.39	2.71	6.20
ad4394	Cre-LBD	0.081	0.22	0.056	1.02
ad4705	LBD-Cre-	ND	ND	ND	ND
	LBD
Cre enzyme activity was measured in the presence or absence of the ligands, tamoxifen, by cotransfecting with the substrate plasmid (ad2265).
BFP intensity (mean intensity/area) was quantified by analyzing fluorescent images captured by a digital camera using IP lab software.
ND, refers to fluorescent intensities that were too weak to measure.
Tet, Tetracycline; tam, tamoxifen; LBD, ligand binding domain

[0145] Deletion of the PolyA Consensus Sequence from Cre or FLP Transcription Units

[0146] To reduce the expression of FLP or Cre recombinase further, the consensus polyA addition signals from the Cre or FLP transcript unit were deleted from vector constructs, leaving polyadenylation dependent on distal downstream sequences, for example, in gene IX. The activity of Crc using type B proviral constructs with or without the polyA signal was measured. As shown Table 4, the construct without polyA signals (AD229.3) showed a significant reduction of GFP intensity compared to a construct bearing the polyA signal (AD230.5). When FLPe constructs of similar structure were evaluated, similar results were found (data not shown). These data show that Cre and FLPe enzyme activity levels can be modulated by attenuating polyadenylation.

TABLE 4
Effect of Deleting polyA Addition Signal From the Cre
Expression Unit on Cre Enzyme Activity Level
		polyA	Relative GFP Intensity
	AD229.3	−	0.25
	AD230.5	+	1

[0147] Post-Transcriptional Regulation of Cre Recombinase Activity

[0148] Post-transcriptional control mechanisms of Cre recombinase activity were also evaluated. Translational fusions between Cre and the ligand binding domain (LBD) of estrogen receptor have been reported to be regulated by estrogen (Feil et al., Proc. Natl. Acad. Sci., U.S.A 93:10887-10890, 1996; Gossen et al., Proc. Natl. Acad. Sci., U.S.A. 89:5547-5551, 1994), or, in the case of mutant estrogen receptors (Metzger et al., Proc. Natl. Acad. Sci. U.S.A. 92:6991-6995, 1995), by the partial antagonist tamoxifen.

[0149] Use of a ligand-dependent recombinase (ad4394 in Table 3), in combination with the HIV LTR-based autoregulated Tet system, allowed for a small degree of regulation by tetracycline, but not by ligand, as assayed using the ad2265 rearrangement assay (Table 3). One interpretation of this finding is that fusion of the estrogen receptor LBD to Cre provides only modest control of recombinase activity, but attenuates enzyme potency to a level so that transcriptional regulation can be measured.

[0150] To increase control of recombinase activity, the LBD was fused both to the N-terminus and C-terminus of Cre (LBD-Cre-LBD) and inserted into the coding sequence of both type A and type B vectors. When the LBD-Cre-LBD construct of type A was transfected into 293 cells, it showed no significant Cre enzyme activity even in the presence of ligand (Table 3). This result confirmed that the Cre recombinase activity is attenuated by N-terminal or C-terminal extension.

[0151] When the LBD fusion Cre enzymes were assayed in the type B vector context, only LBD-Cre-LBD fusions (pk8-ad4626) showed ligand-dependent regulation of Cre enzyme activities (Table 5). It appears that attenuated Cre activity in LBD-Cre-LBD, in the absence of ligand, is low enough to fall below the upper limit of the Cre assay.

TABLE 5
Cre Enzyme Activities of Type B Provirus
	Cre Form	Provirus	−tam	+tam
	Cre	pk8-ad2239	ND	ND
	Cre-LBD	pk8-ad4332	4.1	6
	LBD-Cre-LBD	pk8-ad4626	0.05	4.2
	Cre enzyme activity was measured in the presence or absence of the ligands, tamoxifen. GFP intensity was quantified using IP lab software.
	tam, tamoxifen.

