US20090023196A1 - Stocks of replication-deficient adenovirus - Google Patents

Stocks of replication-deficient adenovirus Download PDF

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US20090023196A1
US20090023196A1 US11/879,421 US87942107A US2009023196A1 US 20090023196 A1 US20090023196 A1 US 20090023196A1 US 87942107 A US87942107 A US 87942107A US 2009023196 A1 US2009023196 A1 US 2009023196A1
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adenovirus
cells
dna
recombinant
e1b
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Frits J. Fallaux
Robert C. Hoeben
Alex Jan Van der Eb
Abraham Bout
Domenico Valerio
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Introgene BV
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Priority to EP95201611.1 priority Critical
Priority to EP95201611 priority
Priority to EP95201728.3 priority
Priority to EP95201728 priority
Priority to US08/793,170 priority patent/US5994128A/en
Priority to PCT/NL1996/000244 priority patent/WO1997000326A1/en
Priority to US09/334,765 priority patent/US6238893B1/en
Priority to US09/506,548 priority patent/US6602706B1/en
Priority to US10/125,751 priority patent/US7105346B2/en
Priority to US10/219,414 priority patent/US20030104626A1/en
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Priority to US11/879,421 priority patent/US20090023196A1/en
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Abstract

Presented are ways to address the problem of replication-competent adenovirus in adenoviral production for use with, for example, gene therapy. Packaging cells having no overlapping sequences with a selected vector are suited for large scale production of recombinant adenoviruses. A system for use with the invention produces replication-defective adenovirus. The system includes a primary cell containing a nucleic acid based on or derived from adenovirus and an isolated recombinant nucleic acid molecule for transfer into the primary cell. The isolated recombinant nucleic acid molecule is based on or derived from an adenovirus, has at least one functional encapsidation signal and at least one functional Inverted Terminal Repeat, and lacks overlapping sequences with the nucleic acid of the cell. Otherwise, the overlapping sequences would enable homologous recombination leading to replication-competent adenovirus in the primary cell into which the isolated recombinant nucleic acid molecule is to be transferred.

Description

    CROSS-REFERENCE TO RELATED APPLICATIONS
  • This patent application is a continuation of U.S. patent application Ser. No. 10/219,414, filed Aug. 15, 2002, pending, which is a continuation of U.S. patent application Ser. No. 10/125,751, filed Apr. 18, 2002, now U.S. Pat. No. 7,105,346, issued Sep. 12, 2006, which is a continuation of U.S. patent application Ser. No. 09/506,548, filed Feb. 16, 2000, now U.S. Pat. No. 6,602,706, issued Aug. 5, 2003, which is a division of U.S. patent application Ser. No. 09/334,765, filed Jun. 16, 1999, now U.S. Pat. No. 6,238,893, issued May 29, 2001, which is a continuation of U.S. patent application Ser. No. 08/793,170, filed Mar. 25, 1997, now U.S. Pat. No. 5,994,128, issued Nov. 30, 1999, which is a national entry under 35 U.S.C. § 371 of PCT International Patent Application PCT/NL96/00244, filed Jun. 14, 1996, which itself claims priority from European Patent Application EP 95201728.3, filed Jun. 26, 1995, and European Patent Application EP 95201611.1, filed Jun. 15, 1995, the disclosures of each of which are hereby incorporated herein in their entirety by this reference.
  • TECHNICAL FIELD
  • The invention relates to the field of recombinant DNA technology, more in particular to the field of gene therapy. In particular, the invention relates to gene therapy using materials derived from adenovirus, specifically human recombinant adenovirus. It especially relates to novel virus-derived vectors and novel packaging cell lines for vectors based on adenoviruses.
  • BACKGROUND
  • Gene therapy is a recently developed concept for which a wide range of applications can be and have been envisioned. In gene therapy, a molecule carrying genetic information is introduced into some or all cells of a host, as a result of which the genetic information is added to the host in a functional format.
  • The genetic information added may be a gene or a derivative of a gene, such as a cDNA, which encodes a protein. This is a functional format in that the protein can be expressed by the machinery of the host cell.
  • The genetic information can also be a sequence of nucleotides complementary to a sequence of nucleotides (either DNA or RNA) present in the host cell. This is a functional format in that the added DNA (nucleic acid) molecule or copies made thereof in situ are capable of base pairing with the complementary sequence present in the host cell.
  • Applications include the treatment of genetic disorders by supplementing a protein or other substance which, because of the genetic disorder, is either absent or present in insufficient amounts in the host, the treatment of tumors, and the treatment of other acquired diseases such as (auto)immune diseases, infections, etc.
  • As may be inferred from the above, there are basically three different approaches in gene therapy: the first directed towards compensating for a deficiency in a (mammalian) host, the second directed towards the removal or elimination of unwanted substances (organisms or cells) and the third towards application of a recombinant vaccine (against tumors or foreign microorganisms).
  • For the purpose of gene therapy, adenoviruses carrying deletions have been proposed as suitable vehicles for genetic information. Adenoviruses are nonenveloped DNA viruses. Gene-transfer vectors derived from adenoviruses (so-called “adenoviral vectors”) have a number of features that make them particularly useful for gene transfer for such purposes. For example, the biology of the adenovirus is characterized in detail, the adenovirus is not associated with severe human pathology, the adenovirus is extremely efficient in introducing its DNA into the host cell, the adenovirus can infect a wide variety of cells and has a broad host-range, the adenovirus can be produced in large quantities with relative ease, and the adenovirus can be rendered replication defective by deletions in the early-region 1 (“E1”) of the viral genome.
  • The adenovirus genome is a linear double-stranded DNA molecule of approximately 36,000 base pairs with the 55 kDa terminal protein covalently bound to the 5′ terminus of each strand. The adenoviral (“Ad”) DNA contains identical Inverted Terminal Repeats (“ITR”) of about 100 base pairs with the exact length depending on the serotype. The viral origins of replication are located within the ITRs exactly at the genome ends. DNA synthesis occurs in two stages. First, the replication proceeds by strand displacement, generating a daughter duplex molecule and a parental displaced strand. The displaced strand is single stranded and can form a so-called “panhandle” intermediate, which allows replication initiation and generation of a daughter duplex molecule. Alternatively, replication may proceed from both ends of the genome simultaneously, obviating the requirement to form the panhandle structure. The replication is summarized in FIG. 14 adapted from Lechner and Kelly (1977).
  • During the productive infection cycle, the viral genes are expressed in two phases: the early phase, which is the period up to viral DNA replication, and the late phase, which coincides with the initiation of viral DNA replication. During the early phase, only the early gene products, encoded by regions E1, E2, E3 and E4, are expressed, which carry out a number of functions that prepare the cell for synthesis of viral structural proteins (Berk, 1986). During the late phase, the late viral gene products are expressed in addition to the early gene products, and host cell DNA and protein synthesis are shut off. Consequently, the cell becomes dedicated to the production of viral DNA and of viral structural proteins (Tooze, 1981).
  • The E1 region of adenovirus is the first region of adenovirus expressed after infection of the target cell. This region consists of two transcriptional units, the E1A and E1B genes, which both are required for oncogenic transformation of primary (embryonic) rodent cultures. The main functions of the E1A gene products are 1) to induce quiescent cells to enter the cell cycle and resume cellular DNA synthesis and 2) to transcriptionally activate the E1B gene and the other early regions (E2, E3, E4). Transfection of primary cells with the E1A gene alone can induce unlimited proliferation (immortalization) but does not result in complete transformation. However, expression of E1A in most cases results in induction of programmed cell death (apoptosis) and only occasionally immortalization (Jochemsen et al., 1987). Co-expression of the E1B gene is required to prevent induction of apoptosis and for complete morphological transformation to occur. In established immortal cell lines, high level expression of E1A can cause complete transformation in the absence of E1B (Roberts et al., 1985).
  • The E1B encoded proteins assist E1A in redirecting the cellular functions to allow viral replication. The E1B 55 kDa and E4 33 kDa proteins, which form a complex that is essentially localized in the nucleus, function in inhibiting the synthesis of host proteins and in facilitating the expression of viral genes. Their main influence is to establish selective transport of viral mRNAs from the nucleus to the cytoplasm concomitantly with the onset of the late phase of infection. The E1B 21 kDa protein is important for correct temporal control of the productive infection cycle, thereby preventing premature death of the host cell before the virus life cycle has been completed. Mutant viruses incapable of expressing the E1B 21 kDa gene product exhibit a shortened infection cycle that is accompanied by excessive degradation of host cell chromosomal DNA (deg-phenotype) and in an enhanced cytopathic effect (cyt-phenotype) (Telling et al., 1994). The deg and cyt phenotypes are suppressed when, in addition, the E1A gene is mutated, indicating that these phenotypes are a function of E1A (White et al., 1988). Furthermore, the E1B 21 kDa protein slows down the rate by which E1A switches on the other viral genes. It is not yet known through which mechanisms E1B 21 kDa quenches these E1A-dependent functions.
  • Vectors derived from human adenoviruses, in which at least the E1 region has been deleted and replaced by a gene of interest, have been used extensively for gene therapy experiments in the preclinical and clinical phase.
  • As stated before, all adenovirus vectors currently used in gene therapy are believed to have a deletion in the E1 region, where novel genetic information can be introduced. The E1 deletion renders the recombinant virus replication defective (Stratford-Perricaudet and Perricaudet, 1991). We have demonstrated that recombinant adenoviruses are able to efficiently transfer recombinant genes to the rat liver and airway epithelium of rhesus monkeys (Bout et al., 1994b; Bout et al., 1994a). In addition, we (Vincent et al., 1996a; Vincent et al., 1996b) and others (see, e.g., Haddada et al., 1993) have observed a very efficient in vivo adenovirus mediated gene transfer to a variety of tumor cells in vitro and to solid tumors in animal models (lung tumors, glioma) and human xenografts in immunodeficient mice (lung) in vivo (reviewed by Blaese et al., 1995).
  • In contrast to (for instance) retroviruses, adenoviruses 1) do not integrate into the host cell genome, 2) are able to infect nondividing cells, and 3) are able to efficiently transfer recombinant genes in vivo (Brody and Crystal, 1994). Those features make adenoviruses attractive candidates for in vivo gene transfer of, for instance, suicide or cytokine genes into tumor cells.
  • However, a problem associated with current recombinant adenovirus technology is the possibility of unwanted generation of replication-competent adenovirus (“RCA”) during the production of recombinant adenovirus (Lochmüller et al., 1994; Imler et al., 1996). This is caused by homologous recombination between overlapping sequences from the recombinant vector and the adenovirus constructs present in the complementing cell line, such as the 293 cells (Graham et al., 1977). RCA is undesirable in batches to be used in clinical trials because RCA 1) will replicate in an uncontrolled fashion, 2) can complement replication-defective recombinant adenovirus, causing uncontrolled multiplication of the recombinant adenovirus, and 3) batches containing RCA induce significant tissue damage and hence strong pathological side effects (Lochmüller et al., 1994). Therefore, batches to be used in clinical trials should be proven free of RCA (Ostrove, 1994).
