Production of viral vectors

FIELD OF THE INVENTION

[0003] The present invention relates to methods and compositions for the production of viral vectors. In particular, the present invention provides methods and compositions for faster, higher titer and higher purity production of adenovirus vectors.

BACKGROUND OF THE INVENTION

[0004] Conventional adenovirus (Ad) gene-delivery vectors are based on replacement of early regions of the viral genome with an expression cassette coding for a gene of interest. Unfortunately, Ad vectors have drawbacks that limit their usefulness for many applications. First, the cloning capacity of these vectors is limited to 8-10 kb. Second, despite deletion of the E1 region, leaky expression of immunogenic viral proteins occurs in vivo, which leads to a host immune response and elimination of gene expression from transduced tissues. Gutted, or helper-dependent, adenoviral vectors may overcome these drawbacks. Gutted vectors contain cis-acting DNA sequences necessary for viral replication and packaging, but usually do not contain viral coding sequences (See U.S. Pat. No. 6,083,750, incorporated by reference). These vectors can accommodate up to 36 kb of exogenous DNA and are unable to express viral proteins. Gutted vectors are produced by replication in the presence of a helper virus, which provides all necessary viral proteins in trans. Since the viral proteins act to replicate both gutted and helper genomes, gutted adenovirus particles are prepared as a mixture with helper virions, though selection against helper virus packaging can reduce this contamination. Particles containing gutted viral genomes, rather than helper genomes, are subsequently purified on the basis of their lower density.

[0005] Generally, the starting point for production of a gutted virus is plasmid DNA. The plasmid contains the viral inverted terminal repeats (ITRs), the viral packaging signal, and exogenous DNA to be carried by the gutted virus. To increase production of gutted virus, most investigators linearize the gutted viral plasmid (some systems require the ligation of viral ITRs after linearization). The plasmid DNA is co-introduced with helper sequences into a cell line that can replicate the helper virus, normally 293 cells. Replication of the helper virus eventually causes lysis of the cells with the lysate containing a large number of helper virions and a comparatively small number of gutted virions.

[0006] To increase the number and proportion of gutted virions in the lysate, the initial mixture is generally serially passaged. Helper-dependent Ad vectors are usually propagated with constant selective pressure against helper virus packaging. During early passages, selection allows for gradual improvement in the ratio of gutted to helper virus. At the last passage selection removes the majority of helper virus before further purification. Unfortunately, growth of vector stocks under selective pressure can lead to rearrangement of helper and gutted viruses.

[0007] The production of gutted virus particles from plasmid DNA in the first step of gutted vector production is so inefficient that titers of less than 100 particles per milliliter have been reported. In some cases no gutted virions can be detected until at least one serial passage has been performed. What is needed is methods and compositions for faster, higher titer and higher purity production of adenovirus vectors.

SUMMARY OF THE INVENTION

[0008] The present invention relates to methods and compositions for the production of viral vectors. In particular, the present invention provides methods and compositions for faster, higher titer and higher purity production of viral vectors (e.g adenoviral vectors). In some embodiments, the present invention provides gutted and helper viruses with corresponding termini. In other embodiments, the present invention provides terminal protein linked adenoviral DNA. In other embodiments, the present invention provides template extended adenoviral DNA (e.g. for increased viral production/recovery and plaquing efficiency). In additional embodiments, the present invention provides methods and compositions for culturing gutted and helper adenoviruses (e.g. with similar or identical termini). For example, the present invention provides compositions and methods for regulated expression of site specific recombinases. In another example, the present invention provides compositions (e.g. cell lines) and methods for culturing adenoviral vectors with adenoviral protein IX.

[0009] In some embodiments, the present invention provides methods for producing helper-dependent viral vectors comprising: a) providing; i) helper-dependent viral DNA comprising a first origin of replication, ii) helper viral DNA comprising a second origin of replication, wherein the second origin of replication has similar activity level in a replication assay as the first origin of replication, and iii) target cells; and b) transfecting the target cells with the helper-dependent viral DNA and the helper viral DNA under conditions such that helper-dependent viral vectors are produced. In particular embodiments, the present invention provides compositions comprising the helper-dependent viral vectors produced with the methods of the present invention. In certain embodiments, the helper-dependent viral DNA comprises adenoviral DNA. In particular embodiments, the helper-dependent viral DNA comprises a heterologous gene sequence. In some embodiments, the helper-dependent viral DNA comprises the left and right inverted terminal repeats (ITRs) of adenovirus, the adenoviral packaging sequence (e.g linked to one of the ITRs), and a heterologous gene sequence.

[0010] In preferred embodiments, the first origin of replication and the second origin of replication have nucleic acid sequences that are identical. In some embodiments, the first and/or second origin of replication lie near the terminus of the viral DNA. In other embodiments, the helper-dependent viral DNA has been released from a plasmid backbone by restriction enzyme digestion. In some embodiments, the helper viral DNA has been realeased from a plasmid backbone. In preferred embodiments, the helper-dependent viral DNA is at least partially linear (in some cases, entirely linear). In other embodiments, the helper viral DNA is at least partially linear (in some cases, entirely linear). In certain embodiments, both the helper-viral DNA and the helper viral DNA lack internal FseI restriction sites (e.g. so plasmids containing both kinds of viral DNA may be digested with FseI to release the viral DNA without cutting viral coding sequences).

[0011] In certain embodiments, the first origin of replication and the second origin of replication have nucleic acid sequences that are similar (e.g. they differ by one base, two bases, or three bases). In additional embodiments, the origins are similar and one of the origins is the natural origin and the other is unnatural (e.g. it has additional sequences attached). In some embodiments, the helper viral DNA is adenoviral helper viral DNA. In preferred embodiments, the first origin of replication and the second origin of replication are not linked to terminal protein or any terminal protein remnant.

[0012] In some embodiments, the helper viral DNA comprises a crippling sequence. In preferred embodiments, the crippling sequence comprises recognition sites for site-specific recombinases (e.g. loxP and Frt). In some embodiments, the target cells express adenoviral DNA polymerase and preterminal protein. In other embodiments, the target cells express adenoviral factor IX.

[0013] In some embodiments, the present invention provides methods for producing helper-dependent viral vectors comprising: a) providing; i) helper-dependent viral DNA comprising a first origin of replication, ii) helper viral DNA comprising a crippling sequence and a second origin of replication, wherein the second origin of replication has similar activity level in a replication assay as the first origin of replication, iii) target cells, and iv) a vector encoding a site-specific recombinase; and b) transfecting the target cells with the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase under conditions such that helper-dependent viral vectors are produced. In preferred embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase all occur at approximately the same time. In particularly preferred embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase all occur at approximately the same time such that the vector expresses the recombinase in a regulated manner (e.g. the amount of recombinase in the transfected cells builds up slowly over time). In some embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase occur at different time (e.g. the helper-dependent viral DNA is transfected before the helper viral DNA, or vice versa). In particular embodiments, the transfecting is accomplished by a method selected from calcium phosphate-DNA co-precipitation, DEAE-dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection, and biolistics.

[0014] In some embodiments, the present invention provides methods for producing helper-dependent viral vectors comprising: a) providing; i) helper-dependent viral DNA comprising a first origin of replication, ii) helper viral DNA comprising a second origin of replication, wherein the second origin of replication has a similar activity level in a replication assay as the first origin of replication, and iii) target cells; b) transfecting the target cells with the helper-dependent viral DNA and the helper viral DNA under conditions such that helper-dependent viral vectors are produced; and c) recovering the helper-dependent vectors. In preferred embodiments, the recovering step yields a helper-dependent titer of up to approximately 30 fold increase compared to transfection/infection protocols in cells expressing adenoviral DNA polymerase and preterminal protein (e.g., at least a 10 fold, at least a 15 fold, at least a 20 fold, or at least 25 fold increase). In particularly preferred embodiments, the recovering step yields a helper-dependent titer of up to approximately 60 fold increase compared to transfection/infection protocols in cells expressing adenoviral DNA polymerase and preterminal protein (e.g., at least 40 fold, at least 50 fold, or at least 55 fold increase).

[0015] In some embodiments, the present invention provides compositions comprising; a) helper-dependent viral DNA comprising a first origin of replication, and b) helper viral DNA comprising a second origin of replication, wherein the second origin of replication has a similar activity level in a replication assay as the first origin of replication. In certain embodiments, the helper-dependent viral DNA comprises adenoviral DNA. In particular embodiments, the helper-dependent viral DNA comprises a heterologous gene sequence. In some embodiments, the helper-dependent viral DNA comprises the left and right inverted terminal repeats (ITRs) of adenovirus, the adenoviral packaging sequence (e.g. linked to one of the ITRs), and a heterologous gene sequence. In preferred embodiments, the first origin of replication and the second origin of replication have nucleic acid sequences that are identical. In certain embodiments, the first origin of replication and the second origin of replication have nucleic acid sequences that are similar (e.g. they differ by one base, two bases, or three bases). In additional embodiments, the origins are similar and one of the origins is the natural origin and the other is unnatural (e.g. it has additional sequences attached). In some embodiments, the helper viral DNA is adenoviral helper viral DNA. In preferred embodiments, the first origin of replication and the second origin of replication are not linked to terminal protein or any terminal protein remnant.

[0016] In some embodiments, the present invention provides kits and systems comprising; i) helper-dependent viral DNA comprising a first origin of replication, and ii) helper viral DNA comprising a second origin of replication, wherein the second origin of replication has similar activity level in a replication assay as the first origin of replication. In preferred embodiments, the kits and systems of the present invention further comprise target cells (e.g., cells expressing adenoviral DNA polymerase and preterminal protein). In other embodiments, the kits and systems of the present invention comprise the helper-dependent viral vectors produced by the methods of the present invention, and one additional component (e.g., an insert component with written instructions for using the components of the kit and system). The kits and systems of the present invention may comprise any of the components listed herein (e.g., helper-dependent viral DNA, helper viral DNA, target cells, insert component, etc.). In particular embodiments, the kits and systems of the present invention comprise a host cell and one additional component, wherein the host cell comprises a) helper-dependent viral DNA comprising a first origin of replication, and b) helper viral DNA comprising a second origin of replication, wherein the second origin of replication has a similar activity level in a replication assay as the first origin of replication.

[0017] In some embodiments, the present invention provides methods for producing helper-dependent viral vectors comprising: a) providing; i) helper-dependent viral DNA comprising an origin of replication linked to a replication-promoting agent, and ii) target cells; and b) transfecting the target cells with the helper-dependent viral DNA under conditions such that helper-dependent viral vectors are produced. In particular embodiments, the present invention provides methods for producing helper-dependent viral vectors comprising: a) providing; i) helper-dependent viral DNA comprising an origin of replication linked to a replication-promoting agent, ii) helper viral DNA, and iii) target cells; and b) transfecting the target cells with the helper-dependent viral DNA and the helper viral DNA under conditions such that helper-dependent viral vectors are produced. In certain embodiments, the present invention provides compositions comprising the helper-dependent viral vectors produced with the methods of the present invention. In preferred embodiments, the replication-promoting agent is selected from Ad2 preterminal protein, Ad2 terminal protein, Ad5 preterminal protein, and Ad5 terminal protein. In other embodiments, replication-promoting agent is selected from at least a portion of Ad2 preterminal protein, Ad2 terminal protein, Ad5 preterminal protein, and Ad5 terminal protein. In preferred embodiments, the replication-promoting agent is Ad5 terminal protein.