[0152] Consistent with this notion, only the construct carrying two LBDs, pk8-ad4626, was able to produce virus (AD121.5) by transfection and propagate in 293 cells, while pk8-ad4332, which carried one LBD, produced virus (AD100.9) initially (following transfection of the cognate DNA), but was unable to propagate in 293 cells (Table 6). In the case of wild type Cre, no virus was produced in 293 cells by transfection.

TABLE 6
Production and Propagation of Type B Adenovirus
			Viral	Viral
		Viral	Prop-	Prop-
	Type B	Production in	agation in	agation in
Cre Form	adenovirus	293 cells	293 cells	#17 cells
Cre	Pack8-2239	−	−	−
Cre-LBD	AD100.9	+	−	+
	(Pack8-4332)
LBD-Cre-LBD	AD121.5	+	+	+
	(Pack8-4626)

[0153] The AD100.9 virus was able to propagate in #17 cells expressing the dominant negative Cre Y324C, demonstrating that modulation of Cre activity is important for viral production. Thus, adenovirus carrying both two loxP sites and Cre in two different configurations were generated by controlling Cre activity.

[0154] Viral Rearrangement in Culture

[0155] Cre/loxP mediated rearrangement of the adenovirus in tissue culture cells has also been analyzed. As shown in FIG. 15A, the AD121.5 virus showed a significant increase in GFP expression in the presence of the ligand, estrogen, suggesting a successful rearrangement of the virus by Cre recombinases. When non-chromosomal DNA (Hirt, J. Mol. Biol. 40:141-144, 1969) was made from the cells and analyzed by DNA blot analysis, the viral DNA from estrogen treated cells was identified mostly in circular form (C in FIG. 15B), while the DNA from cells not treated with estrogen was found mainly in linear form (L in FIG. 15B).

[0156] To evaluate the efficiency of the self-rearranging viruses in vivo, high titer stocks of AD102.7 (a type A virus carrying LBD-Cre, pk8-ad4394) in #17 cells was prepared and purified by CsCl gradient ultracentrifugation. The titer of AD102.7 (4−6×1012/ml by OD) is comparable to or slightly exceeds that of control viruses (2−4×1012/ml by OD), which carry neither Cre nor a loxP site. To determine the efficiency of viral rearrangement in vivo and whether such rearrangement is dependent on the presence of ligand, AD102.7 virus (4×1011 pfu/mouse as determined by optical density) were injected via tail vein into Rag-2 mice that were pretreated with vehicle alone or 110 μg/day of tamoxifen for 7 days as follows.

[0157] Rag-2 mice were injected with either PBS (mock) or 4×1011 adenovirus particles (as determined by OD260) of type A virus, AD102.7, via the tail vein. At various times after injection, animals were sacrificed and the liver tissues were removed and frozen rapidly on dry ice. To visualize GFP expression in animal tissues, mice were anaesthetized and perfused with 4% paraformaldehyde containing 0.2% glutaraldehyde intracardially (Kafri et al., Natl Genet. 17:314-317, 1997), and the liver tissues were removed and fixed overnight at room temperature in the perfusion buffer containing 30% sucrose. The fixed tissues were sectioned serially and observed under confocal scanning laser microscopy. In experiments evaluating the responses of ligand-regulated recombinase, mice were injected either with vehicle (vegetable oil) alone or with 110 μg/day of tamoxifen for 7 days prior to adenoviral injection.

[0158] Liver tissues from these animals were harvested at 2.5 hours post injection (the earliest time point taken after injection) and Hirt DNA from approximately 250 mg of frozen hepatic tissue was prepared and analyzed by blot analysis. As shown in FIG. 16, the majority of adenoviral DNA was found in circular form in tissues from untreated mice, as well as tamoxifen-treated mice. It can be concluded from these data that the Cre enzyme activity present in the tissue, even in the absence of ligand was sufficient for efficient self rearrangement of virus. As expected, the hepatic tissues from the Rag2 mice injected with AD102.7 showed strong expression of GFP (FIG. 17).