  • It was generally thought that E1-deleted vectors would not express any other adenovirus genes. However, recently it has been demonstrated that some cell types are able to express adenovirus genes in the absence of E1 sequences. This indicates that some cell types possess the machinery to drive transcription of adenovirus genes. In particular, it was demonstrated that such cells synthesize E2A and late adenovirus proteins.
  • In a gene therapy setting, this means that transfer of the therapeutic recombinant gene to somatic cells not only results in expression of the therapeutic protein but may also result in the synthesis of viral proteins. Cells that express adenoviral proteins are recognized and killed by Cytotoxic T Lymphocytes, which thus 1) eradicates the transduced cells and 2) causes inflammations (Bout et al., 1994a; Engelhardt et al., 1993; Simon et al., 1993). As this adverse reaction hampers gene therapy, several solutions to this problem have been suggested, such as 1) using immunosuppressive agents after treatment, 2) retention of the adenovirus E3 region in the recombinant vector (see European patent application EP 95202213), and 3) using temperature sensitive (“ts”) mutants of human adenovirus, which have a point mutation in the E2A region rendering them temperature sensitive, as has been claimed in patent WO/28938.
  • However, these strategies to circumvent the immune response have their limitations. The use of ts mutant recombinant adenovirus diminishes the immune response to some extent but was less effective in preventing pathological responses in the lungs (Engelhardt et al., 1994a).
  • The E2A protein may induce an immune response by itself, and it plays a pivotal role in the switch to the synthesis of late adenovirus proteins. Therefore, it is attractive to make temperature sensitive recombinant human adenoviruses.
  • A major drawback of this system is the fact that although the E2 protein is unstable at the nonpermissive temperature, the immunogenic protein is still being synthesized. In addition, it is to be expected that the unstable protein does activate late gene expression, albeit to a low extent. ts125 mutant recombinant adenoviruses have been tested, and prolonged recombinant gene expression was reported (Yang et al., 1994b; Engelhardt et al., 1994a; Engelhardt et al., 1994b; Yang et al., 1995). However, pathology in the lungs of cotton rats was still high (Engelhardt et al., 1994a), indicating that the use of ts mutants results in only a partial improvement in recombinant adenovirus technology. Others (Fang et al., 1996) did not observe prolonged gene expression in mice and dogs using ts125 recombinant adenovirus. An additional difficulty associated with the use of ts125 mutant adenoviruses is that a high frequency of reversion is observed. These revertants are either real revertants or the result of second site mutations (Kruijer et al., 1983; Nicolas et al., 1981). Both types of revertants have an E2A protein that functions at normal temperature and, therefore, have toxicity similar to the wild-type virus.
  • BRIEF SUMMARY OF THE INVENTION
  • In one aspect of the invention, this problem in virus production is solved in that we have developed packaging cells that have no overlapping sequences with a new basic vector and thus are suited for safe large scale production of recombinant adenoviruses. One of the additional problems associated with the use of recombinant adenovirus vectors is the host-defense reaction against treatment with adenovirus.
  • Briefly, recombinant adenoviruses are deleted for the E1 region. The adenovirus E1 products trigger the transcription of the other early genes (E2, E3, E4), which consequently activate expression of the late virus genes.
  • In another aspect of the present invention, we therefore delete E2A coding sequences from the recombinant adenovirus genome and transfect these E2A sequences into the (packaging) cell lines containing E1 sequences to complement recombinant adenovirus vectors.
  • Major hurdles in this approach are 1) that E2A should be expressed to very high levels and 2) that E2A protein is very toxic to cells.
  • The current invention, in yet another aspect, therefore discloses use of the ts125 mutant E2A gene, which produces a protein that is not able to bind DNA sequences at the nonpermissive temperature. High levels of this protein may be maintained in the cells (because it is nontoxic at this temperature) until the switch to the permissive temperature is made. This can be combined with placing the mutant E2A gene under the direction of an inducible promoter, such as, for instance, tet, methallothionein, steroid inducible promoter, retinoic acid β-receptor, or other inducible systems. However, in yet another aspect of the invention, the use of an inducible promoter to control the moment of production of toxic wild-type E2A is disclosed.
  • Two salient additional advantages of E2A-deleted recombinant adenovirus are 1) the increased capacity to harbor heterologous sequences and 2) the permanent selection for cells that express the mutant E2A. This second advantage relates to the high frequency of reversion of ts125 mutation: when reversion occurs in a cell line harboring ts125 E2A, this will be lethal to the cell. Therefore, there is a permanent selection for those cells that express the ts125 mutant E2A protein. In addition, as we in one aspect of the invention generate E2A-deleted recombinant adenovirus, we will not have the problem of reversion in our adenoviruses.
  • In yet another aspect of the invention, as a further improvement, the use of nonhuman cell lines as packaging cell lines is disclosed.
  • For GMP production of clinical batches of recombinant viruses, it is desirable to use a cell line that has been used widely for production of other biotechnology products. Most of the latter cell lines are of monkey origin, which have been used to produce, for example, vaccines.
  • These cells cannot be used directly for the production of recombinant human adenovirus, as human adenovirus cannot replicate or replicates only to low levels in cells of monkey origin. A block in the switch of the early to late phase of the adenovirus lytic cycle underlies defective replication. However, host range mutations in the human adenovirus genome are described (hr400-404), which allow replication of human viruses in monkey cells. These mutations reside in the gene encoding E2A protein (Klessig and Grodzicker, 1979; Klessig et al., 1984; Rice and Klessig, 1985; Klessig et al., 1984). Moreover, mutant viruses have been described that harbor both the hr and temperature-sensitive ts125 phenotype (Brough et al., 1985; Rice and Klessig, 1985).
  • We therefore generate packaging cell lines of monkey origin (e.g., VERO, CV1) that harbor:
      • 1) E1 sequences, to allow replication of E1/E2-defective adenoviruses, and
      • 2) E2A sequences, containing the hr mutation and the ts125 mutation, named ts400 (Brough et al., 1985; Rice and Klessig, 1985) to prevent cell death by E2A overexpression, and/or
      • 3) E2A sequences, just containing the hr mutation, under the control of an inducible promoter, and/or
      • 4) E2A sequences, containing the hr mutation and the ts125 mutation (ts400), under the control of an inducible promoter.
  • Furthermore we disclose the construction of novel and improved combinations of packaging cell lines and recombinant adenovirus vectors. We provide:
      • 1) A novel packaging cell line derived from diploid human embryonic retinoblasts (“HER”) that harbors nt. 80-5788 of the Ad5 genome. This cell line, named 911, deposited under no. 95062101 at the ECACC™, has many characteristics that make it superior to the commonly used 293 cells (Fallaux et al., 1996);
      • 2) Novel packaging cell lines that express just E1A genes and not E1B genes. Established cell lines (and not human diploid cells of which 293 and 911 cells are derived) are able to express E1A to high levels without undergoing apoptotic cell death, as occurs in human diploid cells that express E1A in the absence of E1B. Such cell lines are able to trans-complement E1B-defective recombinant adenoviruses, because viruses mutated for E1B 21 kDa protein are able to complete viral replication even faster than wild-type adenoviruses (Telling et al., 1994). The constructs are described in detail below and are graphically represented in FIGS. 1-5. The constructs are transfected into the different established cell lines and are selected for high expression of E1A. This is done by operatively linking a selectable marker gene (e.g., NEO gene) directly to the E1B promoter. The E1B promoter is transcriptionally activated by the E1A gene product, and, therefore, resistance to the selective agent (e.g., G418 in the case of NEO is used as the selection marker) results in direct selection for desired expression of the E1A gene;
      • 3) Packaging constructs that are mutated or deleted for E1B 21 kDa, but just express the 55 kDa protein;
      • 4) Packaging constructs to be used for generation of complementing packaging cell lines from diploid cells (not exclusively of human origin) without the need for selection with marker genes. These cells are immortalized by expression of E1A. However, in this particular case, expression of E1B is essential to prevent apoptosis induced by E1A proteins. Selection of E1-expressing cells is achieved by selection for focus formation (immortalization), as described for 293 cells (Graham et al., 1977) and 911 cells (Fallaux et al., 1996), that are E1-transformed human embryonic kidney (“HEK”) cells and human embryonic retinoblasts (“HER”), respectively;
      • 5) After transfection of HER cells with construct pIG.E1B (see FIGS. 4A and 4B), seven independent cell lines could be established. These cell lines were designated PER.C1, PER.C3, PER.C4, PER.C5, PER.C6™, PER.C8, and PER.C9. PER denotes PGK-E1-Retinoblasts. These cell lines express E1A and E1B proteins, are stable (e.g., PER.C6™ for more than 57 passages), and complement E1-defective adenovirus vectors. Yields of recombinant adenovirus obtained on PER cells are a little higher than obtained on 293 cells. One of these cell lines (PER.C6™) has been deposited at the ECACC™ under number 96022940;
      • 6) New adenovirus vectors with extended E1 deletions (deletion nt. 459-3510). Those viral vectors lack sequences homologous to E1 sequences in the packaging cell lines. These adenoviral vectors contain pIX promoter sequences and the pIX gene, as pIX (from its natural promoter sequences) can only be expressed from the vector and not by packaging cells (Matsui et al., 1986, Hoeben and Fallaux, personal communication; Imler et al., 1996);
      • 7) E2A-expressing packaging cell lines preferably based on either E1A-expressing established cell lines or E1A-E1B-expressing diploid cells (see under 2-4). Either E2A expression is under the control of an inducible promoter or the E2A ts125 mutant is driven by either an inducible or a constitutive promoter.
      • 8) Recombinant adenovirus vectors as described before (see 6) but carrying an additional deletion of E2A sequences;
      • 9) Adenovirus packaging cells from monkey origin that are able to trans-complement E1-defective recombinant adenoviruses. They are preferably co-transfected with pIG.E1A.E1B and pIG.NEO and selected for NEO resistance. Such cells E1A and E1B are able to transcomplement E1-defective recombinant human adenoviruses but will do so inefficiently because of a block of the synthesis of late adenovirus proteins in cells of monkey origin (Klessig and Grodzicker, 1979). To overcome this problem, we generate recombinant adenoviruses that harbor a host-range mutation in the E2A gene, allowing human adenoviruses to replicate in monkey cells. Such viruses are generated as described in FIG. 12, except DNA from an hr-mutant is used for homologous recombination; and
      • 10) Adenovirus packaging cells from monkey origin as described under 9, except that they will also be co-transfected with E2A sequences harboring the hr mutation. This allows replication of human adenoviruses lacking E1 and E2A (see under 8). E2A in these cell lines is either under the control of an inducible promoter or the tsE2A mutant is used. In the latter case, the E2A gene will thus carry both the ts mutation and the hr mutation (derived from ts400). Replication-competent human adenoviruses have been described that harbor both mutations (Brough et al., 1985; Rice and Klessig, 1985).
  • A further aspect of the invention provides otherwise improved adenovirus vectors, as well as novel strategies for generation and application of such vectors and a method for the intracellular amplification of linear DNA fragments in mammalian cells.