[0018] In some embodiments, the helper-dependent viral DNA comprises adenoviral DNA. In other embodiments, the helper-dependent viral DNA comprises a heterologous gene sequence. In some embodiments, the helper-dependent viral DNA comprises the left and right inverted terminal repeats (ITRs) of adenovirus, the adenoviral packaging sequence (e.g. linked to one of the ITRs), and a heterologous gene sequence. In some embodiments, the helper viral DNA is linked to adenoviral terminal protein. In additional embodiments, the helper viral DNA is adenoviral helper viral DNA. In preferred embodiments, the helper viral DNA comprises a crippling sequence (e.g. loxP). In particular embodiments, the helper viral DNA comprises recognition sites for site-specific recombinases. In certain embodiments, the target cells express adenoviral DNA polymerase and preterminal protein. In other embodiments, the target cells express adenoviral protein IX. In certain embodiments, the target cells express adenoviral DNA polymerase, preterminal protein, and adenoviral protein IX. In some embodiments, the method further comprises recovering the helper-dependent vectors. In particular embodiments, the recovering yields a helper-dependent titer of up to approximately 85 fold increase compared to transfection/infection protocols in cells expressing adenoviral DNA polymerase and preterminal protein (e.g., at least a 40 fold, 55 fold, 70 fold, or 80 fold increase). In preferred embodiments, the recovering yields a helper-dependent titer of up to 170 fold increase compared to transfection/infection protocols in cells expressing adenoviral DNA polymerase and preterminal protein (e.g., at least 100 fold, 120 fold, 140 fold, 150 fold, or 160 fold increase).

[0019] In particular embodiments, the present invention provides methods for producing helper-dependent viral vectors comprising: a) providing; i) helper-dependent viral DNA comprising an origin of replication linked to a replication-promoting agent, ii) helper viral DNA comprising a crippling sequence, and iii) target cells; and b) transfecting the target cells with the helper-dependent viral DNA and the helper viral DNA under conditions such that helper-dependent viral vectors are produced. In preferred embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase all occur at approximately the same time. In particularly preferred embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase all occur at approximately the same time such that the vector expresses the recombinase in a regulated manner (e.g. the amount of recombinase in the transfected cells builds up slowly over time). In some embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase occur at different time (e.g. the helper-dependent viral DNA is transfected before the helper viral DNA, or vice versa). In particular embodiments, the transfecting is accomplished by a method selected from calcium phosphate-DNA co-precipitation, DEAE-dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection, and biolistics.

[0020] In some embodiments, the present invention provides compositions comprising helper-dependent viral DNA comprising an origin of replication linked a replication-promoting agent. In preferred embodiments, the replication-promoting agent is selected from Ad2 preterminal protein, Ad2 terminal protein, Ad5 preterminal protein, and Ad5 terminal protein. In other embodiments, replication-promoting agent is selected from at least a portion of Ad2 preterminal protein, Ad2 terminal protein, Ad5 preterminal protein, and Ad5 terminal protein. In preferred embodiments, the replication-promoting agent is Ad5 terminal protein.

[0021] In some embodiments, the present invention provides kits and systems comprising i) helper-dependent viral DNA comprising an origin of replication linked to a replication-promoting agent, and ii) target cells. In preferred embodiments, the kits and systems of the present invention further comprise helper viral DNA. In other embodiments, the kits and systems of the present invention comprise the helper-dependent viral vectors produced by the methods of the present invention, and one additional component (e.g., an insert component with written instructions). The kits and systems of the present invention may comprise any of the components listed herein (e.g., helper-dependent viral DNA, helper viral DNA, target cells, insert component, etc.).

[0022] In certain embodiments, the present invention provides methods comprising: a) providing; i) a first helper-dependent viral DNA comprising a first origin of replication capable of promoting a first activity level in a replication assay, ii) an agent capable of extending the first origin of replication, and b) contacting the helper-dependent viral DNA with the agent for a period of time sufficient to generate a second helper-dependent viral DNA with an second origin of replication capable of promoting a second activity level in a replication assay, wherein the second activity level in a replication assay is greater than the first activity level in a replication assay. In other embodiments, the present invention provides methods comprising: a) providing; i) a first helper-dependent viral DNA comprising a first origin of replication capable of promoting a first activity level in a replication assay, ii) an agent capable of extending the first origin of replication, iii) helper viral DNA, and iv) target cells; b) contacting the helper-dependent viral DNA with the agent for a period of time sufficient to generate a second helper-dependent viral DNA with an second origin of replication capable of promoting a second activity level in a replication assay, wherein the second activity level in a replication assay is greater than the first activity level in a replication assay; and c) transfecting the target cells with the second helper-dependent viral DNA and the helper viral DNA under conditions such that helper-dependent viral vectors are produced.

[0023] In certain embodiments, the first origin of replication is natural. In some embodiments, the first origin of replication is non-natural (e.g. it has one, two, or three bases added onto the natural origin of replication). In other embodiments, the agent is selected from the group of terminal transferase, T4 DNA ligase, and T4 RNA ligase. In preferred embodiments, the agent is terminal transferase. In some embodiments, the helper-dependent viral DNA comprises adenoviral DNA. In other embodiments, the helper-dependent viral DNA comprises a heterologous gene sequence. In still other embodiments, the helper-dependent viral DNA comprises the left and right inverted terminal repeats (ITRs) of adenovirus, the adenoviral packaging sequence (e.g. linked to of the ITRs), and a heterologous gene sequence. In particular embodiments, the helper viral DNA is adenoviral helper viral DNA. In preferred embodiments, the helper viral DNA comprises a crippling sequence (e.g. a site specific recombinase). In some embodiments, the crippling sequence is loxP. In some embodiments, the target cells express adenoviral DNA polymerase and preterminal protein. In other embodiments, the target cells express adenoviral factor IX. In certain embodiments, the method further comprises recovering the helper-dependent vectors. In preferred embodiments, the second activity level in a replication assay is approximately 2-2.5 fold greater than the first activity level in a replication assay.

[0024] In other embodiments, the present invention provides methods comprising: a) providing; i) a first helper-dependent viral DNA comprising a first origin of replication capable of promoting a first activity level in a replication assay, ii) an agent capable of extending the first origin of replication, iii) helper viral DNA, iv) target cells and v) a vector encoding a site-specific recombinase; b) contacting the helper-dependent viral DNA with the agent for a period of time sufficient to generate a second helper-dependent viral DNA with an second origin of replication capable of promoting a second activity level in a replication assay, wherein the second activity level in a replication assay is greater than the first activity level in a replication assay; and c) transfecting the target cells with the second helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase under conditions such that helper-dependent viral vectors are produced. In certain embodiments, the present invention provides compositions comprising the helper-dependent viral vectors produced with the methods of the present invention. In preferred embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase all occur at approximately the same time. In particularly preferred embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase all occur at approximately the same time such that the vector expresses the recombinase in a regulated manner (e.g. the amount of recombinase in the transfected cells builds up slowly over time). In some embodiments, the transfection of the helper-dependent viral DNA, the helper viral DNA, and the vector encoding a site-specific recombinase occur at different time (e.g. the helper-dependent viral DNA is transfected before the helper viral DNA, or vice versa). In particular embodiments, the transfecting is accomplished by a method selected from calcium phosphate-DNA co-precipitation, DEAE-dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection, retroviral infection and biolistics.

[0025] In some embodiments, the present invention provides kits and systems comprising i) a first helper-dependent viral DNA comprising a first origin of replication capable of promoting a first activity level in a replication assay, and an agent capable of extending the first origin of replication. In other embodiments, the kits and systems further comprise helper viral DNA and/or target cells. In other embodiments, the kits and systems of the present invention comprise the helper-dependent viral vectors produced by the methods of the present invention, and one additional component (e.g., an insert component with written instructions). The kits and systems of the present invention may comprise any of the components listed herein (e.g., helper-dependent viral DNA, helper viral DNA, target cells, insert component, etc.). In particular embodiments, the kits and systems of the present invention comprise a host cell and one additional component, wherein the host cell (e.g., mammalian) stably and constitutively expresses adenovirus preterminal protein, adenovirus DNA polymerase, and adenovirus protein IX.

[0026] In some embodiments the present invention provides mammalian cell lines stably and constitutively expressing adenovirus preterminal protein, adenovirus DNA polymerase, and adenovirus protein IX. In some embodiments, the cell line is D2104#10.

DESCRIPTION OF THE FIGURES

[0027]
FIG. 1 shows; A) the structure of viral origins of replication (both natural and non-natural origins that result when particular restriction enzymes are employed); B) points where viral genome is mutated to remove FseI restriction sites; and C) partial structure of pD1940#3 and pD1940#6.

[0028]
FIG. 2 shows improved gutted virus rescue that is achieved by co-transfection of matching plasmid-derived gutted and helper virus DNAs.

[0029]
FIG. 3 shows a method for conversion of plasmid-derived Ad origins to natural form (creating TP-primer and ligating it to plasmid derived viral DNA).

[0030]
FIG. 4 shows that conversion of plasmid-derived gutted virus to a natural, TP-linked structure facilitates gutted virus rescue.

[0031]
FIG. 5 shows limited extension of template strand of the Ad origin increases plaquing efficiency and gutted virus recovery.

[0032]
FIG. 6 shows that the regulated expression of Cre recombinase improves gutted virus recovery.

[0033]
FIG. 7 shows the recovery of gutted virus in D2104#10 cells.

[0034]
FIG. 8 shows the nucleic acid sequence of (+)lox(+)pol helper virus (SEQ ID NO:1).

[0035]
FIG. 9 shows the nucleic acid sequence of pBSX (SEQ ID NO:12).

[0036]
FIG. 10 show a restriction map of pBSX.

[0037]
FIG. 11 shows the nucleic acid sequence of ΔFseI.4 helper virus (SEQ ID NO:9).

[0038]
FIG. 12 shows pD2076#2.

[0039]
FIG. 13 shows TP-DNA complex from (+)lox(+)pol helper viral DNA; deproteinized Hirt prep DNA from ΔFseI.4; and pD1940#3 and pD1940#6.

[0040]
FIG. 14 shows the nucleic acid sequence of pD1940 (SEQ ID NO:13).

[0041]
FIG. 15 shows the nucleic acid sequence of pD1962delBbsI-pIX (SEQ ID NO:14).

[0042]
FIG. 16 shows a restriction map of pD1962delBsI.

[0043]
FIG. 17 shows the nucleic acid sequence of ΔHIX#3 (SEQ ID NO:15).

[0044]
FIG. 18 shows the nucleic acid sequence for: Ad2 preterminal protein (SEQ ID NO:17); Ad2 terminal protein (SEQ ID NO:18); Ad5 preterminal protein (SEQ ID NO:19); and Ad5 terminal protein (SEQ ID NO:20).

DEFINITIONS

[0045] To facilitate an understanding of the present invention, a number of terms and phrases are defined below:

[0046] The term “oligonucleotide” as used herein is defined as a molecule comprised of two or more deoxyribonucleotides or ribonucleotides, usually more than three (3), and typically more than ten (10) and up to one hundred (100) or more (although preferably between twenty and thirty). The exact size will depend on many factors, which in turn depends on the ultimate function or use of the oligonucleotide. Oligonucleotide may be generated in any manner, including chemical synthesis, DNA replication, reverse transcription, or a combination thereof.

[0047] As used herein, the term “helper dependent viral DNA” or “gutted viral DNA” refers to viral DNA that codes for viral vectors that contain cis-acting DNA sequences necessary for viral replication and packaging, but generally no viral coding sequences (See U.S. Pat. No. 6,083,750, incorporated by reference). These vectors can accommodate up to about 36 kb of exogenous DNA and are unable to express viral proteins sufficient for replication. Helper-dependent viral vectors are produced by replication of the helper dependent viral DNA in the presence of a helper adenovirus, which alone or with a packaging cell line, supplies necessary viral proteins in trans such that the helper-dependent viral DNA is able to be replicated. Gutted vectors may be constructed as described in U.S. Pat. No. 6,083,750.