[0159] Demonstrating that AD102.7 virus, produced efficiently in 293 cells at high titres by the conventional means, can self rearrange efficiently in vivo provides the proof of the concept that potentially safer adenoviral gene therapy vectors can be produced.

[0160] Adenoviruses Carrying Both FRT and FLP Recombinase

[0161] Type A and type B proviral constructs carrying both FRT (FLP recombinase recognition site) and FLP recombinase were also generated. Structures of these viruses are analogous to those of loxP/Cre carrying viruses except that loxP sites are replaced by FRT sites and Cre coding sequence is replaced by FLP coding sequence (FIGS. 18A, 18B).

[0162] Virus Production at Reduced Temperature

[0163] Temperature dependence of the Ef1α promoter using GFP expression as a marker was also examined. As shown in Table 7, Ef1α promoter activity is strongly reduced at 32° C. in comparison to 37° C. or 39° C. The temperature sensitive nature of the Ef1α promoter was used to propagate type B adenovirus carrying FLP at 32° C. following initial production of the virus by DNA transfection (pk8-ad3302) at 37° C. HepG2 cells infected with these viruses (AD41.4) showed strong GFP expression, but with an approximately 12 hour delay compared to GFP expressing viruses, suggesting that FLP recombinase activity may be impaired at 37° C. To improve the activity of FLP recombinase, viral constructs were created using a thermostable FLP (referred to as “FLPe”) described by Buchholz et al. (Nat. Biotechnol. 16:657-662, 1998).

TABLE 7
Effects of Temperature on Ef1α Promoter Strength
as Shown by GFP Intensities
	Arbitrary GFP Intensities
	Tester plasmids		32° C.	37° C.	39° C.
	Ef1α GFP	16 hrs	1475	7886	11409
		41 hrs	6472	36699	50787
		86 hrs	16256	53370	54424
	Ef1α Cre + ad2204	16 hrs	243	1141	2132
		41 hrs	1094	9119	9784
		86 hrs	695	3219	8144
	GFP intensities were measured using a Fluorescent reader.
	ad2204 is a cre substrate plasmid (FIG. 19B).

[0164] The activities of FLP and FLPe using a FLP substrate plasmid (ad2879, FIG. 19A) in 293 cells were compared. As shown in Table 8, FLPe is significantly more active than FLP under these conditions.

TABLE 8
FLPe is Significantly More Active than FLP Recombinase
	Plasmid		Mean GFP intensity
	ad4821	Ef1α FLPe	2.39
	ad2949	Ef1α FLP	0.01
	Plasmid coding either FLPe or FLP was cotransfected with a FLP substrate plasmid (FIG. 19A) into 293 cells. GFP intensity of each transfection was measured using IP lab program.

[0165] In addition, a tamoxifen-regulated FLPe was created by fusing the ligand-binding domain from a mutant form of estrogen receptor to the FLPe coding sequence at its C-terminus (FLPe-LBD). The FLPe-LBD was found to be regulated by the ligand, tamoxifen (Table 9). Although FLP activity was retained by C-terminal fusion (FLP-LBD), addition of a short oligopeptide tag to the N-terminus of FLP abolished its activity (data not shown).

TABLE 9
Tamoxifen Regulation of FLPe as
Determined by GFP Intensities
	Plasmid	FLPe	−tam	+tam
	ad4821 + ad2879	FLPe	++++	++++
	ad5022 + ad2879	FLPe-LBD(tam)	+	+++
	GFP intensity resulting from FLPe mediated recombination was measured using a fluorescent microscope.
	tam, 2 μg/ml tamoxifen.