  • BRIEF DESCRIPTION OF THE DRAWINGS
  • The following figures and drawings may help to understand the invention:
  • FIG. 1 illustrates the construction of pBS.PGK.PCRI;
  • FIG. 2 illustrates the construction of pIG.E1A.E1B.X;
  • FIGS. 3A and 3B illustrate the construction of pIG.E1A.NEO;
  • FIGS. 4A and 4B illustrate the construction of pIG.E1A.E1B;
  • FIG. 5 illustrates the construction of pIG.NEO;
  • FIG. 6 illustrates the transformation of primary baby rat kidney (“BRK”) cells by adenovirus packaging constructs;
  • FIG. 7 illustrates a Western blot analysis of A549 clones transfected with pIG.E1A.NEO and HER cells transfected with pIG.E1A.E1B (PER clones);
  • FIG. 8 illustrates a Southern blot analysis of 293, 911 and PER cell lines. Cellular DNA was extracted, Hind III digested, electrophoresed and transferred to Hybond N+ membranes (Amersham);
  • FIG. 9 illustrates the transfection efficiency of PER.C3, PER.C5, PER.C6™ and 911 cells;
  • FIG. 10 illustrates construction of adenovirus vector pMLPI.TK. pMLPI.TK is designed to have no sequence overlap with the packaging construct pIG.E1A.E1B;
  • FIGS. 11A and 11B illustrate new adenovirus packaging constructs which do not have sequence overlap with new adenovirus vectors;
  • FIG. 12 illustrates the generation of recombinant adenovirus IG.Ad.MLPI.TK;
  • FIG. 13 illustrates the adenovirus double-stranded DNA genome indicating the approximate locations of E1, E2, E3, E4, and L regions;
  • FIG. 14 illustrates the adenovirus genome shown in the top left with the origins of replication located within the left and right ITRs at the genome ends;
  • FIG. 15 illustrates a potential hairpin conformation of a single-stranded DNA molecule that contains the HP/asp sequence (SEQ ID NO:22);
  • FIG. 16 illustrates a diagram of pICLhac;
  • FIG. 17 illustrates a diagram of pICLhaw;
  • FIG. 18 illustrates a schematic representation of pICLI;
  • FIG. 19 is a diagram of pICL (SEQ ID NO:21); and
  • FIGS. 20A-20F recite the nucleotide sequence of pICL 5620BPS DNA (circular) (SEQ ID NO:21).
  • DETAILED DESCRIPTION OF THE INVENTION
  • The so-called “minimal” adenovirus vectors according to the present invention retain at least a portion of the viral genome that is required for encapsidation of the genome into virus particles (the encapsidation signal), as well as at least one copy of at least a functional part or a derivative of the ITR, that is, DNA sequences derived from the termini of the linear adenovirus genome. The vectors according to the present invention will also contain a transgene linked to a promoter sequence to govern expression of the transgene. Packaging of the so-called minimal adenovirus vector can be achieved by coinfection with a helper virus or, alternatively, with a packaging-deficient replicating helper system, as described below.
  • Adenovirus-derived DNA fragments that can replicate in suitable cell lines and that may serve as a packaging-deficient replicating helper system are generated as follows. These DNA fragments retain at least a portion of the transcribed region of the “late” transcription unit of the adenovirus genome and carry deletions in at least a portion of the E1 region and deletions in at least a portion of the encapsidation signal. In addition, these DNA fragments contain at least one copy of an ITR. At one terminus of the transfected DNA molecule an ITR is located. The other end may contain an ITR or alternatively a DNA sequence that is complementary to a portion of the same strand of the DNA molecule other than the ITR. If, in the latter case, the two complementary sequences anneal, the free 3′-hydroxyl group of the 3′ terminal nucleotide of the hairpin structure can serve as a primer for DNA synthesis by cellular and/or adenovirus-encoded DNA polymerases, resulting in conversion into a double-stranded form of at least a portion of the DNA molecule. Further replication initiating at the ITR will result in a linear double-stranded DNA molecule that is flanked by two ITRs and is larger than the original transfected DNA molecule (see FIG. 13). This molecule can replicate itself in the transfected cell by virtue of the adenovirus proteins encoded by the DNA molecule and the adenoviral and cellular proteins encoded by genes in the host-cell genome. This DNA molecule cannot be encapsidated due to its large size (greater than 39,000 base pairs) or due to the absence of a functional encapsidation signal. This DNA molecule is intended to serve as a helper for the production of defective adenovirus vectors in suitable cell lines.
  • The invention also comprises a method for amplifying linear DNA fragments of variable size in suitable mammalian cells. These DNA fragments contain at least one copy of the ITR at one of the termini of the fragment. The other end may contain an ITR or, alternatively, a DNA sequence that is complementary to a portion of the same strand of the DNA molecule other than the ITR. If, in the latter case, the two complementary sequences anneal, the free 3′-hydroxyl group of the 3′ terminal nucleotide of the hairpin structure can serve as a primer for DNA synthesis by cellular and/or adenovirus-encoded DNA polymerases, resulting in conversion of the displaced strand into a double-stranded form of at least a portion of the DNA molecule. Further replication initiating at the ITR will result in a linear double-stranded DNA molecule that is flanked by two ITRs, which is larger than the original transfected DNA molecule. A DNA molecule that contains ITR sequences at both ends can replicate itself in transfected cells by virtue of the presence of at least the adenovirus E2 proteins (viz. the DNA-binding protein (“DBP”), the adenovirus DNA polymerase (“Ad-pol”), and the preterminal protein (“pTP”). The required proteins may be expressed from adenovirus genes on the DNA molecule itself, from adenovirus E2 genes integrated in the host-cell genome, or from a replicating helper fragment, as described above.
  • Several groups have shown that the presence of ITR sequences at the end of DNA molecules are sufficient to generate adenovirus minichromosomes that can replicate if the adenovirus-proteins required for replication are provided in trans, for example, by infection with a helper virus (Hu et al., 1992; Wang and Pearson, 1985; Hay et al., 1984). Hu et al. (1992) observed the presence and replication of symmetrical adenovirus minichromosome-dimers after transfection of plasmids containing a single ITR. The authors were able to demonstrate that these dimeric minichromosomes arise after tail-to-tail ligation of the single ITR DNA molecules. In DNA extracted from defective adenovirus type 2 particles, dimeric molecules of various sizes have also been observed using electron-microscopy (Daniell, 1976). It was suggested that the incomplete genomes were formed by illegitimate recombination between different molecules and that variations in the position of the sequence at which the illegitimate base pairing occurred were responsible for the heterogeneous nature of the incomplete genomes. Based on this mechanism it was speculated that, in theory, defective molecules with a total length of up to two times the normal genome could be generated. Such molecules could contain duplicated sequences from either end of the genome. However, no DNA molecules larger than the full-length virus were found packaged in the defective particles (Daniell, 1976). This can be explained by the size limitations that apply to the packaging. In addition, it was observed that in the virus particles, DNA molecules with a duplicated left end predominated over those containing the right-end terminus (Daniell, 1976). This is fully explained by the presence of the encapsidation signal near that left end of the genome (Gräble and Hearing, 1990; Gräble and Hearing, 1992; Hearing et al., 1987).
  • The major problems associated with the current adenovirus-derived vectors are:
      • 1) The strong immunogenicity of the virus particle;
      • 2) The expression of adenovirus genes that reside in the adenoviral vectors, resulting in a Cytotoxic T-cell response against the transduced cells; and
      • 3) The low amount of heterologous sequences that can be accommodated in the current vectors (up to maximally approximately 8000 base pairs (“bp”) of heterologous DNA).
  • The strong immunogenicity of the adenovirus particle results in an immunological response of the host, even after a single administration of the adenoviral vector. As a result of the development of neutralizing antibodies, a subsequent administration of the virus will be less effective or even completely ineffective. However, a prolonged or persistent expression of the transferred genes will reduce the number of administrations required and may bypass the problem.
  • With regard to problem 2), experiments performed by Wilson and collaborators have demonstrated that after adenovirus-mediated gene transfer into immunocompetent animals, the expression of the transgene gradually decreases and disappears approximately two to four weeks post-infection (Yang et al., 1994a; Yang et al., 1994b). This is caused by the development of a Cytotoxic T-Cell (“CTL”) response against the transduced cells. The CTLs were directed against adenovirus proteins expressed by the viral vectors. In the transduced cells, synthesis of the adenovirus DNA-binding protein (the E2A-gene product), penton, and fiber proteins (late-gene products) could be established. These adenovirus proteins, encoded by the viral vector, were expressed despite deletion of the E1 region. This demonstrates that deletion of the E1 region is not sufficient to completely prevent expression of the viral genes (Engelhardt et al., 1994a).
  • With regard to problem 3), studies by Graham and collaborators have demonstrated that adenoviruses are capable of encapsidating DNA of up to 105% of the normal genome size (Bett et al., 1993). Larger genomes tend to be unstable, resulting in loss of DNA sequences during propagation of the virus. Combining deletions in the E1 and E3 regions of the viral genomes increases the maximum size of the foreign DNA that can be encapsidated to approximately 8.3 kb. In addition, some sequences of the E4 region appear to be dispensable for virus growth (adding another 1.8 kb to the maximum encapsidation capacity). Also, the E2A region can be deleted from the vector when the E2A gene product is provided in trans in the encapsidation cell line, adding another 1.6 kb. It is, however, unlikely that the maximum capacity of foreign DNA can be significantly increased further than 12 kb.
  • We developed a new strategy for the generation and production of helper-free stocks of recombinant adenovirus vectors that can accommodate up to 38 kb of foreign DNA. Only two functional ITR sequences and sequences that can function as an encapsidation signal need to be part of the vector genome. Such vectors are called “minimal adenovectors.” The helper functions for the minimal adenovectors are provided in trans by encapsidation defective-replication-competent DNA molecules that contain all the viral genes encoding the required gene products, with the exception of those genes that are present in the host-cell genome, or genes that reside in the vector genome.
  • The applications of the disclosed inventions are outlined below and will be illustrated in the experimental part, which is only intended for that purpose and should not be used to reduce the scope of the present invention as understood by those skilled in the art.
  • Use of the IG Packaging Constructs Diploid Cells
  • The constructs, in particular pIG.E1A.E1B, will be used to transfect diploid human cells, such as HER, HEK, and Human Embryonic Lung cells (“HEL”). Transfected cells will be selected for transformed phenotype (focus formation) and tested for their ability to support propagation of E1-deleted recombinant adenovirus, such as IG.Ad.MLPI.TK. Such cell lines will be used for the generation and (large-scale) production of E1-deleted recombinant adenoviruses. Such cells, infected with recombinant adenovirus, are also intended to be used in vivo as a local producer of recombinant adenovirus, for example, for the treatment of solid tumors.
  • 911 cells are used for the titration, generation, and production of recombinant adenovirus vectors (Fallaux et al., 1996).