[0048] As used herein the term “helper viral DNA” refers to viral DNA encoding helper viral vectors, that are capable of providing, alone or with a packaging cell line, viral proteins in trans such that a gutted virus is able to replicate. A “helper adenovirus” or “helper virus” refers to an adenovirus which is replication-competent in a particular host cell. The host may provide, for example, Ad gene products such as E1 proteins. The ‘helper virus’ is used to supply in trans functions (e.g., proteins) which are lacking in a second replication-incompetent virus (e.g. a gutted viral vector). Therefore, the first replication-competent virus is said to “help” the second replication-incompetent virus thereby permitting the propagation of the second viral genome in the cell containing the helper and second viruses. Helper virus may include a sequence capable of crippling helper virus replication in the presence of certain crippling agents. An example of a helper virus with a crippling sequence is the (+)lox(+)pol helper virus (SEQ ID NO:1). The (+)lox(+)pol helper virus is an E1-, E3-deleted virus that can be negatively selected using Cre recombinase and carries an alkaline phosphatase reporter gene in its E3 region. The packaging signal, which consists of packaging elements I-V, is flanked by loxP sites in direct repeat orientation, allowing removal of the packaging signal in the presence of Cre (a crippling agent).

[0049] The term “bacteria” refers to any bacterial species including eubacterial and archaebacterial species.

[0050] The term “virus” refers to obligate, ultramicroscopic, intracellular parasites incapable of autonomous replication (i.e., replication requires the use of the host cell's machinery). Adenoviruses are double-stranded DNA viruses. The left and right inverted terminal repeats (ITRs) are short elements located at the 5′ and 3′ termini of the linear Ad genome, respectively, and are required for replication of the viral DNA. The left ITR is located between 1-130 bp in the Ad genome (also referred to as 0-0.5 mu). The right ITR is located from ˜35,800 bp to the end of the genome (also referred to as 99.5-100 mu). The two ITRs are inverted repeats of each other.

[0051] The term “transfection” as used herein refers to the introduction of foreign DNA into eukaryotic cells. Transfection may be accomplished by a variety of means known to the art including, but not limited to, calcium phosphate-DNA co-precipitation, DEAE-dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection and biolistics.

[0052] The term “stable transfection” or “stably transfected” refers to the introduction and integration of foreign DNA into the genome of the transfected cell. The term “stable transfectant” refers to a cell which has stably integrated foreign DNA into the genomic DNA.

[0053] As used herein, the term “gene of interest” or “heterologous gene sequence” refers to a gene inserted into a vector or plasmid whose expression is desired in a host cell. Genes of interest include genes having therapeutic value as well as reporter genes. A variety of such genes are contemplated, including genes of interest encoding proteins which provide a therapeutic function (such as the dystrophin gene, which is capable of correcting the defect seen in the muscle of MD patients), the utrophin gene, the CFTR gene (capable of correcting the defect seen in cystic fibrosis patients), etc.

[0054] The term “reporter gene” indicates a gene sequence that encodes a reporter molecule (including an enzyme). A “reporter molecule” is detectable in detection systems, including, but not limited to enzyme (e.g., ELISA, as well as enzyme-based histochemical assays), fluorescent, radioactive, and luminescent systems. Examples of reporter molecules include, but are not limited to, beta-galactosidase gene (available from Pharmacia Biotech, Pistacataway, N.J.), green fluorescent protein (GFP) (commercially available from Clontech, Palo Alto, Calif.), the human placental alkaline phosphatase gene, and the chloramphenicol acetyltransferase (CAT) gene. Other reporter genes are known to the art and may be employed.

[0055] As used herein, the term “activity level in a replication assay” refers to the level of activity observed for a particular type of viral origin of replication as measured in a replication assay. Examples of replication assays include, but are not limited to, plaque assays, rate of initiation of DNA replication assays, and replication factor affinity assays.

[0056] As used herein, the term “plaque assay” refers to a means for measuring the frequency with which virus or viral DNA can replicate productively (See, Graham, F. L. and Prevec, L. Manipulation of Adenovirus Vectors in Gene Transfer and Expression Protocols, Clifton: The Humana Press, Inc., 1991, hereby incorporated by reference). The assay may be performed, for example, by using either virus (by infection) or viral DNA (by transfection). For purposes of measuring the activity of an origin of replication the assay is performed using viral DNA. When viral DNA is introduced into cells by transfection, some transfected cells allow replication of the genome and progeny virions are produced. If the cells have been overlayed with agarose, the progeny virions diffuse to and infect only nearby cells. Thus, after several rounds of replication, foci of dead cells are observed (e.g. their presence may be highlighted through use of dyes like neutral red). These foci of dead cells are referred to as “plaques”. To measure the activity of an origin of replication in this assay, the origin is linked to helper-independent viral DNA and transfected into cells which support growth of the virus. The cells are overlayed with agarose, and the investigator waits for the appearance of plaques (e.g. 3-14 days). After plaques have appeared, their appearance may be highlighted with dye, and their number counted. The higher the number of plaques, the more often the viral DNA has been converted into replicating virus, and the higher the activity of the origin of replication is found to be. The number of plaques observed is also correlated with the amount of DNA transfected, so the results of a plaque assay may be expressed as “specific activity”; that is, the number of plaques observed per weight of DNA transfected. An origin of replication that is more active than a second origin will tend to display more plaques in the plaque assay.

[0057] As used herein, the term “rate of initiation of DNA replication assays” refers to methods for determining the rate of initiation of DNA replication on a given origin (See, Challberg M D., Rawlins Dr., P.N.A.S., 81(1):100-4, 1984, herein incorporated by reference). The rate of initiation of DNA replication on a given origin may be measured, for example, by incubating the origin together with all the viral and cellular factors required for initiation, and then noting the rate with which new copies of the non-template strand appear. Generally, the steps in such an assay include: isolation of cellular and viral factors from infected cells; incubation of the isolated factors with origin fragments and radioactive nucleotides; observation of new DNA copies using an assay method such as gel electrophoresis followed by autoradiography. For each origin, the analysis is usually performed at several time points, so that the appearance of new DNA copies may be charted over time. Using this information, the rate of their appearance can be calculated. An origin of replication that is more active than a second origin will tend to cause the rate of appearance of new DNA copies to be more rapid in this assay.

[0058] As used herein, the term “replication factor affinity assays” refers to methods for determining the ability of viral DNA to attract viral replication factors (e.g. adenovirus DNA polymerase, adenovirus preterminal protein, NFI, and NFIII, See Pronk et al., Nucleic Acids Research, 25(10):2293-300, 1993, herein incorporated by reference). The affinity of a replication factor for an origin of replication may be measured, for example, by incubating the two together at a variety of concentrations and then determining, at each concentration, the amount of origin DNA that was bound by factor. One example of a method used to determine the amount of bound origin DNA is an “electrophoretic mobility shift assay” (EMSA). In this assay, the presence of factor bound to DNA causes the mobility of the origin-containing DNA to be reduced in polyacrylamide gels. Using radioactive origin DNA, the amount of DNA bound by factor can therefore be determined by measuring the amount of radioactivity found in an electrophoretic band of reduced mobility—the larger the amount of radioactivity, the larger the amount of DNA bound by factor. The affinity of an origin of replication for a replication factor is indicated by the concentration levels at which substantial binding can occur: the lower the concentration at which binding occurs, the higher the affinity is said to be. The relative affinities of two origins for a replication factor could be compared by incubating radioactive samples of each origin together with different concentrations of replication factor, usually in the presence of random DNA fragments to inhibit non-specific interactions. If the first origin has a higher affinity for factor than the second origin, a lesser concentration of factor will be required to bind a given amount of origin DNA. For example, a lesser concentration of factor will be required to retard the migration of a certain proportion of DNA sequences containing the first origin than DNA sequences containing the second, as determined by EMSA.

[0059] As used herein, the term “target cells” refers to any cells that may be transfected with viral DNA. Target cells include, but are not limited to, bacterial cells, mammalian cells, and insect cells. Target cells may from any source including, but not limited to, bacterial colonies, cell lines, tissue samples, and blood samples.

[0060] As used herein the term “expresses said recombinase in a regulated manner” refers to the expression of recombinase in a target cell such that the level of recombinase in the cell gradually increases over time. This gradual increase in expression allows the helper viral DNA to replicate at a greater rate initially after transfection (when the level of recombinase is lower), and slows the replication rate of the helper virus as the level of recombinase increases. One example expression of recombinase in a regulated manner is provided in Example 6.

[0061] As used herein, the term “similar activity level in a replication assay” refers to the situation where two origins of replication have about the same activity level in a replication assay (e.g. plaque assay, replication factor affinity assay, or rate of initiation of DNA replication assay). For example, similar activity level includes a difference of 20 fold or less, preferably 10 fold or less, more preferably 5 fold or less, and most preferably 2 fold or less.

[0062] As used herein, the phrase “wherein said second activity level in a replication assay is greater than said first activity level in a replication assay” refers to a second activity level of at least 5% greater, preferably 10%, more preferably 20% greater, most preferably 50% greater, than said first activity level.

[0063] As used herein the phrase “at about the same time” refers to transfection steps that occur within approximately one hour of each other.

[0064] As used herein, the term “under conditions such that helper-dependent viral vectors are produced” refers to conditions such that help dependent viral DNA is able to replicate inside a cell (e.g. may require helper viral DNA) such that helper-dependent viral vectors (particles) are produced.

[0065] As used herein, the term “origin of replication” refers to the DNA sequence elements that are necessary and sufficient to direct replication of a DNA molecule to which they are attached. Generally, the sequence elements include binding sites for replication factors and usually span the points at which the synthesis of new DNA strand begin. Origins of replication can often be identified by the fact that their mutation or removal prevents replication of DNA molecules to which they had been attached and which had formerly replicated in a given system. In addition, the attachment of an origin of replication to a formerly inert molecule should be sufficient to cause its replication in a given system. For example, the origin of replication for adenoviral DNA has been identified as including at least the first 50 base pairs of the adenoviral genome and commonly refers to approximately the first 100 base pairs of the adenoviral genome also known as the inverted terminal repeat (ITR). Removal of the ITRs from adenoviral genome prevents its replication; the addition of ITRs to most DNA molecules is sufficient to allow their replication in cells that have been infected by helper independent adenovirals, which provides viral replication factors.

[0066] As used herein the term “viral recovery” refers to collection and storage of progeny virions produced by cells (e.g. infected by helper-dependent and helper viral DNA). This can be accomplished with or without purification of the virions to remove cellular contaminants. For example, a simple method for viral recovery is to collect lysed cells and store them in the freezer. The presence of virions may be revealed through an examination of the lysate by any of several methods including, but not limited to, plaque assay, a transduction assay that reveals the presence of a marker genes like beta-galactosidase, or physical methods such as chromatography followed by spectroscopy.

[0067] As used herein, the term “transfection/infection protocol” refers to the standard protocol where helper-dependent viral DNA is introduced into cells by a transfection method at approximately the same time (e.g. plus or minus 24 hours) that intact helper independent viral particles (e.g. contain adenoviral terminal protein linked to the origin of replication) are allowed to contact the cells and infect them. After a variable period of time the cells lyse due to replication of the virus. At that point, the progeny viral particles are collected.

