Apoptosis inducing proteinaceous substance

Abstract

The invention relates to the field of apoptosis. The invention provides novel therapeutic possibilities, for example novel combinatorial therapies or novel therapeutic compounds that can work alone, sequentially to, or jointly with Apoptin, especially in those cases wherein p53 is (partly) non-functional and/or Bcl-2 is over-expressed and/or functional caspase-3 is lacking. The invention further describes that a proteinaceous substance according to the invention induces apoptosis tumor specific and does not or at least not significantly induce apoptosis in normal cells. The invention comprises an anti-tumor agent, which specifically kill tumor cells and not normal cells.

Description

TECHNICAL FIELD

[0002] The invention relates generally to biology and biotechnology, and specifically to the field of apoptosis.

BACKGROUND

[0003] Apoptosis is an active and programmed physiological process for eliminating superfluous, altered or malignant cells (Earnshaw, 1995, Duke et al., 1996).

[0004] Apoptosis is characterized by shrinkage of cells, segmentation of the nucleus, condensation and cleavage of DNA into domain-sized fragments, in most cells followed by internucleosomal degradation. The apoptotic cells fragment into membrane-enclosed apoptotic bodies. Finally, neighboring cells and/or macrophages will rapidly phagocytose these dying cells (Wyllie et al., 1980, White, 1996). Cells grown under tissue-culture conditions and cells from tissue material can be analyzed for being apoptotic with DNA-staining agents, such as e.g. DAPI, which stains normal DNA strongly and regularly, whereas apoptotic DNA is stained weakly and/or irregularly (Noteborn et al., 1994, Telford et al., 1992).

[0005] The apoptotic process can be initiated by a variety of regulatory stimuli(Wyllie, 1995, White 1996, Levine, 1997). Changes in the cell survival rate play an important role in human pathogenesis, e.g. in cancer development and auto-immune diseases, which is caused by enhanced proliferation but also by decreased cell death (Kerr et al., 1994, Paulovich, 1997). A variety of chemotherapeutic compounds and radiation have been demonstrated to induce apoptosis in tumor cells, in many instances via wild-type p53 protein (Thompson, 1995, Bellamy et al., 1995, Steller, 1995, McDonell et al., 1995).

[0006] Many tumors, however, acquire a mutation in p53 during their development, often correlating with poor response to cancer therapy. Transforming genes of tumorigenic DNA viruses can inactivate p53 by directly binding to it (Teodoro, 1997). An example of such an agent is the large T antigen of the tumor DNA virus SV40. For several (leukemic) tumors, a high expression level of the proto-oncogene Bcl-2 or Bcr-abl is associated with a strong resistance to various apoptosis-inducing chemotherapeutic agents (Hockenberry 1994, Sachs and Lotem, 1997).

[0007] For such cancers (representing more than half of the tumors) alternative anti-tumor therapies are under development based on induction of apoptosis independent of p53 (Thompson 1995, Paulovich et al., 1997). For this one has to search for the factors involved in induction of apoptosis that do not need p53 and/or cannot be blocked by anti-apoptotic activities, such as Bcl-2 or Bcr-abl-like ones. These factors might be part of a distinct apoptosis pathway or being(far) downstream to the apoptosis inhibiting compounds.

[0008] Apoptin (or VP3, the terms may be used interchangeable herein) is a small protein derived from chicken anemia virus (CAV; Noteborn and De Boer, 1996, Noteborn et al., 1991, Noteborn et al., 1994; 1998a), which can induce apoptosis in human malignant and transformed cell lines (the terms tumorigenic, transformed and malignant will be used interchangeable herein), but not in untransformed human cell cultures. lit vitro, Apoptin fails to induce apoptosis in normal limphoid, dermal, epidermal, endothelial and smooth-muscle cells. However, when normal cells are transformed they become susceptible to apoptosis by Apoptin. Long-term expression of Apoptin in normal human fibroblasts revealed that Apoptin has no toxic or transforming activity in these cells (Danen-van Oorschot, 1997 and Noteborn, 1996). In normal cells, Apoptin was found predominantly in the cytoplasm, whereas in transformed or malignant cells i.e. characterized by hyperplasia, metaplasia or dysplasia, it was located in the nucleus, suggesting that the localization of Apoptin is related to its activity (Danen-van Oorschot et al. 1997).