  • HER cells transfected with pIG.E1A.E1B have resulted in seven independent clones (called PER cells). These clones are used for the production of E1-deleted (including non-overlapping adenovirus vectors) or E1-defective recombinant adenovirus vectors and provide the basis for introduction of, for example, E2B or E2A constructs (e.g., tsl25E2A, see below), E4 etc., that will allow propagation of adenovirus vectors that have mutations in, for example, E2A or E4.
  • In addition, diploid cells of other species that are permissive for human adenovirus, such as the cotton rat (Sigmodon hispidus) (Pacini et al., 1984), Syrian hamster (Morin et al., 1987), or chimpanzee (Levrero et al., 1991), will be immortalized with these constructs. Such cells infected with recombinant adenovirus are also intended to be used in vivo for the local production of recombinant adenovirus, for example, for the treatment of solid tumors.
  • Established Cells
  • The constructs, in particular pIG.E1A.NEO, can be used to transfect established cells, for example, A549 (human bronchial carcinoma), KB (oral carcinoma), MRC-5 (human diploid lung cell line), or GLC cell lines (small cell lung cancer) (de Leij et al., 1985; Postmus et al., 1988) and selected for NEO resistance. Individual colonies of resistant cells are isolated and tested for their capacity to support propagation of E1-deleted recombinant adenovirus, such as IG.Ad.MLPI.TK. When propagation of E1-deleted viruses on E1A-containing cells is possible, such cells can be used for the generation and production of E1-deleted recombinant adenovirus. They can also be used for the propagation of E1A-deleted/E1B-retained recombinant adenovirus.
  • Established cells can also be co-transfected with pIG.E1A.E1B and pIG.NEO (or another NEO-containing expression vector). Clones resistant to G418 are tested for their ability to support propagation of E1-deleted recombinant adenovirus, such as IG.Ad.MLPI.TK, and used for the generation and production of E1-deleted recombinant adenovirus and will be applied in vivo for local production of recombinant virus, as described for the diploid cells (see previous discussion). All cell lines, including transformed diploid cell lines or NEO-resistant established lines, can be used as the basis for the generation of “next generation” packaging cell lines that support propagation of E1-defective recombinant adenoviruses and that also carry deletions in other genes, such as E2A and E4. Moreover, they will provide the basis for the generation of minimal adenovirus vectors as disclosed herein.
  • E2-Expressing Cell Lines
  • Packaging cells expressing E2A sequences are and will be used for the generation and large scale production of E2A-deleted recombinant adenovirus.
  • The newly generated human adenovirus packaging cell lines or cell lines derived from species permissive for human adenovirus (E2A or ts125E2A: E1A+E2A; E1A+E1B+E2A; E1A−E2A/ts125; E1A+E1B−E2A/ts125) or nonpermissive cell lines such as monkey cells (hrE2A or hr+ts125E2A; E1A+hrE2A; E1A+E1B+hrE2A; E1A+hrE2A/ts125; E1A−E1B+hrE2A/ts125) are and will be used for the generation and large scale production of E2A-deleted recombinant adenovirus vectors. In addition, they will be applied in vivo for local production of recombinant virus, as described for the diploid cells (see previous discussion).
  • Novel Adenovirus Vectors
  • The newly developed adenovirus vectors harboring an E1 deletion of nt. 459-3510 will be used for gene transfer purposes. These vectors are also the basis for the development of further deleted adenovirus vectors that are mutated for, for example, E2A, E2B or E4. Such vectors will be generated, for example, on the newly developed packaging cell lines described above.
  • Minimal Adenovirus Packaging System
  • We disclose adenovirus packaging constructs (to be used for the packaging of minimal adenovirus vectors) which have the following characteristics:
      • 1) the packaging construct replicates;
      • 2) the packaging construct cannot be packaged because the packaging signal is deleted;
      • 3) the packaging construct contains an internal hairpin-forming sequence (see FIG. 15);
      • 4) because of the internal hairpin structure, the packaging construct is duplicated, that is, the DNA of the packaging construct becomes twice as long as it was before transfection into the packaging cell (in our sample, it duplicates from 35 kb to 70 kb). This duplication also prevents packaging. Note that this duplicated DNA molecule has ITRs at both termini (see, e.g., FIG. 13);
      • 5) this duplicated packaging molecule is able to replicate like a “normal adenovirus” DNA molecule;
      • 6) the duplication of the genome is a prerequisite for the production of sufficient levels of adenovirus proteins required to package the minimal adenovirus vector; and
      • 7) the packaging construct has no overlapping sequences with the minimal vector or cellular sequences that may lead to generation of RCA by homologous recombination.
  • This packaging system is used to produce minimal adenovirus vectors. The advantages of minimal adenovirus vectors, for example, for gene therapy of vaccination purposes, are well known (accommodation of up to 38 kb; gutting of potentially toxic and immunogenic adenovirus genes).
  • Adenovirus vectors containing mutations in essential genes (including minimal adenovirus vectors) can also be propagated using this system.
  • Use of Intracellular E2-Expressing Vectors
  • Minimal adenovirus vectors are generated using the helper functions provided in trans by packaging-deficient replicating helper molecules. The adenovirus-derived ITR sequences serve as origins of DNA replication in the presence of at least the E2 gene products. When the E2 gene products are expressed from genes in the vector genome (the gene(s) must be driven by an E1-independent promoter), the vector genome can replicate in the target cells. This will allow a significantly increased number of template molecules in the target cells and, as a result, an increased expression of the genes of interest encoded by the vector. This is of particular interest for application of gene therapy in cancer treatment.
  • Applications of Intracellular Amplification of Linear DNA Fragments
  • A similar approach could also be taken if amplification of linear DNA fragments is desired. DNA fragments of known or unknown sequence could be amplified in cells containing the E2 gene products if at least one ITR sequence is located near or at its terminus. There are no apparent constraints on the size of the fragment. Even fragments much larger than the adenovirus genome (36 kb) should be amplified using this approach. It is thus possible to clone large fragments in mammalian cells without either shuttling the fragment into bacteria (such as E. coli) or using the polymerase chain reaction (“PCR”). At the end stage of a productive adenovirus infection, a single cell can contain over 100,000 copies of the viral genome. In the optimal situation, the linear DNA fragments can be amplified to similar levels. Thus, one should be able to extract more than 5 μg of DNA fragment per 10 million cells (for a 35-kbp fragment). This system can be used to express heterologous proteins equivalent to the Simian Virus 40-based COS cell system for research or for therapeutic purposes. In addition, the system can be used to identify genes in large fragments of DNA. Random DNA fragments may be amplified (after addition of ITRs) and expressed during intracellular amplification. Election or selection of those cells with the desired phenotype can be used to enrich the fragment of interest and to isolate the gene.
  • EXPERIMENTS Generation of Cell Lines Able to Transcomplement E1-Defective Recombinant Adenovirus Vectors
  • 911 Cell Line
  • We have generated a cell line that harbors E1 sequences of adenovirus type 5 (“Ad5”) able to trans-complement E1-deleted recombinant adenovirus (Fallaux et al., 1996). This cell line was obtained by transfection of diploid human embryonic retinoblasts (“HER”) with pAd5XhoIC, which contains nt. 80-5788 of Ad5. One of the resulting transformants was designated 911. This cell line has been shown to be very useful in the propagation of E1-defective recombinant adenovirus. It was found to be superior to 293 cells. Unlike 293 cells, 911 cells lack a fully transformed phenotype, which most likely is the cause of its better performance as an adenovirus packaging line:
      • 1) plaque assays can be performed faster (four to five days instead of eight to fourteen days, as on 293),
      • 2) monolayers of 911 cells survive better under agar overlay, as required for plaque assays, and
      • 3) higher amplification of E1-deleted vectors is obtained.
  • In addition, unlike 293 cells that were transfected with sheared adenoviral DNA, 911 cells were transfected using a defined construct. Transfection efficiencies of 911 cells are comparable to those of 293.
  • New Packaging Constructs—Source of Adenovirus Sequences
  • Adenovirus sequences are derived either from pAd5.SalB, containing nt. 80-9460 of human adenovirus type 5 (Bernards et al., 1983), or from wild-type Ad5 DNA. pAd5.SalB was digested with SalI and XhoI, the large fragment was relegated, and this new clone was named pAd5.X/S. The pTN construct (constructed by Dr. R. Vogels, IntroGene, Leiden, The Netherlands) was used as a source for the human PGK promoter and the NEO gene.
  • Human PGK Promoter and NEOR Gene
  • Transcription of E1A sequences in the new packaging constructs is driven by the human PGK promoter (Michelson et al., 1983; Singer-Sam et al., 1984), derived from plasmid pTN (gift of R. Vogels), which uses pUC119 (Vieira and Messing, 1987) as a backbone. This plasmid was also used as a source for the NEO gene fused to the Hepatitis B Virus (“HBV”) poly-adenylation signal.
  • Fusion of PGK Promoter to E1 Genes
  • As shown in FIG. 1, in order to replace the E1 sequences of Ad5 (ITR, origin of replication, and packaging signal) by heterologous sequences, we have amplified E1 sequences (nt.459 to nt. 960) of Ad5 by PCR, using primers Ea-1 (SEQ ID NO:1) and Ea-2 (SEQ ID NO:2) (see Table I). The resulting PCR product was digested with ClaI and ligated into Bluescript (Stratagene), predigested with ClaI and EcoRV, resulting in construct pBS.PCR1.