[0068] As used herein, the term “replication-promoting agent” refers to a compound or molecule that may be ligated to viral DNA terminus such that the activity level in a replication assay of such viral DNA is increased (compared to not having the replication-promoting agent ligated to the viral terminus). Examples of replication-promoting agents include, but are not limited to, Ad5 adnenoviral preterminal protein, Ad5 adenoviral protein, Ad2 preterminal protein, and Ad2 terminal protein.

[0069] As used herein, the term “agent capable of extending said first origin of replication” refers to any agent that is capable of adding single nucleotides, or oligonucleotides (e.g. 10 mers) to the terminal end of viral DNA. Examples of such agents include, but are not limited to, terminal transferase, T4 DNA ligase, and T4 RNA ligase.

[0070] As used herein, the phrase “contacting said helper-dependent viral DNA with said agent for a period of time sufficient to generate”, in regards to time, refers to the length of time required to expose viral DNA origins (natural or un-natural) to an agent capable of extending such origins, such that the activity level in a replication assay of such extended origin is increased (as compared to not extended origins). This time period may vary according to the agent employed and other conditions (e.g. type and concentrations of nucleotides). One example of determining the appropriate length of time is provided in Example 5.

[0071] As used herein, the phrase “said first origin of replication and said second origin of replication have nucleic acid sequences that are substantially similar” refers to the situation where the first and second origins, while not identical, have origins of replication that are similar in nature (e.g. they both have additional nucleotides added to the natural origin of replication such that the ability). One example of substantially similar origins is provided in FIG. 1A, comparing the structure of the PacI digested viral DNA origin to the FseI digested viral DNA origin.

DESCRIPTION OF THE INVENTION

[0072] The present invention relates to methods and compositions for the production of viral vectors. In particular, the present invention provides methods and compositions for faster, higher titer and higher purity production of viral vectors (e.g. adenoviral vectors). In some embodiments, the present invention provides gutted and helper viruses with corresponding termini. In other embodiments, the present invention provides terminal protein linked adenoviral DNA. In other embodiments, the present invention provides template extended adenoviral DNA (e.g. for increased viral production/recovery and plaquing efficiency). In additional embodiments, the present invention provides methods and compositions for culturing gutted and helper adenoviruses (e.g. with similar or identical termini). For example, the present invention provides compositions and methods for regulated expression of site specific recombinases. In another example, the present invention provides compositions (e.g. cell lines) and methods for culturing adenoviral vectors with adenoviral protein IX.

[0073] I. Gutted and Helper Viruses with Similar or Identical Termini

[0074] In typical gutted virus-helper virus rescue production methods, the helper virus eventually comes to dominate the contents of the packaging cell (to the detriment of the gutted adenovirus). The number and proportion of gutted virions is small because plasmid DNA, whether circular (with fused ITRs) or linear, is a poor substrate for initiation of adenoviral DNA replication. As a result, replication of the helper virus occurs in many cells without concomitant production of gutted virus, despite the presence of gutted viral plasmid substrate.

[0075] As mentioned above, to increase the number and proportion of gutted virions in the lysate, the initial mixture is generally serially passaged. Helper-dependent Ad vectors are usually propagated with constant selective pressure against helper virus packaging. During early passages, selection allows for gradual improvement in the ratio of gutted to helper virus. Unfortunately, growth of vector stocks under selective pressure can lead to rearrangement of helper and gutted viruses. In addition, serial passage is time consuming.

[0076] Published protocols for rescue of helper-dependent Ad vectors employ gutted viral DNA derived from plasmids and helper viral DNA derived from replicating virus. Most investigators transfect gutted viral DNA and then infect with replication-competent helper virus the “transfection/infection” protocol. Others have compared transfection/infection to co-transfection of gutted viral DNA from plasmids and helper viral DNA prepared from replicating virus and found that co-transfection is more efficient. In these protocols, the helper and gutted viral DNAs have different structures at their origins of replication.

[0077] The present invention provides gutted and helper viral DNA with similar corresponding termini or linked to terminal protein, thus alleviating some of the problems of normal viral rescue protocols. While not limited to any mechanism, providing gutted and viral DNA that are substantially similar at the origin of replication allows parallel amplification of both types of vectors, thus preventing the helper viruses production from dominating over gutted virus production. Again, while not limited to any mechanism, it is believed that substantially similar termini or origins of replication (or identical termini or origins of replication) allow parallel amplification of both types of vectors because neither type of virus has a competitive advantage for attracting replication factors (such as adenoviral polymerase, transcription factors, etc.).

[0078] The present invention provides gutted and helper viruses with corresponding termini, and methods of employing such vectors for increased production yields (and faster production) of adenoviral vectors (which, may then be used, for example, for gene therapy applications). In some embodiments, gutted adenoviral DNA and helper adenoviral DNA (e.g. both located on plasmids) are released from their plasmids with the same restriction enzyme (cutting at the termini) such that the termini of the linearized DNA are the same (i.e. the gutted and helper adenoviral DNA have corresponding termini). Any type of restriction enzyme (or other enzyme that will cut DNA) may be used, as long as at least one viral terminus is released from its host vector or the ends of the DNA are able to be cut, leaving corresponding termini on both the gutted and helper DNA. In particular embodiments, different restriction enzymes are employed. In such embodiments, the ends of the viral DNA may not be identical, but the ability of the ends to promote replication in cells is approximately the same (e.g. neither type of DNA has a substantial competitive advantage after transfection, such that replication of both types of viruses proceeds at approximately the same pace). In preferred embodiments, the same restriction enzyme is used to generate the termini of both the gutted and helper viral DNA.

[0079] Preferably, restriction enzymes are employed that cut close to or at the termini of helper and gutted viral DNA. In some embodiments, creating gutted and helper adenoviral DNA with identical or similar termini requires that particular restriction sites be removed from one or both types of DNA (to prevent the digestion of the viral DNA). An example of removing unwanted restriction sites (FseI sites) from viral DNA (the Ad5 genome) is provided in Example 1. A similar procedure can be employed to remove other types of unwanted restriction sites from viral DNA. In this regard, any restriction enzyme could be employed to create identical (or similar) termini if the suitable modification are made (if necessary) in the viral DNA.

[0080] To confirm that the restriction enzyme employed is capable of releasing replication-competent viral DNA from flanking DNA sequences (e.g. plasmid DNA), an assay similar to Example 2 may be employed (transfecting gutted and helper DNA into cells known to replicate adenoviral DNA). Such a technique may also be employed to test the relative efficiency of production of viral particles from viral DNA with various termini.

[0081] In certain embodiments, neither the gutted or the helper viral DNA contain terminal protein, and both types are transfected into a cell line as DNA (e.g. the helper DNA is transfected as DNA, instead of a viral particle). In such embodiments, the identity of the termini of the helper and gutted viral DNA is not critical, as long as the termini both do not contain terminal protein or any terminal protein remnant (e.g. one serine residue). In certain embodiments, the gutted and helper viral DNA are co-transfected into a packaging cell line.

[0082] II. Replication-Promoting Agent Linked Adenoviral DNA

[0083] Another method for increasing viral production is linking gutted adenoviral DNA (e.g. the adenoviral origin) to a replication-promoting agent (e.g. adenoviral preterminal protein or adenoviral terminal protein). The normal substrate for initiation of adenoviral DNA replication is terminal protein-DNA complex. Plasmid-based substrates propagated in, for example, E. coli, normally lack terminal protein. As such, replication is greatly increased by linking gutted adenoviral DNA (and, in some embodiments, helper viral DNA) to adenoviral terminal protein.

[0084] In the transfection/infection protocol, or when helper virus terminal protein-DNA complex is used for co-transfection, the helper virus DNA is already attached to adenoviral terminal protein. While not limited to any mechanism, it is believed that linking the gutted adenoviral DNA termini to a replication-promoting agent (e.g. adenoviral terminal protein) reduces the competitive advantage helper virus has when supplied as viral particles (or DNA) that is already attached to terminal protein. In this regard, both types of viral DNA have a similar ability to attract replication factors and replicate into viral particles. Again, while not limited to any mechanism, it is believed that the presence of a replication-promoting agent (e.g. adenoviral preterminal protein) bound to the template confers higher affinity for incoming Ad polymerase-preterminal protein complex, an essential viral replication factor.

[0085] One method for preparing gutted viral genomes linked to adenoviral terminal protein (i.e. terminal protein serves as the replication-promoting agent) involves purifying terminal protein-containing fragments. Terminal protein-containing fragments (e.g. isolated from intact virus), can be purified away from other viral DNA fragments before ligation. It is desired that such purification be employed as the presence of other viral fragments would tend to inhibit the desired ligation reaction, since both partners in the desired ligation (gutted viral genomes and terminal protein-containing fragments) would likely be ligated to contaminating, more numerous random viral fragments in a mixed reaction. A second purification step may be performed after ligation, when unligated terminal protein-DNA fragments are removed. As these fragments contain natural Ad origins, failure to remove them could reduce the yield of gutted virus by inhibiting viral replication. Another method for obtaining terminal protein is purification of terminal protein-gutted genome complex from gutted virus preparations.

[0086] In a preferred embodiments, gutted Ad genomes are linked to normal Ad origins (FIG. 4). This method requires relatively small amounts of terminal protein DNA-complex (e.g. 2-4 moles of terminal protein-DNA complex are sufficient to convert approximately 1 mole of gutted viral genomes to the natural, terminal protein-containing form). Conveniently, the reaction can be performed without purification of the terminal protein-DNA reagent either before or after origin conversion (See Example 3).

[0087] In some embodiments, the compound used in the conversion process is terminal protein linked to single-stranded DNA (e.g. from the non-template strand of an Ad ITR). Another term for terminal protein linked to single-stranded DNA is “TP-primer”. Example 3 provides one example of the preparation of TP-primer, employing a restriction enzyme digest of viral TP-DNA complex (employing Bsh12361, AluI, and HinfI) followed by λ exonuclease treatment. Other restriction enzymes may be employed in this process. Preferably, restriction enzymes are chosen that leave a substantial length of nucleic acid (i.e. ‘primer’) on the TP-primer reagent. For example, Bsh1236I, employed in Example 3, is known to cut between base pairs 73 and 74 of the Ad5 ITR, so this type of digestion results in terminal protein linked to a 73-bp, double stranded DNA molecule. This method may also employ other exonucleases (i.e. besides λ exonuclease), preferably 5′ to 3′ exonucleases (e.g. T7 gene 6 exonuclease).

[0088] In some embodiments, the TP-primer reagent is purified after it is constructed (e.g. to remove any mononucleotides or oligonucleotides created as a result of the enzyme digests). For example, as the TP-primer contains single-stranded DNA, any type of solid-phase purification strategy may be used (e.g. paramagnetic beads linked to single-stranded DNA that is complementary to the DNA in the TP-primer reagent—after binding of TP-primer to the beads, the beads could be collected and the TP-primer reagent released through heating). Other suitable purification/collection techniques are known in the art.

[0089] TP-primer may also be constructed synthetically. Such a synthetic reagent would contain, for example, a peptide fragment (or entire protein) of the Ad terminal protein linked to any number of bases from an adenovirus ITR. Synthesis techniques for polypeptides and nucleic acid are well known in the art.

[0090] A natural or synthetic “primer” sequence, for generating a TP-primer molecule, is selected to be substantially or completely complementary to a strand of specific sequence of the gutted viral template. A primer must be sufficiently complementary to hybridize with a template strand (e.g. such that primer elongation can occur). A primer sequence need not reflect the exact sequence of the template. Non-complementary bases or longer sequences can be interspersed into the primer, provided that the primer sequence has sufficient complementarity with the sequence of the template to hybridize and thereby form a template primer complex. Complementarity need not be perfect, stable duplexes may contain mismatched base pairs or unmatched bases. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the oligonucleotide, ionic strength and incidence of mismatched base pairs.