[0166] Inhibition of FLPe Activities by Anti-sense FLPe

[0167] An anti-sense approach to inhibit FLP enzyme activity was also employed. This approach tested the notion that incorporation of an open reading frame into an antisense transcript would stabilize the transcript and potentiate antisense activity. Two approaches were utilized. In one approach, the BFP coding sequence was placed upstream of anti-FLPe. In the second approach, an anti-FLPe was placed upstream of an internal ribosome entry sequence (IRES) and the BFP coding sequence (FIG. 20). The ability of these constructs to inhibit FLPe was assayed using a FLP substrate plasmid, ad2879 (FIG. 19A) and the result is shown in FIG. 21. These data show that anti-sense FLPe is more effective in inhibiting FLPe function when it is fused to BFP, which can presumably be replaced with any other stable protein.

Other Self-Rearranging Adenoviruses

[0168] Mixed Infection With Adenoviruses Carrying loxP/FLP and FRT/Cre

[0169] One of the ways to produce adenoviruses that can be rearranged in target cells, but not producer cells, is to engineer two separate viruses, each carrying one recombinase and the target sequence for the other. To test this system, type B adenoviral constructs carrying Cre recombinase and FRT sites and FLPe recombinase and loxP sites were created (FIG. 22). In target cells infected with both viruses, Cre catalyzes recombination between the two loxP sites in the FLP virus, and FLP carries out FRT mediated recombination in the Cre virus, resulting in two circular plasmids. The loxP virus contained BFP, whereas the FRT virus contained GFP. Measurement of the fluorescent intensities of GFP and BFP, after cotransfecting the two constructs, revealed that BFP expression (mediated by Cre enzyme) was greater than GFP expression (mediated by FLP enzyme), suggesting that the Cre enzyme functions more efficiently than FLP.

[0170] Accordingly, these two recombinase activities in the target cells need to be balanced for complete circularization of both viral vectors. Exemplary methods for modulating Cre/FLP activity include the use of transcriptional regulation (such as by varying promoter strength and/or with or without poly A addition signal sequence) and translational and/or post-translational regulation (such as by changing FLP to FLPe and making LBD fusion proteins), and post viral production control (such as by changing the ratio of two viruses).

[0171] In one approach, Cre was replaced by Cre-LBD and FLP was replaced by FLPe. To improve identification of the rearrangement products, BFP was replaced with RFP as a marker for Cre recombination. As shown in Table 10, in the presence of estrogen, expression of GFP (FLPe mediated) and RFP (Cre mediated) were similar.

TABLE 10
RFP and GFP Expression of Cells Cotransfected
With Type B Proviral Constructs
Carrying Cre-LBD/FRT(GFP) or FLPe/loxP (RFP)
		GFP	RFP
Plasmids	Genotypes	intensity	intensity
pk8-ads120 +	Cre-LBD/FRT (GFP) +	Estrogen
pk8-ads113	FLPe/loxP (RFP)	−	+	−	+
		3222	3183	46	1954

[0172] To insure that both Cre and FLP carrying viruses with an optimal ratio infect each target cell, these viruses can be cross-linked prior to infection. For example, Cre carrying virus is labeled by biotin while FLP carrying virus is labeled by avidin. Mixing two types of modified viruses generates virus complexes of desired proportions as well. Biotinylation or avidinylation can be carried out using commercially available reagents such as EZ-Link TFP-PEO biotin (Pierce) and EZ-Link maleimide activated NeutrAvidin (Pierce). The extent of the biotin/virus and avidin/virus will be empirically determined to ensure the viability of the virus and to obtain an optimal ratio of two viruses in the complex. Optimal ratios will be those resulting in 1:1 Cre and FLP recombinase activities in target cells. The modifications will be done following manufacture's instructions.

[0173] This approach not only increases the effective capacity of adenoviral vector but also opens new avenue of applications involving multiple proteins, some of which cannot be coexpressed in production cell line as a result of combination toxicity.

[0174] All references mentioned herein are hereby incorporated by reference.

[0175] Other embodiments are within the claims.