  • TABLE I
    Name
    (SEQ ID NO) Sequence Function
    Primer Ea-1 CGTGTAGTGT ATTTATACCC PCR amplification Ad5
    (SEQ ID NO:1) a G nt459 ->
    Primer Ea-2 TCGTCACTGG GTGGAAAGCC PCR amplification Ad5
    (SEQ ID NO:2) a A nt960 <-
    Primer Ea-3 TACCCGCCGT CCTAAAATGG nt1284-1304 of Ad5
    (SEQ ID NO:3) a C genome
    Primer Ea-5 TGGACTTGAG CTGTAAACGC nt1514-1533 of Ad5
    (SEQ ID NO:4) a genome
    Primer Ep-2 GCCTCCATGGAGGTCAGATG nt1721-1702 of Ad5:
    (SEQ ID NO:5) a T introduction of NcoI
    site
    Primer Eb-1 GCTTGAGCCC GAGACATGTC nt3269-3289 of Ad5
    (SEQ ID NO:6) a genome
    Primer Eb-2 CCCCTCGAGC TCAATCTGTA nt3508-3496 of Ad5
    (SEQ ID NO:7) a TCTT genome: introduction
    of XhoI site
    Primer 5V40-1 GGGGGATCCG AACTTGTTTA Introduction Bam-H
    (SEQ ID NO:8) a TTGCAGC site (nt2182-2199 of
    adaption of
    recombinant
    adenoviruses
    Primer 5V40-2 GGGAGATCTA GACATGATAA Introduction BglII site
    (SEQ ID NO:9) a GATAC (nt2312-2297 of pMLP.TK)
    Primer Ad5-1 GGGAGATCTG TACTGAAATG Introduction of BglII
    (SEQ ID NO:10) a TGTGGGC site (nt 2496-2514 of
    pMLP.TK)
    Primer Ad5-2 GGAGGCTGCA GTCTCCAACG Rnt2779-2756 of PMLP.TK
    (SEQ ID NO:11) a GCGT
    Primer ITR1 GGGGGATCCT CAAATCCTCA nt35737-35757 of Ad5
    (SEQ ID NO:12) a CTTCCGT (introduction of BamHI
    site)
    Primer ITR2 GGGGTCTAGA CATCATCAAT nt35935-35919 of Ad5
    (SEQ ID NO:13 a AATATAC (introduction of XbaI
    site)
    PCR primer PCR/MLP1 GCCGAATTCG TCGACATCAT (Ad5 nt. 10-18)
    (SEQ ID NO:14) b CAATAATATA CC
    PCT primer PCR/MLP2 GGCGAATTCG GTACCATCAT (Ad5 nt. 10-18)
    (SEQ ID NO:15) b CAATAATATA CC
    PCT primer PCR/MLP3 CTGTCTACAC CGGCGCA (Ad5 nt. 200-184)
    (SEQ ID NO:16) b
    PCT primer HP/asp1 5′-GTACACTGAC CTAGTGCCGC
    (SEQ ID NO:17) c CCGGGCAAAG CCCGGGCGGC
    ACTAGGTCAG
    PCT primer HP/asp2 5′-GTACCTGACC TAGTGCCGCC
    (SEQ ID NO:18) c CGGGCTTTGC CCGGGCGGCA
    CTAGGTCAGT
    PCT primer HP/cla1 5′-GTACATTGAC CTAGTGCCGC
    (SEQ ID NO:19) d CCGGCCAAAG CCCGCGCGGC
    ACTAGGTCAA TCGAT
    PCT primer HP/cla2 5′-GTACATCGAT TGACCTAGTG
    (SEQ ID NO:20) d CCGCCCGGGC TTTGCCCGGG
    CGGCACTAGG TCAAT
    a-Primers used for PCR amplification of DNA fragments used for generation of constructs described in this patent application.
    b-PCR primer sets to be used to create the SalI and Asp718 sites juxtaposed to the ITR sequences.
    c-Synthetic oligonucleotide pair used to generate a synthetic hairpin, recreates an Asp718 site at one of the termini if inserted in the Asp718 site.
    d-Synthetic oligonucleotide pair used to generate a synthetic hairpin, contains the ClaI recognition site to be used for hairpin formation.
  • Vector pTN was digested with restriction enzymes EcoRI (partially) and ScaI, and the DNA fragment containing the PGK promoter sequences was ligated into PBS.PCRI digested with ScaI and EcoRi. The resulting construct pBS.PGK.PCR1 contains the human PGK promoter operatively linked to Ad5 E1 sequences from nt. 459 to nt. 916.
  • Construction of pIG.E1A.E1B.X
  • As shown in FIG. 2, pIG.E1A.E1B.X was made by replacing the ScaI-BspEI fragment of pAT.X/S by the corresponding fragment from pBS.PGK.PCR1 (containing the PGK promoter linked to E1A sequences). pIG.E1A.E1B.X contains the E1A and E1B coding sequences under the direction of the PGK promoter. As Ad5 sequences from nt. 459 to nt. 5788 are present in this construct, pIX protein of adenovirus is also encoded by this plasmid.
  • Construction of pIG.E1A.NEO
  • As shown in FIG. 3A, in order to introduce the complete E1B promoter and to fuse this promoter in such a way that the AUG codon of E1B 21 kDa functions exactly as the AUG codon of NEOR, we amplified the E1B promoter using primers Ea-3 (SEQ ID NO:3) and Ep-2 (SEQ ID NO:5), where primer Ep-2 (SEQ ID NO:5) introduces an NcoI site in the PCR fragment. The resulting PCR fragment, named PCRII, was digested with HpaI and NcoI and ligated into pAT-X/S, which was predigested with HpaI and with NcoI. The resulting plasmid was designated pAT.X/S.PCR2. The NcoI-StuI fragment of pTN, containing the NEO gene and part of the HBV polyadenylation signal, was cloned into pAT.X/S.PCR2 (digested with NcoI and NruI). The resulting construct: pAT.PCR2.NEO.
  • As shown in FIG. 3B, the polyadenylation signal was completed by replacing the ScaI-SalI fragment of pAT-PCR2-NEO with the corresponding fragment of pTN (resulting in pAT.PCR2.NEO.p(A)). The ScaI-XbaI of pAT.PCR2.NEO.p (A) was replaced by the corresponding fragment of pIG.EIA.E1B.X, containing the PGK promoter linked to E1A genes. The resulting construct was named pIG.E1A.NEO, and thus contains Ad5 E1 sequences (nt. 459 to nt. 1713) under the control of the human PGK promoter.
  • Construction of pIG.EIA.E1B
  • As shown in FIGS. 4A and 4B, pIG.E1A.E1B was made by amplifying the sequences encoding the N-terminal amino acids of E1B 55 kDa using primers Eb-1 (SEQ ID NO:6) and Eb-2 (SEQ ID NO:7) (introduces an XhoI site). The resulting PCR fragment was digested with BglII and cloned into BglII/NruI of pAT-X/S, thereby obtaining pAT.PCR3.
  • pIG.E1A.E1B was constructed by introducing the HBV poly(A) sequences of pIG.E1A.NEO downstream of E1B sequences of pAT.PCR3 by exchange of the XbaI-SalI fragment of pIG.E1A.NEO and the XbaI XhoI fragment of pAT.PCR3.
  • pIG.E1A.E1B contains nt. 459 to nt. 3510 of Ad5 Ad5, which encode the E1A and E1B proteins. The E1B sequences are terminated at the splice acceptor at nt. 3511. No pIx sequences are present in this construct.
  • Construction of pIG.NEO
  • As shown in FIG. 5, pIG.NEO was generated by cloning the HpaI-ScaI fragment of pIG.E1A.NEO, containing the NEO gene under the control of the Ad.5 E1B promoter, into pBS digested with EcoRV and ScaI.
  • This construct is of use when established cells are transfected with E1A.E1B constructs and NEO selection is required. Because NEO expression is directed by the E1B promoter, NEO resistant cells are expected to co-express E1A, which is also advantageous for maintaining high levels of expression of E1A during long-term culture of the cells.
  • Testing of Constructs
  • The integrity of the constructs pIG.E1A.NEO, pIG.E1A.E1B.X and pIG.E1A.E1B was assessed by restriction enzyme mapping; furthermore, parts of the constructs that were obtained by PCR analysis were confirmed by sequence analysis. No changes in the nucleotide sequence were found.
  • The constructs were transfected into primary Baby Rat Kidney (“BRK”) cells and tested for their ability to immortalize (pIG.E1A.NEC) or fully transform (pAd5.XhoIC, pIG.E1A.E1B.X, and pIG.E1A.E1B) these cells.
  • Kidneys of six-day old WAG-Rij rats were isolated, homogenized, and trypsinized. Subconfluent dishes (diameter 5 cm) of the BRK cell cultures were transfected with 1 or 5 μg of pIG.NEO, pIG.E1A.NEO, pIG.E1A.E1B, pIG.E1A.E1B.X, pAd5XhoIC, or pIG.E1A.NEO together with PDC26 (Van der Elsen et al., 1983), carrying the Ad5.E1B gene under control of the SV40 early promoter. Three weeks post-transfection, when foci were visible, the dishes were fixed, Giemsa stained, and the foci counted.
  • An overview of the generated adenovirus packaging constructs and their ability to transform BRK is presented in FIG. 6. The results indicate that the constructs pIG.E1A.E1B and pIG.E1A.E1B.X are able to transform BRK cells in a dose-dependent manner. The efficiency of transformation is similar for both constructs and is comparable to what was found with the construct that was used to make 911 cells, namely pAd5. XhoIC.
  • As expected, pIG.E1A.NEO was hardly able to immortalize BRK. However, co-transfection of an E1B expression construct (PDC26) did result in a significant increase in the number of transformants (18 versus 1), indicating that E1A encoded by pIG.E1A.NEO is functional. We conclude, therefore, that the newly generated packaging constructs are suited for the generation of new adenovirus packaging lines.
  • Generation of Cell Lines with New Packaging Constructs, Cell Lines, and Cell Culture
  • Human A549 bronchial carcinoma cells (Shapiro et al., 1978), human embryonic retinoblasts (“HER”), Ad5-E1-transformed human embryonic kidney (“HEK”) cells (293; Graham et al., 1977), and Ad5-transformed HER cells (911; Fallaux et al., 1996)) and PER cells were grown in Dulbecco's Modified Eagle Medium (“DMEM”) supplemented with 10% Fetal Calf Serum (“FCS”) and antibiotics in a 5% CO2 atmosphere at 37° C. Cell culture media, reagents, and sera were purchased from Gibco Laboratories (Grand Island, N.Y.). Culture plastics were purchased from Greiner (Nürtingen, Germany) and Corning (Corning, N.Y.).
  • Viruses and Virus Techniques
  • The construction of adenoviral vectors IG.Ad.MLP.nls.lacZ, IG.Ad.MLP.luc, IG.Ad.MLP.TK, and IG.Ad.CMV.TK is described in detail in European patent application EP 95202213. The recombinant adenoviral vector IG.Ad.MLP.nls.lacZ contains the E. coli lacZ gene, encoding β-galactosidase, under control of the Ad2 major late promoter (“MLP”). IG.Ad.MLP.luc contains the firefly luciferase gene driven by the Ad2 MLP. Adenoviral vectors IG.Ad.MLP.TK and IG.Ad.CMV.TR contain the Herpes Simplex Virus thymidine kinase (“TK”) gene under the control of the Ad2 MLP and the Cytomegalovirus (“CMV”) enhancer/promoter, respectively.
  • Transfections
  • All transfections were performed by calcium-phosphate precipitation DNA (Graham and Van der Eb, 1973) with the GIBCO Calcium Phosphate Transfection System (GIBCO BRL Life Technologies Inc., Gaithersburg, Md., USA), according to the manufacturer's protocol.
  • Western Blotting
  • Subconfluent cultures of exponentially growing 293, 911 and Ad5-E1-transformed A549 and PER cells were washed with PBS and scraped in Fos-RIPA buffer (10 mM Tris (pH 7.5), 150 mM NaCl, 1% NP4O, 1% sodium dodecyl sulphate (“SDS”), 1% NA-DOC, 0.5 mM phenyl methyl sulphonyl fluoride (“PMSF”), 0.5 mM trypsin inhibitor, 50 mM NaF and 1 mM sodium vanadate). After ten minutes at room temperature, lysates were cleared by centrifugation. Protein concentrations were measured with the Biorad protein assay kit, and 25 μg total cellular protein was loaded on a 12.5% SDS-PAA gel. After electrophoresis, proteins were transferred to nitrocellulose (one hour at 300 mA). Prestained standards (Sigma, USA) were run in parallel. Filters were blocked with 1% bovine serum albumin (“BSA”) in TBST (10 mM Tris, pH 8.15 mM NaCl, and 0.05% TWEEN™-20) for one hour. The first antibodies were the mouse monoclonal anti-Ad5-E1B-55-kDa antibody A1C6 (Zantema et al., unpublished) and the rat monoclonal anti-Ad5-E1B-221-kDa antibody C1G11 (Zantema et al., 1985). The second antibody was a horseradish peroxidase-labeled goat anti-mouse antibody (Promega). Signals were visualized by enhanced chemiluminescence (Amersham Corp, UK).