[0091] TP-primer molecules (or similar molecules) are used to convert viral origins to “natural” viral origins of replication. In a preferred embodiment, TP-primer is used to convert plasmid derived gutted viral genomes to natural adenoviral origins by attaching TP-primer to the terminus of adenoviral DNA. Any type of method may be employed. For example, gutted viral genomic DNA (flanked by restriction enzyme sites) may be digested with the appropriate restriction enzyme to release the gutted viral DNA. The products of this are then subjected to limited digestion with a 5′ to 3′ exonuclease (limited digestion with this type of enzyme exposes single-stranded regions near the gutted vector genomic termini, see FIG. 3B). Any type of 5′ to 3′ exonuclease may be employed (e.g. T7-gene-6 exonuclease, λ exonuclease, etc.). Digestion with the 5′ to 3′ nuclease is for a limited time (e.g. about 1-2 minutes), such that enough single strand template is exposed to hybridize to the nucleic acid in the TP-primer, but not so much that the entire strand is digested. The longer the single-stranded nucleic acid is on the TP-primer compound, the more 5′ to 3′ digestion is needed to expose a single-stranded template for hybridization. The exonuclease is preferably inactivated (e.g. by heating) prior to the introduction of the TP-primer.

[0092] TP-primer is then added to the digested product that is created after exonuclease digestion. The nucleic acid portion of the TP-primer (i.e. the ‘primer’ portion) will hybridize to its complement on the partially digested viral DNA. In preferred embodiments, the nucleic acid portion of the TP-primer is relatively long (e.g. 25 or more bases) such that the TP-primer reagent can bind efficiently to the exonuclease digest gutted DNA, even at low molar ratios. However, any length of ‘primer’ nucleic acid capable of hybridizing to the exonuclease digested viral DNA may be employed (see discussion above). Once the TP-primer reagent is added to the digested viral DNA, the mixture may be subjected to conditions that promote rapid hybridization. For example, the temperature of the mixture may be raised (e.g. to 75° C.) and allowed to cool (e.g. the temperature is allowed to fall slowly over 2-3 hours to room temperature).

[0093] Hybridized TP-primer molecules are then extended (e.g. using T4 DNA polymerase, Taq polymerase, etc.) and nicks are repaired (e.g. using T4 DNA ligase) in the presence of dNTPs. In some embodiments, products of the extension and nick repair are incubated for a period of time (e.g. 5 minutes) at 0°, then a period of time (e.g. 5 minutes) at room temperature, and then a period of time (e.g. 2 hours) at 37° C. In certain embodiments, EDTA is then added to this mixture, and the mixture is stored on ice. In particular embodiments, the reaction products are dialyzed against transfection buffer before being used (e.g. before being used to transfect cells).

[0094] In particular embodiments, the successful addition of TP-primer to the origin of replication (e.g of gutted adenoviral DNA) is confirmed. Confirmation may be performed by any method. For example, a restriction digestion may be performed on the TP-primer-viral DNA molecules followed by agarose gel electrophoresis (See FIG. 4A, and Example 3). Another example of a method that may be employed to confirm the successful addition of TP-primer to the origin of replication is determining if these molecules have increased specific activity of these molecules (e.g. Example 4).

[0095] Linking gutted viral DNA to adenoviral terminal protein (e.g. by attaching TP-primer) increased the yield of gutted virus produced in a gutted viral rescue procedure. In some embodiments, co-transfection of terminal protein linked gutted DNA with terminal protein DNA complex from helper virus results in an 85 fold increase in virus production, when compared to transfection/infection protocols using C7 cells without linking the gutted viral DNA to adenoviral terminal protein. In other embodiments, co-transfection of adenoviral terminal linked gutted and helper adenoviral DNA results in greater than a 2.5 fold increase in adenoviral production (e.g. 2.7 fold increase), compared to not linking either viral DNA to adenoviral terminal protein.

[0096] The replication-promoting agent may be adenoviral terminal protein. Viral DNA may also be linked to adenoviral preterminal protein. Any source of terminal or preterminal protein (e.g. natural or synthetic) from any type of adenovirus (e.g. Ad5 and Ad2). The terminal protein or preterminal protein may be made synthetically by, for example, transfecting cells with an expression vector (e.g. plasmid) with a gene sequence encoding a least a portion of adenoviral terminal, or preterminal, protein. Examples of such nucleic acid sequences that may be express in such a recombinant fashion include, but are not limited to, SEQ ID NO:18 (Ad2 terminal protein, FIG. 18) and SEQ ID NO:20 (Ad5 terminal protein, FIG. 18). Examples of preterminal protein nucleic acid sequences include, but are not limited to, SEQ ID NO:17 (Ad2 preterminal protein, FIG. 18) and SEQ ID NO:19 (Ad5 preterminal protein). The sequences, or portions thereof, may linked to viral DNA as described above. The present invention also contemplates other replication promoting agents, including lipids, other proteins, carbohydrates, and nucleic acids, as long as they are capable of promoting the replication of viral DNA when linked to the origin of the viral DNA.

[0097] Another method for creating terminal protein-linked viral DNA is by the use of Cre recombinase to transfer a segment of DNA linked to terminal protein. For example, gutted viral plasmid DNA containing a loxP site near at least one terminus is incubated with terminal protein-DNA complex from a helper virus whose genome contains a loxP site. Cre is then added to the reaction to facilitate intermolecular exchange.

[0098] The present invention contemplates terminal protein linked gutted adenoviral DNA that is transfected with helper viral DNA that is either linked to terminal protein (e.g. natural adenoviral DNA), or not linked to helper viral DNA (e.g. deproteinized helper viral DNA). For example, terminal protein linked gutted viral DNA may be used in conjunction with adenovirus (e.g. transfection/infection protocol), deproteinized viral DNA or terminal transferase treated (see below) helper viral DNA. In some embodiments, the helper virus does not contain terminal protein. In other embodiments, the helper virus does not contain terminal protein and is used at a higher concentration than the gutted viral DNA. These sequence may also be mutated (e.g. directed evolution) to increase their ability to promote replication (See, e.g. U.S. Pat. No. 5,811,238, hereby incorporated by reference).

[0099] III. Template Strand Extended Adenoviral DNA

[0100] The present invention provides a further method for increasing gutted virus production (and recovery), as well as methods for increasing the plaquing efficiency of adenoviral DNA after transfection into cells. In particular, limited extension of adenoviral DNA termini (e.g. gutted adenoviral termini) increases plaquing efficiency (e.g. approximately 10 fold increase in efficiency, see Example 5 and FIG. 5) as well as increasing gutted virus recovery (e.g. an increase of 2.5 fold gutted viral recovery).

[0101] In preferred embodiments, the terminus of an adenoviral DNA is extended for a time sufficient to allow increased plaquing efficiency and/or gutted virus recovery. As demonstrated in Example 5, various time points may be tested to determine the appropriate limited template extension (e.g. in Example 5, approximately 30 minutes of extension in the presence of terminal transferase was optimal, with 6 minutes being less than optimal and 150 minutes being worse than no template extension). In some embodiments, adenoviral template DNA is extended from approximately 6 minutes to approximately 100 minutes. In preferred embodiments, the adenoviral DNA is extended for approximately 20 minutes to approximately 40 minutes. In particularly preferred embodiments, the adenoviral DNA is extended for approximately 30 minutes (e.g. 25-35 minutes). The time required to achieve a successful limited extension may be determined empirically employing methods similar to Example 5 and will vary depending on the conditions used (e.g. extending enzymes employed, concentrations of dNTPs, etc.).

[0102] Any type of enzyme capable of extending viral template DNA may be employed. For example, Taq polymerase, T4 polymerase, T4 DNA or RNA ligase, or terminal transferase may be used. In preferred embodiments, terminal transferase is employed. In some embodiments, the viral template DNA sequence is linearized by digesting with restriction enzyme(s) before template strand extension.

[0103] Template strand extension of viral DNA templates (e.g. gutted adenoviral DNA) employs molecule(s) capable of adding deoxyribonucleotide triphosphates (dNTPs) to the viral template DNA. In some embodiments, all four dNTPs are provided in the reaction mixture (i.e. guanine, cytosine, adenine, thymine). In other embodiments, only two or three of the dNTPs are provided (e.g. guanine and adenine, or guanine, adenine, and cytosine). In preferred embodiments, only guanine, adenine, and cytosine are supplied to the reaction mixture (i.e. not thymine).

[0104] Limited template extension of viral DNA increases plaquing efficiency and gutted virus recovery. In certain embodiments, the plaquing efficiency is increased two fold (i.e. the plaquing efficiency is double compared to controls that do not have limited extension of the template DNA). In preferred embodiments, the plaquing efficiency is more than doubled (e.g 3 fold, 4 fold, and 5 fold increased efficiency). In particularly preferred embodiments, the plaquing efficiency is increased approximately 10 fold. In some embodiments, the recovery of gutted virus is increased two fold. In preferred embodiments, the recovery of gutted virus is increased more than two fold (e.g. 2.5 fold). In some embodiments, template extended gutted viral DNA is transfected into cells, followed later by infection by helper virus (i.e. a transfection/infection protocol is employed). In preferred embodiments, helper and gutted viral DNA are co-transfected into cells (See Example 5, and FIG. 5D).

[0105] Extensions of viral DNA may also be accomplished by ligating various length oligos to the viral origin (i.e. ligation of oligonucleotides is employed instead of or in addition to the methods described above). For example, T4 DNA ligase may be used to ligate various oligonucleotides (e.g. ranging from 2-100 base pairs in length, and mixtures of various lengths) to viral origins in order to increase the activity of these origins. Again, assays may be employed to determine the optimal length of oligonucleotides to employ and the amount of time ligation is allowed to proceed.

[0106] IV. Culturing Gutted and Helper Adenoviruses

[0107] Methods and compositions are also provided by the present invention to increase viral recovery. In particular, improved selection strategies are provided (particularly well suited for gutted and helper adenoviral DNA with identical or similar termini). The present invention also provides cells lines expressing protein IX (and methods for allowing cells to express factor IX) to increase viral recovery.

[0108] A. Regulated Expression of Site-Specific Recombinases

[0109] Site-specific recombinases have been used to reduce helper contamination and improve gutted virus titer during serial passage. In these systems, the packaging element of the helper virus is flanked by recognition sites for site-specific recombinases like Cre or Flp. In these systems, the yield of gutted virus after rescue from plasmid is low, so improvement in gutted virus titer during serial passage is paramount. Use of a site-specific recombinase improves gutted virus titer by improving the gutted:helper ratio after lysis of a plate, so that a higher percentage of particles produced contain gutted viral genomes. This method results in a higher gutted virus titer at the following passage, since each infected cell contains a higher proportion of gutted genomes.

[0110] Such systems are typically designed for infection of each producer cell by at least one helper virus particle. This protocol typically allows for complete lysis of the plate despite the action of recombinase, which acts to prevent packaging and spread of helper virus, but does not prevent death of infected cells. In these systems, high-level production of the site-specific recombinase is desirable. Since each cell is infected by helper virus, viral spread is not necessary; higher production of recombinase leads to lower contamination with helper virus but does not compromise gutted virus production.

[0111] As described above, gutted virus rescue is most efficient when gutted and helper viral genomes with identical origin structure are co-transfected into producer cells (see also, Example 2). Employing gutted and helper viral genomes with identical (or similar) origin structure, however, a smaller fraction of transfected cells convert the helper virus DNA into replicating virus. This fact is confirmed by the observation that lysis of transfected plates takes about a week, although the time for a single round of viral replication is on the order of 24 hours. Virus produced by those few cells that converted transfected DNA to replicating virus must spread through the plate before complete lysis occurs. Under these conditions, constitutive, high-level expression of recombinase is not appropriate (See Example 6). In the presence of high levels of recombinase, the few cells that can produce virus produce very little, which often is not sufficient to lyse the plate, typically a requirement for high titers of gutted virus.