Claims

1. A replicatable viral DNA vector encoding a site-specific DNA-altering enzyme and a DNA target recognized by said enzyme, said enzyme selectively converting, in a cell expressing said enzyme, said DNA vector to a rearranged form.

2. The vector of claim 1, wherein said rearranged form comprises an autonomously replicating episome.

3. The vector of claim 1, wherein said rearranged form comprises linear and circular DNAs.

4. The vector of claim 1, wherein said vector comprises adenoviral DNA.

5. The vector of claim 1, wherein said vector comprises a genetically-engineered recombination site.

6. The vector of claim 5, wherein said recombination site comprises a target of Cre or FLP.

7. The vector of claim 1, wherein said enzyme comprises a recombinase or an integrase.

8. The vector of claim 7, wherein said recombinase is Cre or FLP recombinase.

9. The vector of claim 1, wherein said enzyme is functional in a mammalian cell.

10. The vector of claim 5, wherein said recombination site comprises a recognition sequence of a site-specific DNA-altering enzyme.

11. The vector of claim 1, wherein said vector comprises an origin of replication functioning in a mammalian cell.

12. The vector of claim 11, wherein said origin of replication is an Epstein Barr Virus replicon.

13. The vector of claim 1, wherein said vector comprises a gene of interest.

14. A method for assembling a recombinant adenoviral DNA said method comprising the steps of: (a) providing a first linearized DNA vector comprising a restriction site and a cos site and a second linearized DNA vector comprising said restriction site, an adenoviral nucleic acid molecule, and a cos site; and (b) ligating said first and second linearized DNA vectors, said ligation assembling a recombinant adenoviral DNA.

15. The method of 14, wherein said first linearized DNA vector comprises a selectable marker.

16. The method of claim 14, wherein said first linearized DNA vector comprises an adenoviral left end-inverted terminal repeat.

17. The method of claim 14, wherein said first linearized DNA vector comprises a gene of interest.

18. The method of claim 14, wherein said second linearized DNA vector comprises a selectable marker.

19. The method of claim 14, wherein said second linearized DNA vector comprises an adenoviral right-end inverted terminal repeat.

20. The method of claim 14, said method further comprising packaging said assembled adenoviral DNA into a phage and infecting a host cell.

21. The method of claim 14, wherein said first and second linearized DNAs comprise a cosmid vector.

22. The method of claim 14, wherein said adenoviral DNA is flanked by cleavage sites.

23. The method of claim 22, wherein said cleavage sites comprise intron endonuclease cleavage sites.

24. An adenovirus producer cell comprising a nucleic acid molecule that expresses a dominant negative site-specific DNA-altering enzyme.

25. The producer cell of claim 24, wherein said site-specific DNA altering enzyme is a dominant negative recombinase.

26. The producer cell of claim 25, wherein said recombinase is a Cre or Flp recombinase.

27. The producer cell of claim 26, wherein said dominant negative recombinase is CreY324C.

28. The producer cell of claim 26, wherein said Flp recombinase is Flpe.

29. The producer cell of claim 24, wherein said cell is a 293 human embryonic kidney cell.

30. A vector comprising, in the 5′ to 3′ direction, a first genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; a gene of interest; a lineage-specific gene promoter; a second genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; and a nucleic acid molecule encoding a site-specific DNA altering enzyme.

31. A vector comprising, in the 5′ to 3′ direction, a first genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; a gene of interest; a bi-directional promoter, comprising a second genetically engineered cis-acting target recognized by a site-specific DNA altering enzyme; and a nucleic acid molecule encoding a site-specific DNA altering enzyme.

32. A method of gene therapy comprising the administration to a patient in need of gene therapy a therapeutically effective amount of the vector of any one of claims 1, 30, or 31 which is expressed in said patient

33. A population of cells transfected with the vector of any one of claims 1, 30, or 31.

34. A method of gene therapy comprising the administration to a patient in need of gene therapy a therapeutically effective amount of the population of cells of claim 33.