  • Southern Blot Analysis
  • High molecular weight DNA was isolated and 10 μg was digested to completion and fractionated on a 0.7% agarose gel. Southern blot transfer to Hybond N+ (Amersham, UK) was performed with a 0.4 M NaOH, 0.6 M NaCl transfer solution (Church and Gilbert, 1984). Hybridization was performed with a 2463-nt SspI-HindIII fragment from pAd5.SalB (Bernards et al., 1983). This fragment consists of Ad5 bp. 342-2805. The fragment was radiolabeled with α-32p-dCTP with the use of random hexanucleotide primers and Klenow DNA polymerase. The Southern blots were exposed to a Kodak XAR-5 film at −80° C. and to a Phospho-Imager screen that was analyzed by B&L Systems' Molecular Dynamics software.
  • A549
  • Ad5-E1-transformed A549 human bronchial carcinoma cell lines were generated by transfection with pIG.E1A.NEO and selection for G418 resistance. Thirty-one G418 resistant clones were established. Co-transfection of pIG.E1A.E1B with pIG.NEO yielded seven G418 resistant cell lines.
  • PER
  • Ad5-E1-transformed HER cells were generated by transfection of primary HER cells with plasmid pIG.E1A.E1B. Transformed cell lines were established from well-separated foci. We were able to establish seven clonal cell lines, which we called PER.C1, PER.C3, PER.C4, PER.C5, PER.C6™, PER.C8, and PER.C9. One of the PER clones, namely PER.C6™, has been deposited under the Budapest Treaty under number ECACC™ 96022940 with the Centre for Applied Microbiology and Research of Porton Down, UK, on Feb. 29, 1996. In addition, PER.C6™ is commercially available from IngroGene, B.V., Leiden, NL.
  • Expression of Ad5 E1A and E1B Genes in Transformed A549 and PER Cells
  • Expression of the Ad5 E1A and the 55 kDa and 21 kDa E1B proteins in the established A549 and PER cells was studied by means of Western blotting with the use of monoclonal antibodies (“Mab”). Mab M73 recognizes the E1A products, whereas Mabs AIC6 and C1G11 are directed against the 55 kDa and 21 kDa E1B proteins, respectively.
  • The antibodies did not recognize proteins in extracts from the parental A549 or the primary HER cells (data not shown). None of the A549 clones that were generated by co-transfection of pIG.NEO and pIG.E1A.E1B expressed detectable levels of E1A or E1B proteins (not shown). Some of the A549 clones that were generated by transfection with pIG.E1A.NEO expressed the Ad5 E1A proteins (see FIG. 7), but the levels were much lower than those detected in protein lysates from 293 cells. The steady-state E1A levels detected in protein extracts from PER cells were much higher than those detected in extracts from A549-derived cells. All PER cell lines expressed similar levels of E1A proteins (FIG. 7). The expression of the E1B proteins, particularly in the case of E1B 55 kDa, was more variable. Compared to 911 and 293, the majority of the PER clones express high levels of E1B 55 kDa and 21 kDa. The steady-state level of E1B 21 kDa was the highest in PER.C3. None of the PER clones lost expression of the Ad5 E1 genes upon serial passage of the cells (not shown). We found that the level of E1 expression in PER cells remained stable for at least 100 population doublings. We decided to characterize the PER clones in more detail.
  • Southern Analysis of PER Clones
  • To study the arrangement of the Ad5-E1 encoding sequences in the PER clones, we performed Southern analyses. Cellular DNA was extracted from all PER clones and from 293 and 911 cells. The DNA was digested with HindIII, which cuts once in the Ad5 E1 region. Southern hybridization on HindIII-digested DNA, using a radiolabeled Ad5-E1-specific probe, revealed the presence of several integrated copies of pIG.E1A.E1B in the genome of the PER clones. FIG. 8 shows the distribution pattern of E1 sequences in the high molecular weight DNA of the different PER cell lines. The copies are concentrated in a single band, which suggests that they are integrated as tandem repeats. In the case of PER.C3, C5, C6, and C9, we found additional hybridizing bands of low molecular weight that indicate the presence of truncated copies of pIG.E1A.E1B. The number of copies was determined with the use of a Phospho-Imager. We estimated that PER.C1, C3, C4, C5, C6, C8, and C9 contain 2, 88, 5, 4, 5, 5, and 3 copies of the Ad5 E1 coding region, respectively, and that 911 and 293 cells contain 1 and 4 copies of the Ad5 E1 sequences, respectively.
  • Transfection Efficiency
  • Recombinant adenovectors are generated by co-transfection of adaptor plasmids and the large ClaI fragment of Ad5 into 293 cells (see European patent application EP 95202213). The recombinant virus DNA is formed by homologous recombination between the homologous viral sequences that are present in the plasmid and the adenovirus DNA. The efficacy of this method, as well as that of alternative strategies, is highly dependent on the transfectability of the helper cells. Therefore, we compared the transfection efficiencies of some of the PER clones with 911 cells, using the E. coli β-galactosidase-encoding lacZ gene as a reporter (see FIG. 9).
  • Production of Recombinant Adenovirus
  • Yields of recombinant adenovirus obtained after inoculation of 293, 911, PER.C3, PER.C5, and PER.C6™ with different adenovirus vectors are presented in Table II. The results indicate that the yields obtained on PER cells are at least as high as those obtained on the existing cell lines. In addition, the yields of the novel adenovirus vector IG.Ad.MLPI.TK are similar or higher than the yields obtained for the other viral vectors on all cell lines tested.
  • TABLE II
    Pas-
    sage Pro-
    num- IG.Ad. IG.Ad. IG.Ad. ducer
    Cell ber CMV.lacZ CMV.TK MLPI.TK d1313 Mean
    293 6.0 5.8 24 34 17.5
    911 8 14 34 180 59.5
    PER.C3 17 8 11 44 40 25.8
    PER.C5 15 6 17 36 200 64.7
    PER.C6 ™ 36 10 22 58 320 102
    Yields × 10−8 pfu/T175 flask.
  • Table II. Yields of different recombinant adenoviruses obtained after inoculation of adenovirus E1 packaging cell lines 293, 911, PER.C3, PER.C5, and PER.C6™. The yields are the mean of two different experiments. IG.Ad.CMV.lacZ and IG.Ad.CMV.TK are described in European patent application EP 95202213. The construction of IG.Ad.MLPI.TK is described in this patent application. Yields of virus per T80 flask were determined by plaque assay on 911 cells, as described (Fallaux, 1996 #1493).
  • Generation of New Adenovirus Vectors
  • The used recombinant adenovirus vectors (see European patent application EP 95202213) are deleted for E1 sequences from nt. 459 to nt. 3328.
  • As construct pE1A.E1B contains Ad5 sequences nt. 459 to nt. 3510, there is a sequence overlap of 183 nt. between E1B sequences in the packaging construct pIG.E1A.E1B and recombinant adenoviruses, such as, for example, IG.Ad.MLP.TK. The overlapping sequences were deleted from the new adenovirus vectors. In addition, noncoding sequences derived from lacZ, which are present in the original constructs, were deleted as well. This was achieved (see FIG. 10) by PCR amplification of the SV40 poly(A) sequences from pMLP.TK using primers SV40-1 (SEQ ID NO:8) (introduces a BamHI site) and SV40-2 (SEQ ID NO:9) (introduces a BglII site). In addition, Ad5 sequences present in this construct were amplified from nt. 2496 (Ad5-1 (SEQ ID NO:10), introduces a BglII site) to nt. 2779 (Ad5-2 (SEQ ID NO:11)). Both PCR fragments were digested with BglII and were ligated. The ligation product was PCR amplified using primers SV40-1 (SEQ ID NO:8) and Ad5-2 (SEQ ID NO:11). The PCR product obtained was cut with BamHI and AflII and was ligated into pMLP.TK predigested with the same enzymes. The resulting construct, named pMLPI.TK, contains a deletion in adenovirus E1 sequences from nt. 459 to nt. 3510.
  • Packaging System
  • The combination of the new packaging construct pIG.E1A.E1B and the recombinant adenovirus pMLPI.TK, which do not have any sequence overlap, are presented in FIGS. 11A and 11B. In these figures, the original situation is also presented with the sequence overlap indicated.
  • The absence of overlapping sequences between pIG.E1A.E1B and pMLPI.TK (FIG. 11A) excludes the possibility of homologous recombination between packaging construct and recombinant virus, and is therefore a significant improvement for production of recombinant adenovirus as compared to the original situation.
  • In FIG. 1B, the situation is depicted for pIG.E1A.NEO and IG.Ad.MLPI.TK. pIG.E1A.NEO, when transfected into established cells, is expected to be sufficient to support propagation of E1-deleted recombinant adenovirus. This combination does not have any sequence overlap, preventing generation of RCA by homologous recombination. In addition, this convenient packaging system allows the propagation of recombinant adenoviruses that are deleted just for E1A sequences and not for E1B sequences. Recombinant adenoviruses expressing E1B in the absence of E1A are attractive, as the E1B protein, in particular E1B 19 kDa, is able to prevent infected human cells from lysis by Tumor Necrosis Factor (“TNF”) (Gooding et al., 1991).
  • Generation of Recombinant Adenovirus Derived from pMLPI.TK
  • Recombinant adenovirus was generated by co-transfection of 293 cells with SalI linearized pMLPI.TK DNA and ClaI linearized Ad5 wt DNA. The procedure is schematically represented in FIG. 12.
  • Outline of the Strategy to Generate Packaging Systems for Minimal Adenovirus Vector
  • Name convention of the plasmids used:
      • p plasmid
      • I ITR (Adenovirus Inverted Terminal Repeat)
      • C CMV Enhancer/Promoter Combination
      • L Firefly Luciferase Coding Sequence hac,haw Potential hairpin that can be formed after digestion with restriction endonuclease Asp718 in its correct orientation and in the reverse orientation, respectively (FIG. 15 (SEQ ID NO:22)).
  • For example, pICLhaw is a plasmid that contains the adenovirus ITR followed by the CMV-driven luciferase gene and the Asp718 hairpin in the reverse (nonfunctional) orientation.
  • Experiment Series 1
  • The following demonstrates the competence of a synthetic DNA sequence that is capable of forming a hairpin structure to serve as a primer for reverse strand synthesis for the generation of double-stranded DNA molecules in cells that contain and express adenovirus genes.
  • Plasmids pICLhac, pICLhaw, pICLI and pICL (SEQ ID NO:21) were generated using standard techniques. The schematic representation of these plasmids is shown in FIGS. 16-19.