[0112] Regulated expression of site specific recombinase is provided by the present invention in order to take advantage of the beneficial activity of site specific recombinases, yet avoid the detrimental results evidenced in cells expressing site specific recombinase constitutively. Site specific recombinase may be regulated in time, with minimal to no expression at early times after transfection and high expression at later time points. While not limited to any mechanism, it is believed that the expression of a site-specific recombinase is detrimental at early times after transfection, when transfected helper genomes are being converted to replicating virus, thus providing helper particles that should spread through the plate. At later time points, however, when helper and gutted virus particles are replicating in tandem, expression of site-specific recombinase could increase the proportion of viral particles that contain gutted genomes, thereby assisting in gutted virus recovery. One example of providing such temporal expression employs co-transfection of site specific expression vectors (e.g. Cre recombinase expression vector) with viral genomes (e.g. gutted and helper viral genomes with identical origins of replication) (See Example 6). In this manner, transfected cells are not expressing Cre at the time of transfection, and after transfection, some time will pass before the appearance of the first molecules of Cre protein, since RNA and then protein must be synthesized. Finally, the level of Cre will increase to some equilibrium level on a time scale that depends on the half life of the RNA, the half life of the protein, and the strength of the promoter used to drive Cre recombinase expression.

[0113] The amount of the recombinase expression vector employed will depend on many factors. Importantly, transfecting cells with a level of recombinase expression vector that is too high to allow the helper virus DNA to replicate at a high enough level to infect most of the cells, and lyse the plate is to be avoided (See Example 6, where 176 ng of pOG231 is less effective than providing no Cre at all). Likewise, transfecting cells with a level of recombinase expression vector that is too low to prevent the helper virus from dominating the type of virus being expressed is also to be avoided (See Example 6, where 1.41 ng of pOG231 was no more effective than providing no Cre at all). Determining the appropriate level of recombinase expression level to employ for a given type of cell type, recombinase, promoters employed, etc., is within the skill in the art. For example, a concentration type assay may be employed as exemplified in Example 6. As demonstrated in this example, various levels of recombinase expression vector may be tested to determine the optimal levels of starting recombinase expression vector that should be employed. Examples of appropriate levels of recombinase expression level are provided in Example 6 (for the types of conditions employed in this assay). For example, appropriate levels of pOG231, as determined in example 6 include approximately 5-37 ng of expression vector, preferably 7-36 ng of expression vector, more preferably 16-35 ng of expression vector. Of course, altering the type of vector, cells, conditions, etc., may change the appropriate level as described above.

[0114] B. Culturing Adenovirus in Cells Expressing Adenoviral Protein IX

[0115] In order to improve production, gutted and helper adenovirus are co-transfected in cells expressing adenoviral protein IX (pIX). The protein IX gene of the adenoviruses encodes a minor component of the outer adenoviral capsid which stabilizes the group-of-nine hexons which compose the majority of the viral capsid (See U.S. Pat. Nos. 5,932,210 and 5,824,544, hereby incorporated by reference). Based upon study of adenovirus deletion mutants, protein IX initially was thought to be a non-essential component of the adenovirus, although its absence was associated with greater heat lability than observed with wild-type virus. More recently it was discovered that protein IX is essential for packaging full length viral DNA into capsids and that in the absence of protein IX, only genomes at least 1 kb smaller than wild-type could be propagated as recombinant viruses.

[0116] In one embodiment, an expression vector encoding protein IX is co-transfected with the gutted and helper adenovirus. In some embodiments, gutted and helper adenovirus are transfected in a cell line that expresses adenoviral protein IX. In preferred embodiments, the cell stably and constitutively expresses adenoviral protein IX. In particularly preferred embodiments, the cell line also expresses E2B proteins. One example of a cell line expressing E2B proteins (adenoviral DNA polymerase and preterminal protein) is the C7 cell line (See, U.S. Pat. No. 6,083,750). Creating a cell line that stably and constitutively expresses adenoviral protein IX, in addition to adenoviral DNA polymerase and preterminal protein, may be accomplished, for example by stably transfecting C7 cells (or other cells expressing E2B proteins) with a vector expressing adenoviral protein IX (See Example 7, creating the D2104#10 cell line).

[0117] Additional cell lines that stably and constitutely expresses adenoviral protein IX, in addition to adenoviral DNA polymerase and preterminal protein are contemplated. For example, any type of cell known to effectively allow adenoviral replication may be transfected with an expression vector encoding adenoviral protein IX (preferably with a selectable marker). Preferably, the cells also express preterminal protein and adenoviral DNA polymerase. Transfected cells may be grown on selective media. Clones are then screened for expression by transfection with an adenoviral protein IX negative genome, and clones producing virus after transfection are isolated.

[0118] V. Heterologous Gene Sequences

[0119] As described above, the present invention is useful for the production of adenoviral vectors (e.g helper-dependent adenoviral vectors). The adenoviral vectors produced, in preferred embodiments, comprise a heterologous gene sequence, such that the vectors may be useful for various applications (protein expression in vitro, therapeutic applications, etc). Suitable heterologous DNA sequences include, for example, nucleic acid sequences that encode a protein that is defective or missing in a recipient subject, or a heterologous gene that encodes a protein having a desired biological or therapeutic effect (e.g. an antibacterial, antiviral, or antitumor function). Other suitable heterologous nucleic acids include, but are not limited to, those encoding for proteins used for the treatment of endocrine, metaloic, hematologic, cardiovascular, neurologic, musculoskeletal, urologic, pulmonary, and immune disorders, including such disorders as inflammatory diseases, autoimmune disease, chronic and infectious diseases, such as AIDS, cancer, hypercholestemia, insulin disorders such as diabetes, growth disorders, various blood disorders including various enemias, thalassemias, and hemophilia; genetic defects such as cystic fibrosis, Gaucher's disease, Hurler's disease, adenosine deaminase (ADA) deficiency, and emphysema.

[0120] The therapeutic or diagnostic nucleic acid sequence, in some embodiments, will code for a protein antigen. The antigen may include a native protein or protein fragment, or a synthetic protein or protein fragment or peptide. Examples of antigens include, but are not limited to, those that are capable of eliciting an immune response against viral or bacterial hepatitis, influenza, diphtheria, tetanus, pertussis, measles, mumps, rubella, polio, pneumococcus, herpes, respiratory syncytial virus, hemophilus influenza type b, chlamydia, varicella-zoster virus or rabies. The nucleic acid sequence may also be a normal muscle gene that is effected in a muscle disease (e.g. muscular dystrophies like Duchenne muscular dystrophy, limb-girdle muscular dystrophy, Landouzy-Dejerine muscular dystrophy, Becker's muscular dystrophy, ocular myopathy, and myotonic muscular dystrophy). For such muscular dystrophies, the nucleic acid may be a heterologous gene encoding the full length dystrophin gene (or cDNA sequence), BMD-minigene, ΔH2-R19 minigene, Laminin-α2, utrophin, α-sarcoglycan, and emerin. BMD mini-gene refers to dystrophin cDNAs containing internal truncations corresponding to specific exons of the gene, in particular, a deletion of the sequences encoded on exons 17-48 [Amalfitano et al., in Lucy J, and Brown S. (eds): Dystrophin: Gene, Protein, and Cell Biology (Cambridge University Press, 1997), Chpt. 1, 1-26, herein incorporated by reference]. ΔH2-R19 refers to a specific dystrophin cDNA containing internal deletions corresponding to specific functional domains of the gene, in particular, a deletion of the sequences that encode ‘hinge 2’ through ‘spectrin-like repeat’ 19 [See Amalfitano et al.].

[0121] Nucleic acid sequences may also be antisense molecules (e.g. for blocking the expression of an abnormal muscle gene). The nucleic acid sequence may also code for proteins that circulate in mammalian blood or lymphatic systems. Examples of circulating proteins include, but are not limited to, insulin, peptide hormones, hemoglobin, growth factors, liver enzymes, clotting factors and enzymes, complement factors, cytokines, tissue necrosis factor and erythropoietin. Heterologous genes may also include gene encoding proteins that are to be produced (e.g. commercially produced) in muscle cells in vitro or in vivo. For example, the improved expressions systems of the present invention may be applied to preexisting, working muscle expression systems to improve the level of expression of protein product from a gene of interest. The present invention also contemplates employing any gene of interest (heterologous or endogenous).

[0122] VI. Using Adenoviral Vectors

[0123] The adenoviral vectors produced as described above may be used, for example, in drug screen or in gene therapy methods. In one screening method, an adenoviral vector (e.g. helper-dependent adenoviral vector, produced according to the above methods) contain adenoviral DNA operably linked to a heterologous gene encoding an factor (e.g. enzyme, protein, antisense molecule) with a known function (e.g. alcohol dehydrogenase), is contacted in vitro with a tissue culture sample (e.g. a muscle cell containing tissue culture) such that the heterologous gene is expressed. A candidate compound is added along with a substrate for the enzyme (e.g. ethanol), and a parallel assay is run without the candidate compound. The level of enzyme activity is detected (e.g. amount of substrate remaining over time) in each assay. The results of both assays are compared in order to determine the affect of the candidate compound on the activity of the enzyme. In other embodiments, the candidate compound many comprise a factor suspected of altering gene expression of the heterologous gene and the assay detects that degree and/or ability of the candidate compound to reduce the activity of the expressed factor. One of ordinary skill in the art will appreciate that many other screening methods can be used. The adenoviral vectors may also be used advantageously in gene therapy to replace a defective gene in subject with a heterologous gene.

EXPERIMENTAL

[0124] The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof.

[0125] In the experimental disclosure which follows, the following abbreviations apply: N (normal); M (molar); mM (millimolar); μM (micromolar); mol (moles); mmol (millimoles); μmol (micromoles); nmol (nanomoles); pmol (picomoles); g (grams); mg (milligrams); μg (micrograms); ng (nanograms); l or L (liters); ml (milliliters); μl (microliters); cm (centimeters); mm (millimeters); μm (micrometers); nm (nanometers); ° C. (degrees Centigrade); Sigma (Sigma Chemical Co., St. Louis, Mo.); and

EXAMPLE 1

[0126] Generating Gutted and Helper Virus with Identical Termini

[0127] This example describes the deletion of internal FseI sites in the nucleic acid sequence of an Ad5-based helper virus, and insertion of this nucleic acid sequence into a plasmid such that it is removable with FseI.

[0128] The FseI recognition sequence, “GGCCGGCC”, contains cytosine residues and can be arranged to overlap with the first nucleotide of viral DNA so that only one additional base pair is attached to viral DNA removed from plasmid vectors with this enzyme (FIG. 1A). In addition, FseI is rare in cloning vector polylinkers and mammalian sequences, so it is ideal for removal of gutted viral genomes from plasmid vectors. FseI has been used previously for linearization of viral shuttle vectors, which contain a portion of the Ad genome; however, it could not be used to liberate the entire Ad5 genome from plasmid DNA, because the Ad5 genome contains two FseI sites.

[0129] In order to remove the FseI sites in the (+)lox(+)pol helper virus DNA sequence (SEQ ID NO:1), mutations were created that destroy both FseI sites while maintaining the ability of the virus to replicate (transitions were made at nucleotides 12587 and 17756, creating SEQ ID NO:9, FIG. 11, see also FIG. 1B). The mutation at nucleotide 12587 was chosen so as to preserve the amino acid sequence of capsid protein IIIa. Primers 9252I, CGGAATTCGGATCCAGCGACCGCGAGCTGAT (SEQ ID NO:2) and 9253I, CGGAATTCAGCCGGCTTCGTCGGGCCGGATGGC (SEQ ID NO:3) were used in a PCR reaction to simultaneously amplify approximately 540 base pairs of the Ad5 sequence, to introduce the G to A transition at nucleotide 12587, and to flank the resulting DNA sequence with EcoRI sites. The product was digested with EcoRI and ligated to the large, approximately 2.2 kb ApoI fragment of pBSX (pBSX—SEQ ID NO:12, FIG. 9, which is a minor modification of a Bluescript vector, with alterations to the polylinker sequence, See FIG. 10) to yield pD1858#7. Primers 9254I, CGCGGATCCGCCGGCTACGGCCTGACGGGCGG (SEQ ID NO:4) and 9255I, CGGAATTCACACACATACGACACGTTAG (SEQ ID NO:5) were used to amplify approximately 1 kb of Ad5 sequence, to introduce the C to T transition at nucleotide 17756, and to append an EcoRI site to the rightmost end of the resulting DNA fragment. The product was digested with EcoRI and NgoMI, then ligated to EcoRI-, NgoMI-digested pD1858#7 to yield pD1863#4. This plasmid was digested with NgoMI and ligated to the 5162-bp NgoMI fragment from the Ad5 genome, resulting in pD1866#17, which contains both transitions mentioned above. To create a virus lacking FseI sites, pD1866#17 was digested with EcoRI and co-transfected with FseI-digested terminal protein-DNA complex from (+)lox(+)pol Ecd-AP helper virus. The sequence for (+)lox(+)pol Ecd-AP is SEQ ID NO:1, FIG. 8. After one week of incubation, the transfected cells showed evidence of viral cytopathic effect, indicating that they contained replicating virus, designated ΔFseI.4 (SEQ ID NO:9, FIG. 1B). The DNA was extracted from these cells by Hirt prep (DNA episomal extraction method employing lysis in 0.6% SDS/10 mM EDTA, followed by addition of salt, incubation at 4° C., and centrifugation to remove contaminants, Hirt, B., J. Mol. Biol. 26:365 [1967]) and shown not to contain FseI sites by restriction digest.

[0130] To confirm that FseI could be used to release replication-competent viral DNA from flanking DNA sequences, ΔFseI.4 genomic DNA was cloned into a plasmid vector, where it was flanked by FseI sites (FIG. 1C). Primers 8270I, CGGAATTCGGCCGGCCATCATCAATAATATAC (SEQ ID NO:6) and 8274I, CGGTCGATTCAATTGCTGGCAAGCTTCGGCCCTAGACAAATAT (SEQ ID NO:7) were used in a PCR reaction to amplify approximately 400 bp from the left end of (+)lox(+)pol Ecd-AP helper virus and to introduce flanking restriction sites: EcoRI and FseI at the left end of the fragment and HindIII, MfeI, and TfiI at the right end. The product was digested with EcoRI and TfiI and cloned into the 1.86 kb ApoI/TfiI fragment of pBSX (See, FIG. 9), generating pD1812#1. Primers 8270I (SEQ ID NO:6) and 8273I, CTATGCTAACCAGCGTAGC (SEQ ID NO:8) were used to amplify approximately 1 kb from the right end of (+)lox(+)pol Ecd-AP helper virus and to add FseI and EcoRI sites at the right end of the fragment. The product was digested with HindIII and EcoRI and cloned into HindIII-, MfeI-digested pD1812#1, generating pD1821#8. To clone ΔFseI.4 viral genomic DNA into pD1821#8, the plasmid was digested with HindIII and recombined with ΔFseI.4 Hirt prep DNA in BJ5183 bacterial cells (BJ5183 bacterial cells, see Hanahan, D., J. Mol. Biol., 166:557 [1983]). The resulting plasmids, including pD1940#3 and pD1940#6, were shown by restriction digest to contain the entire ΔFseI.4 genome flanked by FseI sites (FIG. 1C). No internal FseI sites were detected, confirming that virus ΔFseI.4 contains mutations that destroy these sites.

[0131] To show that FseI digestion could release replication-competent Ad DNA from plasmids, pD1940#3 and pD1940#6 were digested with FseI and transfected into C7 cells (C7 cells express both Ad DNA polymerase and preterminal protein, see U.S. Pat. No. 6,083,750, hereby incorporated by reference). Plasmid pFG140 [See, Graham, F. L., The EMBO J., 3:2917 (1984)] known to produce replicating adenovirus after transfection, was used as a control. Both sets of transfected cells were overlaid with agarose after transfection and stained with neutral red 10 days after overlay. It was determined that FseI-digested pD1940#3 and pD1940#6 produced 36 and 56 plaques per microgram, respectively; pFG140 produced 38 plaques per microgram. This result indicates that mutation of internal FseI sites did not prevent replication of adenovirus and that FseI is an appropriate enzyme for release of viral DNA from plasmids.

EXAMPLE 2

[0132] Rescue of Helper-Dependent Ad Vectors Using Plasmid-Derived Substrates With Corresponding Termini

[0133] This example describes the rescue of helper-dependent Ad vectors using plasmid-derived substrates with corresponding termini. To demonstrate that efficient gutted virus rescue depends on the relative specific activities of gutted and helper viral DNA, a FseI-terminated gutted virus was co-transfected with various forms of helper virus DNA or transfection/infection was performed (FIG. 2). The gutted adenovirus DNA employed was pD2076#2, which contains a gutted Ad genome flanked by FseI recognition sites and carries an inducible beta-galactosidase expression cassette (FIG. 12). This plasmid was digested with FseI, and 4.4 micrograms of digested DNA were transfected into C7 cells.

[0134] For co-transfection assays, 4.4. micrograms of helper viral DNA (either TP-DNA, Hirt DNA, or FseI-terminated DNA) were co-transfected with pD2076#2 DNA. For transfection/infection, helper virus particles were added immediately following transfection at an MOI of 10 transducing units per cell. For the TP-DNA complex co-transfection, terminal protein-DNA complex was isolated from (+)lox(+)pol helper virus (SEQ ID NO:1) was isolated and transfected into cells to provide helper activity (FIG. 13). For the Hirt DNA samples, ΔFseI.4 DNA (SEQ ID NO:9) was isolated from infected cells and deproteinized (FIG. 13). For FseI-terminated samples, pD1940#3 or pD1940#6 (See FIG. 13) was digested with FseI and the released DNA was used to provide helper activity (SEQ ID NO:13, FIG. 14). Digestion with FseI releases what is essentially ΔFseI.4 (SEQ ID NO:9), except with a couple of extra nucleotides at the end (as shown in FIG. 1).

[0135] Transfection/infection was found to be very inefficient (See FIG. 2), although it is the method most frequently reported in the literature. In co-transfections, an inverse correlation was observed between the specific activity of the helper virus DNA from and the yield of gutted virus produced. Co-transfection of gutted viral DNA with plasmid-derived helper viral DNA, carrying a physically identical origin of replication (constructed as described in Example 1), was by far the most efficient method for rescue of gutted adenovirus (See, FIG. 2). After co-transfection of plasmid-derived, FseI-terminated genomes, the average gutted viral titer observed was 5.6×106 ml−1. This yield represents an improvement of approximately 30 fold over typical titers obtained by transfection/infection into C7 cells and 300 fold over typical titers obtained by transfection/infection into 293 cells.

EXAMPLE 3

[0136] Conversion of Plasmid-Derived Viral Replication Origins to Natural, Terminal Protein-Linked Origins.

[0137] This example describes the conversion of plasmid derived viral replication origins to natural, terminal protein-linked origins. This conversion employs “TP-primer”, which is terminal protein DNA linked to single-stranded DNA from the non-template strand of an Ad ITR (FIG. 3A). TP Primer was prepared in the following manner. Terminal protein-DNA complex prepared from (+)lox(+)pol Ecd-AP virus was digested for at least 16 hours at 37° C. with 2.5 U/μg Bsh1236I, 1.33 U/μg AluI, and 0.69 U/μg HinfI. Bsh12361 cuts between base pairs 73 and 74 of the Ad5 ITR (CATCATCAATAATATACCTTATTTTGGATTGAAGCCAATATGATAATGAGGG GGTGGAGTTTGTGACGTGGCGCGGGGCGTGGGAACGGGGCGGGTGACGTAG, SEQ ID NO:10), so this digestion results in terminal protein linked to a 73-bp, double-stranded DNA molecule (one of the two strands is as follows, CATCATCAATAATATACCTTATTTTGGATTGAAGCCAATATGATAATGAGGG GGTGGAGTTTGTGACGTGGCG, SEQ ID NO:11). The products of restriction digestion were then treated with 2.5 U/μg DNA of lambda exonuclease for 20 minutes at 37° C. This enzyme catalyzes the removal of 5′ mononucleotides from duplex DNA. Since the enzyme acts in a 5′ to 3′ direction, strands linked to terminal protein are not degraded; all other strands are degraded until a single-stranded region is reached.

[0138] The products of this digestion, therefore, include: 1) terminal protein linked to 73 unpaired bases (SEQ ID NO:11) of the non-template strand of the Ad5 ITR (TP-primer); 2) many random, small, single-stranded DNA molecules resulting from the degradation of approximately half of the restriction fragments present in the reaction; and 3) mononucleotides. The first of these is the desired and useful product; however, the other products do not interfere with subsequent steps. The enzymes in the reaction were then inactivated by incubation at 75° C. for 20 minutes.

[0139] TP-primer was then used to convert plasmid-derived gutted viral genomes to natural Ad origins by the following method (FIG. 3B). First, a plasmid containing gutted viral genomic DNA (pD2076#2), flanked by FseI sites, was digested with PseI to release gutted viral DNA. The products were subjected to very limited digestion with T7 gene 6 exonuclease (0.76 U/μg for 1 minute, 40 seconds) and the exonuclease was inactivated by incubation at 80° C. for 15 minutes. T7 gene 6 exonuclease, like lambda exonuclease, is a 5′ to 3′ exonuclease, so limited digestion with this enzyme exposes single-stranded regions near the gutted vector genomic termini. These regions are complementary to the single-stranded DNA found in the TP-primer reagent. Due to the long (73 bp) stretch of complementary DNA sequence and the absence of competing binding partners, the TP-primer reagent can bind efficiently to T7 gene 6-digested gutted DNA even at low molar ratios.

[0140] We added TP-primer reagent, prepared as described above, to the digested gutted DNA, raised the temperature of the mixture to 75° C., and allowed the temperature to fall slowly (over 2-3 hours) to room temperature. Hybridized TP-primer molecules were then extended using T4 DNA polymerase and nicks were repaired using T4 DNA ligase. This was accomplished by addition of 0.5 mM each dNTP, 1 mM ATP, 2.5 units T4 polymerase per μg DNA, and 2 Weiss units T4 ligase per μg DNA. A small amount of buffer (10 mM Tris-HCl, 10 mM MgCl2, 50 mM NaCl, and 1 mM DTT, pH 7.9 at 25C) was also added such that the final concentration of gutted vector genomic DNA was 0.04 μg/μL when a 2:1 (TP-primer:gutted genome) ratio was used or 0.029 μg/μL when a 4:1 ratio was used. The reaction was then incubated for 5 minutes at 0° C., 5 minutes at room temperature, and 2 hours at 37° C. EDTA was added to a final concentration of 15 mM and the reaction was stored on ice.