  • Plasmid pICL (SEQ ID NO:21) is derived from the following plasmids:
  •   nt. 1-457 pMLP10 (Levrero et al., 1991);
     nt. 458-1218 pCMVβ (Clontech, EMBL Bank No. U02451);
    nt. 1219-3016 pMLP.luc (IntroGene, Leiden, NL, unpublished); and
    nt. 3017-5620 pBLCAT5 (Stein and Whelan, 1989).
  • The plasmid has been constructed as follows:
  • The tet gene of plasmid pMLP10 has been inactivated by deletion of the BamHI-SalI fragment to generate pMLP10ΔSB. Using primer set PCR/MLP1 (SEQ ID NO:14) and PCR/MLP3 (SEQ ID NO:16), a 210 bp fragment containing the Ad5-ITR, flanked by a synthetic SalI restriction site, was amplified using pMLP10 DNA as the template. The PCR product was digested with the enzymes EcoRI and SgrAI to generate a 196 bp fragment. Plasmid pMLP10ΔSB was digested with EcoRI and SgrAI to remove the ITR. This fragment was replaced by the EcoRI-SgrAI-treated PCR fragment to generate pMLP/SAL. Plasmid pCMV-Luc was digested with PvuII to completion and recirculated to remove the SV40-derived polyadenylation signal and Ad5 sequences with the exception of the Ad5 left-terminus. In the resulting plasmid, pCMV-lucΔAd, the Ad5 ITR was replaced by the Sal-site-flanked ITR from plasmid pMLP/SAL by exchanging the XmnI-SacII fragments. The resulting plasmid, pCMV-lucΔAd/SAL, the Ad5 left terminus, and the CMV-driven luciferase gene were isolated as an SalI-SmaI fragment and inserted in the SalI and HpaI digested plasmid pBLCATS to form plasmid pICL (SEQ ID NO:21). Plasmid pICL is represented in FIG. 19; its sequence is presented in FIGS. 20A-20F (SEQ ID NO:21).
  • The plasmid pICL (SEQ ID NO:21) contains the following features:
  •   nt. 1-457 Ad5 left terminus (Sequence 1-457 of human adenovirus
    type 5);
     nt. 458-969 Human cytomegalovirus enhancer and immediate early
    promoter (see Boshart et al., A Very Strong Enhancer is
    Located Upstream of an Immediate Early Gene of
    Human Cytomegalovirus,” Cell 41, pp. 521-530 (1985),
    hereby incorporated herein by reference) (from plasmid
    pCMVβ, Clontech, Palo Alto, USA);
     nt. 970-1204 SV40 19S exon and truncated 16/19S intron (from
    plasmid pCMVβ);
    nt. 1218-2987 Firefly luciferase gene (from pMLP.luc);
    nt. 3018-3131 V40 tandem polyadenylation signals from late transcript,
    derived from plasmid pBLCAT5);
     t. 3132-5620 UC12 backbone (derived from plasmid pBLCAT5); and
     t. 4337-5191 β-lactamase gene (Amp-resistance gene, reverse
    orientation).

    Plasmids pICLhac and pICLhaw
  • Plasmids pICLhac and pICLhaw were derived from plasmid pICL (SEQ ID NO:21) by digestion of the latter plasmid with the restriction enzyme Asp718. The linearized plasmid was treated with Calf-Intestine Alkaline Phosphatase to remove the 51 phosphate groups. The partially complementary synthetic single-stranded oligonucleotide Hp/asp1 (SEQ ID NO:17) and Hp/asp2 (SEQ ID NO:18) were annealed and phosphorylated on their 5′ ends using T4-polynucleotide kinase.
  • The phosphorylated double-stranded oligomers were mixed with the dephosphorylated pICL fragment and ligated. Clones containing a single copy of the synthetic oligonucleotide inserted into the plasmid were isolated and characterized using restriction enzyme digests. Insertion of the oligonucleotide into the Asp718 site will at one junction recreate an Asp718 recognition site, whereas at the other junction, the recognition site will be disrupted. The orientation and the integrity of the inserted oligonucleotide were verified in selected clones by sequence analyses. A clone containing the oligonucleotide in the correct orientation (the Asp718 site close to the 3205 EcoRI site) was denoted pICLhac. A clone with the oligonucleotide in the reverse orientation (the Asp718 site close to the SV40-derived poly signal) was designated pICLhaw. Plasmids pICLhac and pICLhaw are represented in FIGS. 16 and 17.
  • Plasmid pICLI was created from plasmid pICL (SEQ ID NO:21) by insertion of the SalI-SgrAI fragment from pICL containing the Ad5-ITR into the Asp718 site of pICL. The 194 bp SalI-SgrAI fragment was isolated from pICL (SEQ ID NO:21), and the cohesive ends were converted to blunt ends using E. coli DNA polymerase I (Klenow fragment) and dNTPs. The Asp718 cohesive ends were converted to blunt ends by treatment with mungbean nuclease. Clones that contain the ITR in the Asp718 site of plasmid pICL (SEQ ID NO:21) were generated by ligation. A clone that contained the ITR fragment in the correct orientation was designated pICLI (see FIG. 18). Generation of adenovirus Ad-CMV-hcTK recombinant adenovirus was constructed according to the method described in European patent application EP 95202213. Two components are required to generate a recombinant adenovirus. First, an adaptor-plasmid containing the left terminus of the adenovirus genome containing the ITR and the packaging signal, an expression cassette with the gene of interest, and a portion of the adenovirus genome which can be used for homologous recombination. In addition, adenovirus DNA is needed for recombination with the aforementioned adaptor plasmid. In the case of Ad-CMV-hcTK, the plasmid PCMV.TK was used as a basis. This plasmid contains nt. 1-455 of the adenovirus type 5 genome, nt. 456-1204 derived from pCMVP (Clontech, the PstI-StuI fragment that contains the CMV enhancer promoter and the 16S/19S intron from Simian Virus 40), the HSV TK gene (described in European patent application EP 95202213), the SV40-derived polyadenylation signal (nt 2533-2668 of the SV40 sequence), followed by the BglII-ScaI fragment of Ad5 (nt. 3328-6092 of the Ad5 sequence). These fragments are present in a pMLP10-derived (Levrero et al., 1991) backbone. To generate plasmid pAD-CMVhc-TK, plasmid pCMV.TK was digested with ClaI (the unique ClaI-site is located just upstream of the TK open reading frame) and dephosphorylated with Calf-Intestine Alkaline Phosphate. To generate a hairpin structure, the synthetic oligonucleotides HP/cla1 (SEQ ID NO:19) and HP/cla2 (SEQ ID NO:20) were annealed and phosphorylated on their 5-OH groups with T4-polynucleotide kinase and ATP. The double-stranded oligonucleotide was ligated with the linearized vector fragment and used to transform E. coli strain “Sure.” Insertion of the oligonucleotide into the ClaI site will disrupt the ClaI recognition sites. The oligonucleotide contains a new ClaI site near one of its termini. In selected clones, the orientation and the integrity of the inserted oligonucleotide was verified by sequence analyses. A clone containing the oligonucleotide in the correct orientation (the ClaI site at the ITR side) was denoted pAd-CMV-hcTK. This plasmid was co-transfected with ClaI-digested wild-type Adenovirus type 5 DNA into 911 cells. A recombinant adenovirus in which the CMV-hcTK expression cassette replaces the E1 sequences was isolated and propagated using standard procedures.
  • To study whether the hairpin can be used as a primer for reverse strand synthesis on the displaced strand after replication had started at the ITR, the plasmid pICLhac is introduced into 911 cells (human embryonic retinoblasts transformed with the adenovirus E1 region). The plasmid pICLhaw serves as a control, which contains the oligonucleotide pair HP/asp1 (SEQ ID NO:17) and HP/asp2 (SEQ ID NO:18) in the reverse orientation but is further completely identical to plasmid pICLhac. Also included in these studies are plasmids pICLI and pICL (SEQ ID NO:21). In the plasmid pICLI, the hairpin is replaced by an adenovirus ITR. Plasmid pICL (SEQ ID NO:21) contains neither a hairpin nor an ITR sequence. These plasmids serve as controls to determine the efficiency of replication by virtue of the terminal-hairpin structure. To provide the viral products other than the E1 proteins (these are produced by the 911 cells) required for DNA replication, the cultures are infected with the virus IG.Ad.MLPI.TK after transfection. Several parameters are being studied to demonstrate proper replication of the transfected DNA molecules. First, DNA extracted from the cell cultures transfected with the aforementioned plasmids and infected with IG.Ad.MLPI.TK virus is being analyzed by Southern blotting for the presence of the expected replication intermediates, as well as for the presence of the duplicated genomes. Furthermore, virus is isolated from the transfected and IG.Ad.MLPI.TK infected cell populations that is capable of transferring and expressing a luciferase marker gene into luciferase negative cells.
  • Plasmid DNA of plasmids pICLhac, pICLhaw, pICLI, and pICL (SEQ ID NO:21) have been digested with restriction endonuclease SalI and treated with mungbean nuclease to remove the four nucleotide single-stranded extension of the resulting DNA fragment. In this manner, a natural adenovirus 5′ ITR terminus on the DNA fragment is created. Subsequently, both the pICLhac and pICLhaw plasmids were digested with restriction endonuclease Asp718 to generate the terminus capable of forming a hairpin structure. The digested plasmids are introduced into 911 cells, using the standard calcium phosphate co-precipitation technique, four dishes for each plasmid. During the transfection, for each plasmid two of the cultures are infected with the IG.Ad.MLPI.TK virus using five infectious IG.Ad.MLPI.TK particles per cell. At twenty hours post-transfection and forty hours post-transfection, one Ad.tk-virus-infected and one uninfected culture are used to isolate small molecular-weight DNA using the procedure devised by Hirt. Aliquots of isolated DNA are used for Southern analysis. After digestion of the samples with restriction endonuclease EcoRI using the luciferase gene as a probe, a hybridizing fragment of approximately 2.6 kb is detected only in the samples from the adenovirus infected cells transfected with plasmid pICLhac. The size of this fragment is consistent with the anticipated duplication of the luciferase marker gene. This supports the conclusion that the inserted hairpin is capable of serving as a primer for reverse strand synthesis. The hybridizing fragment is absent if the IG.Ad.MLPI.TK virus is omitted or if the hairpin oligonucleotide has been inserted in the reverse orientation.
  • The restriction endonuclease DpnI recognizes the tetranucleotide sequence 5′-GATC-3′ but cleaves only methylated DNA (that is, only plasmid DNA propagated in and derived from E. coli, not DNA that has been replicated in mammalian cells). The restriction endonuclease MboI recognizes the same sequences, but cleaves only unmethylated DNA (viz. DNA propagated in mammalian cells). DNA samples isolated from the transfected cells are incubated with MboI and DpnI and analyzed with Southern blots. These results demonstrate that only in the cells transfected with the pICLhac and the pICLI plasmids are large DpnI-resistant fragments present that are absent in the MboI treated samples. These data demonstrate that only after transfection of plasmids pICLI and pICLhac does replication and duplication of the fragments occur.