[0141] An assay was performed to confirm the successful addition of terminal protein to the origin of replication of the gutted virus. Specifically, a restriction digest employing NotI was performed on circular pD2076#2, the TP-primer linked pD2076#2 (FseI digested), and FseI digested pD2076#2 (negative control). This digestion was followed by agarose gel electrophoresis (FIG. 4A). The results confirmed the successful addition of the TP-primer as approximately two-thirds of the gutted DNA terminal fragments were retained in the wells of the agarose gel, behavior that is typical of protein-linked DNA (FIG. 4A).

EXAMPLE 4

[0142] TP-Primer Increases the Specific Activity of Plasmid-Derived Ad DNA

[0143] This example describes the ability of TP-primer to increase the specific activity of plasmid derived Ad DNA. In particular, replication-competent helper virus genomes were excised from plasmids pD1940#3 or pD1940#6 and the origins of DNA replication were modified as described above (See Example 3, adding TP-primer to Ad DNA). Reaction mixtures were then diluted into 0.1× TE such that transfection mixtures contained either one microgram or 0.1 micrograms of modified plasmid DNA. Parallel transfection mixtures were prepared using unmodified FseI-digested pD1940 plasmid (SEQ ID NO:13, FIG. 14). The DNA was co-precipitated with calcium phosphate, and added to plates of C7 cells. Plates were washed 16 hours after addition of precipitates and overlayed with noble agar (See, Graham, F. L. and Prevec, L. Manipulation of Adenovirus Vectors in Gene Transfer and Expression Protocols, Clifton: The Humana Press, Inc., 1991). Eight to ten days after overlay, the plates were stained with neutral red and plaques were counted. Specific activity was calculated as the number of plaques observed divided by the weight of transfected DNA.

[0144] It was found that the specific activity of treated genomes was increased by an average of 24 or 27 fold after treatment with a 2:1 or 4:1 molar ratio of TP-primer, respectively. We also examined the effect of TP-primer treatment on the rescue of gutted Ad vectors from their plasmid-derived precursors. For these experiments, since large amounts of DNA were transfected, reaction mixtures were dialyzed against 1× HBS to avoid dilution. Conversion of gutted vector origins to natural, TP-linked form resulted in improved competition with helper virus DNA (FIG. 4B). Strikingly, co-transfection of TP-gutted DNA and untreated, FseI-terminated helper virus DNA prevented lysis of the transfected cells, indicating that the specific activity of TP-gutted DNA is high enough to prevent robust helper replication.

[0145] Co-transfection of TP-gutted DNA with terminal protein-DNA complex from helper virus resulted in an average gutted viral titer of 1.5×107 per ml. This titer represents an improvement of approximately 85 fold over typical titers obtained by transfection/infection into C7 cells, 850 fold over titers obtained by transfection/infection into 293 cells, and 2.7 fold over titers obtained by co-transfection of plasmid-derived, FseI-liberated gutted and helper genomes (See FIG. 4B).

EXAMPLE 5

[0146] Terminal Transferase Template Strand Extension of Adenoviral DNA

[0147] This example describes terminal transferase (TdT) template strand extension of adenoviral DNA, and how limited extensions increase the specific activity in plaque assays and allow for more efficient recovery of gutted adenovirus.

[0148] pD1940#3 or pD1940#6 viral DNA was digested to completion with FseI. The restriction enzyme reaction was diluted 3.125-fold into 1× TdT reaction buffer (Promega, Madison, Wis.) and supplemented with 80 micromolar dNTPs and 10 units TdT per picomole DNA termini. The reaction was mixed well, incubated for a variable length of time at 37° C., and the TdT was inactivated by incubation at 75° C. for 10 minutes. The reaction mixture was extracted with 0.5 volumes of phenol-chloroform and DNA was precipitated. Samples were resuspended in 0.1× TE and transfected into C7 cells using the calcium phosphate co-precipitation method.

[0149] To determine whether TdT treatment had improved the ability of viral DNA to replicate in cells, the specific activity of treated and untreated DNA in transfected cells was measured (‘specific activity’ was defined as the number of viral plaques observed per microgram of DNA transfected; higher specific activity indicates that a lesser weight of viral DNA must be transfected to produce actively replicating virus). The results of the this assay indicate that the specific activity of pD1940 DNA was increased by approximately 5 fold after 30 minutes of treatment but less so after 6 minutes or 2.5 hours (FIG. 5C). Control reactions lacking the TdT enzyme showed no evidence of increased plaquing efficiency (FIG. 5C).

[0150] To test whether the identity of added nucleotides is important for the observed effect, we supplemented individual TdT reactions with various single and mixed nucleotides. The various reactions were precipitated individually, transfected into cells, and developing viral plaques were counted after 7-10 days. The effectiveness of TdT treatment was found to vary with the identity of the nucleotides included in the reaction (FIG. 5C). It was determined that the addition of single nucleotides was not effective; in fact, addition of thymidine or cytosine residues alone markedly reduced plaquing efficiency. It was also determined that the most effective combination was addition of guanine, adenine, and cytosine (dGAC), which increased plaquing efficiency by approximately 10 fold (FIG. 5C and data not shown).

[0151] An assay was also conducted involving TdT treatment of gutted Ad virus, and rescue from bacterial plasmids. In this example, gutted Ad genomes excised from pD2076#2 with the restriction enzyme FseI were employed. These excised genomes were treated with the combination of guanine, adenine, and cytosine as described above. 8.8 micrograms of treated DNA were transfected into approximately 2 million C7 cells in a 60-mm plate. 16 hours later the cells were washed and then infected with 20 million transducing units of ΔFseI.4 helper virus (SEQ ID NO:9). Two to three days after this procedure, the plates displayed viral cytopathic effect and lysates were harvested. By measuring the titer of gutted virus in the recovered lysates, it was determined that TdT treatment of the gutted vector doubled the amount of gutted virus produced by the cells after rescue (FIG. 5D). By co-transfecting plasmid-derived helper and gutted DNAs, as described above, the baseline titer obtained without TdT treatment was increased (FIG. 5D). After treatment of gutted plasmid DNA with TdT, a further 2.5-fold increase in gutted virus titer was obtained (FIG. 5D).

EXAMPLE 6

[0152] Regulated Expression of Site-Specific Recombinase Improves Gutted Virus Rescue

[0153] This example describes the use of regulated expression of Cre recombinase to improve gutted virus rescue when gutted and helper virus with identical ends are co-transfected. Initially, the effect of constitutive expression of Cre recombinase in packing cells co-transfected with gutted and helper viruses with identical ends was examined. ΔFseI.4 helper virus (SEQ ID NO:9) is an E1-, E3-deleted virus that can be negatively selected using Cre recombinase and carries an alkaline phosphatase reporter gene in its E3 region. The packaging signal, which consists of packaging elements I-V, is flanked by loxP sites in direct repeat orientation, allowing removal of the packaging signal in the presence of Cre. The E1 region (map units 1-9.2) has been removed. The E3 region (map units 78.3-85.8) has also been removed and replaced with an expression cassette, oriented from left to right in the viral genome, that consists of the inducible ecdysone promoter, the coding region for human placental alkaline phosphatase, polyadenylation sequences from SV40, and approximately 2 kb of “stuffer” DNA derived from an intron of the human dystrophin gene. For these experiments, ΔFseI.4 genomes were released from pD1940#3 or pD1940#6 by digestion with FseI.

[0154] Specifically, FseI-terminated gutted and helper viral genomes were co-transfected into either C7 cells or C7-Cre-8.2 cells, which constitutively express Cre recombinase. The plate of transfected C7-Cre-8.2 cells showed no signs of lysis even after 12 days of incubation and the resulting titer of gutted virus was approximately 100 times lower than that observed in C7 cells (FIG. 6). This result indicates that when gutted and helper viral genomes with identical origin structures are co-transfected, constitutive expression Cre recombinase in the packaging cells is not desirable.

[0155] Cre recombinase, however, may still be employed to improve gutted virus recovery. Instead of constitutive expression of Cre recombinase, the recombinase expression is regulated over time. This was accomplished by co-transfection of a Cre recombinase expression vector (the level of Cre recombinase will increase gradually over time). Specifically, C7 cells were transfected with FseI-terminated gutted virus, FseI-terminated helper virus, and varying amounts of a Cre recombinase expression vector (pOG231). The results of this experiment show very low amounts of pOG231 had minimal effects on gutted virus production, with increasing amounts of pOG231, gutted virus production was improved (FIG. 6). The results also indicate that using the highest amounts of pOG231, little viral replication was observed and gutted virus titers were reduced (indicating that Cre protein levels increased to a level beyond which lysis could not proceed). Maximal improvement in gutted virus titers was observed using 16-35 ng of Cre expression vector, at which level average gutted titers more than doubled, to 1.3×107 ml-1 (FIG. 6). High levels of gutted virus were also observed using 7.04 ng of the Cre expression vector.

[0156] This selection strategy was also shown to be effective for gutted virus rescue from TdT-modified and TP-primer-modified genomes. For TdT-modified genomes, co-transfection with 35.2 ng Cre increased gutted virus production by an average of 3 fold. For TP-primer-modified genomes, use of 0.88 μg Cre approximately doubled gutted virus production, to 2.5×107 ml-1.

EXAMPLE 7

[0157] Generating An Adenoviral Protein IX Expressing Cell Line

[0158] This example describes the generation of a cell line expressing adenoviral protein IX (pIX), in addition to E2B proteins (adenoviral DNA polymerase and preterminal protein). C7 cells (that already express adenoviral DNA polymerase and preterminal protein) were transfected with PvuI-linearized pD1962delBbsI-pIX (SEQ ID NO:14, FIG. 15), a plasmid that contains expression cassettes directing expression of adenoviral protein IX and puromycin N-acetyl transferase (See FIG. 16). Positive clones were selected in the presence of 2 micrograms puromycin per milliliter of medium. Clones were screened for expression of pIX by transfection with FseI-digested HΔIX#3 (SEQ ID NO:15, FIG. 17), a plasmid that contains an E1-, E3-, and pIX-negative Ad genome of approximately 35.6 kb in size. Clone pD2104#10 produced virus after transfection with HΔIX#3.

[0159] D2104#10 cells and C7 cells were then transfected with FseI-digested pD1940#6, which contains a pIX-positive Ad genome. The cells were then overlayed with agarose to allow for counting of plaques, each representing the successful conversion of a transfected genome to a replicating virus. It was determined that D2104#10 cells displayed three times as many plaques as C7 cells (FIG. 7). Additionally, plaques formed on D2104#10 cells were larger than those formed on C7 cells.

[0160] D2104#10 cells were then tested for the ability to rescue gutted virus from a plasmid-based precursor, either in the presence or absence of regulated Cre expression (FIG. 7). Plates of each cell type were transfected with FseI-terminated gutted and helper genomes at a 1:1 ratio, together with varying amounts (15.74 ng, 35.2 ng, and 78.71 ng) of the Cre expression plasmid pOG231. Plates of D2104#10 cells were found to lyse before plates of C7 cells that had been transfected under the same conditions, reflecting the higher proportion of transfected cells that initiated replication of the helper. The co-transfection of C7 cells in the presence of 79 ng of pOG231 failed to produce lysis even after 13 days, whereas D2104#10 cells lysed within 10 days. More gutted virus was produced in D2104#10 cells under all the conditions tested (FIG. 7). In the absence of Cre selection, D2104#10 cells produced twice as much virus as C7 cells. Examining the highest level of selection tested (79 ng), D2104#10 cells produced twice as much virus as C7 cells did under their highest selection conditions (16 ng).

[0161] All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in material science, chemistry, and molecular biology or related fields are intended to be within the scope of the following claims.

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