  • These data demonstrate that in adenovirus-infected cells, linear DNA fragments that have on one terminus an adenovirus-derived ITR and at the other terminus a nucleotide sequence that can anneal to sequences on the same strand when present in single-stranded form thereby generate a hairpin structure and will be converted to structures that have inverted terminal repeat sequences on both ends. The resulting DNA molecules will replicate by the same mechanism as the wild-type adenovirus genomes.
  • Experiment Series 2
  • The following demonstrates that the DNA molecules that contain a luciferase marker gene, a single copy of the ITR, the encapsidation signal, and a synthetic DNA sequence that is capable of forming a hairpin structure are sufficient to generate DNA molecules that can be encapsidated into virions.
  • To demonstrate that the above DNA molecules containing two copies of the CMV-luc marker gene can be encapsidated into virions, virus is harvested from the remaining two cultures via three cycles of freeze-thaw crushing and is used to infect murine fibroblasts. Forty-eight hours after infection, the infected cells are assayed for luciferase activity. To exclude the possibility that the luciferase activity has been induced by transfer of free DNA, rather than via virus particles, virus stocks are treated with DNaseI to remove DNA contaminants. Furthermore, as an additional control, aliquots of the virus stocks are incubated for 60 minutes at 56° C. The heat treatment will not affect the contaminating DNA but will inactivate the viruses. Significant luciferase activity is only found in the cells after infection with the virus stocks derived from IG.Ad.MLPI.TK-infected cells transfected with the pICLhac and pICLI plasmids. In neither the noninfected cells nor the infected cells transfected with the pICLhaw and pICL (SEQ ID NO:21) can significant luciferase activity be demonstrated. Heat inactivation, but not DNaseI treatment, completely eliminates luciferase expression, demonstrating that adenovirus particles, and not free (contaminating) DNA fragments, are responsible for transfer of the luciferase reporter gene.
  • These results demonstrate that these small viral genomes can be encapsidated into adenovirus particles and suggest that the ITR and the encapsidation signal are sufficient for encapsidation of linear DNA fragments into adenovirus particles. These adenovirus particles can be used for efficient gene transfer. When introduced into cells that contain and express at least part of the adenovirus genes (viz. E1, E2, E4, and L, and VA), recombinant DNA molecules that consist of at least one ITR, at least part of the encapsidation signal, and a synthetic DNA sequence that is capable of forming a hairpin structure have the intrinsic capacity to autonomously generate recombinant genomes that can be encapsidated into virions. Such genomes and vector system can be used for gene transfer.
  • Experiment Series 3
  • The following demonstrates that DNA molecules that contain nucleotides 3510-35953 (viz. 9.7-100 map units) of the adenovirus type 5 genome (thus lacking the E1 protein-coding regions, the right-hand ITR, and the encapsidation sequences) and a terminal DNA sequence that is complementary to a portion of the same strand of the DNA molecule when present in single-stranded form other than the ITR, and as a result is capable of forming a hairpin structure, can replicate in 911 cells.
  • In order to develop a replicating DNA molecule that can provide the adenovirus products required to allow the above-mentioned pICLhac vector genome and alike minimal adenovectors to be encapsidated into adenovirus particles by helper cells, the Ad-CMV-hcTK adenoviral vector has been developed. Between the CMV enhancer/promoter region and the thymidine kinase gene, the annealed oligonucleotide pair HP/cla1 (SEQ ID NO:19) and 2 (SEQ ID NO:20) is inserted. The vector Ad-CMV-hcTK can be propagated and produced in 911 cell using standard procedures. This vector is grown and propagated exclusively as a source of DNA used for transfection. DNA of the adenovirus Ad-CMV-hcTK is isolated from virus particles that had been purified using CsC1 density-gradient centrifugation by standard techniques. The virus DNA has been digested with restriction endonuclease ClaI. The digested DNA is size-fractionated on a 0.7% agarose gel, and the large fragment is isolated and used for further experiments. Cultures of 911 cells are transfected with the large ClaI-fragment of the Ad-CMV-hcTK DNA using the standard calcium phosphate coprecipitation technique. Much like in the previous experiments with plasmid pICLhac, the AD-CMV-hc will replicate starting at the right-hand ITR. Once the one strand is displaced, a hairpin can be formed at the left-hand terminus of the fragment. This facilitates the DNA polymerase to elongate the chain towards the right-hand side. The process will proceed until the displaced strand is completely converted to its double-stranded form. Finally, the right-hand ITR will be recreated, and in this location the normal adenovirus replication-initiation and elongation will occur. Note that the polymerase will read through the hairpin, thereby duplicating the molecule. The input DNA molecule of 33250 bp, which had on one side an adenovirus ITR sequence and at the other side a DNA sequence that had the capacity to form a hairpin structure, has now been duplicated in a way that both ends contain an ITR sequence. The resulting DNA molecule will consist of a palindromic structure of approximately 66500 bp.
  • This structure can be detected in low-molecular-weight DNA extracted from the transfected cells using Southern analysis. The palindromic nature of the DNA fragment can be demonstrated by digestion of the low-molecular-weight DNA with suitable restriction endonucleases and Southern blotting with the HSV-TK gene as the probe. This molecule can replicate itself in the transfected cells by virtue of the adenovirus gene products that are present in the cells. In part, the adenovirus genes are expressed from templates that are integrated in the genome of the target cells (viz. the E1 gene products); the other genes reside in the replicating DNA fragment itself. Note, however, that this linear DNA fragment cannot be encapsidated into virions. Not only does it lack all the DNA sequences required for encapsidation, but its size is also much too large to be encapsidated.
  • Experiment Series 4
  • The following demonstrates that DNA molecules that contain nucleotides 3503-35953 (viz. 9.7-100 map units) of the adenovirus type 5 genome (thus lacking the E1 protein-coding regions, the right-hand ITR, and the encapsidation sequences) and a terminal DNA sequence that is complementary to a portion of the same strand of the DNA molecule other than the ITR, and as a result is capable of forming a hairpin structure, can replicate in 911 cells and can provide the helper functions required to encapsidate the pICLI- and pICLhac-derived DNA fragments.
  • The following series of experiments aims to demonstrate that the DNA molecule described in Experiment Series 3 could be used to encapsidate the minimal adenovectors described in Experiment Series 1 and 2.
  • In the experiments, the large fragment isolated after endonuclease ClaI-digestion of Ad-CMV-hcTK DNA is introduced into 911 cells (in conformity with the experiments described in part 1.3) together with endonuclease SalI, mungbean nuclease, endonuclease Asp718-treated plasmid pICLhac, or, as a control, similarly treated plasmid pICLhaw. After 48 hours, virus is isolated by freeze-thaw crushing of the transfected cell population. The virus preparation is treated with DNaseI to remove contaminating free DNA. The virus is used subsequently to infect Rat2 fibroblasts. Forty-eight hours post-infection, the cells are assayed for luciferase activity. Significant luciferase activity can be demonstrated only in the cells infected with virus isolated from the cells transfected with the pICLhac plasmid and not with the pICLhaw plasmid. Heat inactivation of the virus prior to infection completely abolishes the luciferase activity, indicating that the luciferase gene is transferred by a viral particle. Infection of 911 cells with the virus stock did not result in any cytopathological effects, demonstrating that the pICLhac is produced without any infectious helper virus that can be propagated on 911 cells. These results demonstrate that the proposed method can be used to produce stocks of minimal adenoviral vectors that are completely devoid of infectious helper viruses and are able to replicate autonomously on adenovirus-transformed human cells or on nonadenovirus-transformed human cells.
  • Besides the system described in this application, another approach for the generation of minimal adenovirus vectors has been disclosed in International Patent Publication WO 94/12649. The method described in WO 94/12649 exploits the function of the protein IX for the packaging of minimal adenovirus vectors (Pseudo Adenoviral Vectors (“PAV”) in the terminology of WO 94/12649). PAVs are produced by cloning an expression plasmid with the gene of interest between the left-hand (including the sequences required for encapsidation) and the right-hand adenoviral ITRs. The PAV is propagated in the presence of a helper virus. Encapsidation of the PAV is preferred compared with the helper virus because the helper virus is partially defective for packaging (either by virtue of mutations in the packaging signal or by virtue of its size; virus genomes greater than 37.5 kb package inefficiently). In addition, the authors propose that in the absence of the protein IX gene, the PAV will be preferentially packaged. However, neither of these mechanisms appear to be sufficiently restrictive to allow packaging of only PAVs/minimal vectors. The mutations proposed in the packaging signal diminish packaging but do not provide an absolute block, as the same packaging activity is required to propagate the helper virus. Also, neither an increase in the size of the helper virus nor the mutation of the protein IX gene will ensure that PAV is packaged exclusively. Thus, the method described in WO 94/12649 is unlikely to be useful for the production of helper-free stocks of minimal adenovirus vectors/PAVs.
  • Although the application has been described with reference to certain preferred embodiments and illustrative examples, the scope of the invention is to be determined by reference to the appended claims.
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Claims (8)

1. A stock of recombinant adenoviruses, wherein each recombinant adenovirus has a genome, the genome comprising:
a nucleic acid encoding pIX gene product;
an expression cassette encoding a nonadenovirus gene product;
an adenoviral encapsidation signal; and
a 5′ adenoviral ITR or a derivative thereof and a 3′ adenoviral ITR or a derivative thereof;
wherein the recombinant adenovirus genome does not contain sequences of adenovirus E1A, E1B 21 kDa and E1B 55 kDa coding regions; and
wherein said stock of the recombinant adenoviruses is free of replication-competent adenovirus.
2. The stock of claim 1, wherein the deletion in the at least part of the E1 region comprises a deletion of nucleotides corresponding nt. 459 to nt. 3510 of the adenovirus 5 genome.
3. The stock of claim 1, wherein said recombinant adenovirus is capable of replication in a packaging cell line.
4. The stock of claim 3, wherein said packaging cell line comprises a cell line deposited at the European Collection of Animal Cell Cultures under No. 96022940.
5. The stock of claim 1, wherein the genome of said recombinant adenovirus further comprises other adenovirus sequences capable of allowing replication of said recombinant adenovirus in an E1-complementing cell.
6. The stock of claim 2, wherein the genome of said recombinant adenovirus further comprises other adenovirus sequences capable of allowing replication of said recombinant adenovirus in an E1-complementing cell.
7. The stock of claim 4, wherein the stock of recombinant adenoviruses is capable of being produced in the packaging cell line on a large scale.
8. A stock of recombinant adenoviruses, each recombinant adenovirus thereof having a genome, the genome comprising:
a nucleic acid encoding pIX gene product;
an expression cassette encoding a nonadenovirus gene product;
an adenoviral encapsidation signal; and
a 5′ adenoviral ITR or a derivative thereof and a 3′ adenoviral ITR or a derivative thereof;
wherein the genome does not contain sequences of adenovirus E1A, E1B 21 kDa and E1B 55 kDa coding regions and further has a deletion of one or more of adenovirus E2A and adenovirus E3; and
wherein said stock is free of replication-competent adenovirus.
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