[0009] Apoptin-induced apoptosis occurs in the absence of functional p53 (Zhuang et al., 1995a), and cannot be blocked by Bcl-2, Bcr-abl (Zhuang et al., 1995), the Bcl associating protein BAG-1 and not by the caspase-inhibitor cowpox protein CrmA (Danen-Van Oorschot, 1997a, Noteborn, 1996). Therefore, Apoptin is a particularly useful therapeutic compound for the destruction of tumor cells, or other hyperplasia, metaplasia or dysplasia which have become3 0 resistant to (chemo)-therapeutic induction of apoptosis, due to for example the lack of functional p53 and (over)-expression of Bcl-2 and other apoptosis-inhibiting agents (Noteborn and Pietersen, 1998).

[0010] It appears, that even pre-malignant, minimally transformed cells, are sensitive to the death-inducing effect of Apoptin. In addition, Notebom and Zhang (1998) have shown that Apoptin-induced apoptosis can be used as diagnosis of cancer-prone cells and treatment of cancer-prone cells.

[0011] The fact that Apoptin does not induce apoptosis in normal human cells, at least not in vitro, implies that there would be little or no toxic effect of Apoptin treatment in vivo. Noteborn and Pietersen (1998) and Pietersen et al. (1999)have provided evidence that adenovirus expressed Apoptin does not have an acute toxic effect in vivo. In addition, in nude mice it was shown that Apoptin has a strong anti-tumor activity.

[0012] However, to further enlarge the array of therapeutic anti-cancer or anti-auto-immune-disease compounds available in the art, additional therapeutic compounds are desired that are designed to work alone, sequentially to, or jointly with Apoptin or other apoptosis inducing substances, especially in those cases wherein the tumor suppressor p53 is (partly) non-functional and or anti-apoptosis proteins such as Bcl-2 are over-expressed.

DISCLOSURE OF THE INVENTION

[0013] The invention provides novel therapeutic possibilities, for example novel combinatorial therapies or novel therapeutic compounds that can work alone, sequentially or jointly with Apoptin, especially in those cases wherein p53 is(partly) non-functional and/or Bcl-2 is over-expressed and/or functional caspase-3, an essential protease of the apoptotic machinery, is lacking.

[0014] In a first embodiment, the invention provides an apoptosis inducing2 5 proteinaceous substance, capable of providing apoptosis, alone or in combination with other apoptosis-inducing substances, such as Apoptin, the proteinaceous substance encoded by an isolated or recombinant nucleic acid or functional equivalent and/or fragment thereof derivable from a mammalian gyrovirus-like virus nucleic acid.

[0015] Mammalian gyrovirus-like viruses, which are circovirus-like single-stranded circular DNA viruses distinct from for example porcine circovirus or relatives thereof, have been found which surprisingly can be used to provide a substance providing apoptosis, thereby providing functional equivalent proteinaceous substances and/or fragments thereof having similar features as CAV-derived Apoptin or fragments thereof. In particular, the invention provides a proteinaceous substance according to the invention wherein the mammalian gyrovirus-like virus includes a single-stranded circular DNA virus, such as for example a TTV-like virus, such as seen with the recently discovered novel human single-stranded circular DNA virus TTV (Charlton et al., 1998; Miyata et al., 1999). In a preferred embodiment, the invention provides a proteinaceous substance or functional equivalent and/or fragment thereof, the substance encoded by an isolated or recombinant nucleic acid which is at least 60% homologous preferably at least 70%, more preferably at least 80%, even more preferably at least 90%, most preferably at least 95% to a TTV-like virus nucleic acid as shown in FIG. 1.

[0016] Surprisingly, such a proteinaceous substance according to the invention is capable of providing apoptosis alone or in combination with another apoptosis-inducing substance, as for example shown in FIG. 4, in particular wherein apoptosis-inducing substance includes Apoptin or a functional fragments thereof. In a particular advantageous embodiment of the invention, the proteinaceous substance according to the invention is capable of providing apoptosis independent of p53 and/or does not need a functional caspase Preferable the proteinaceous substance according to the invention provides tumor-specific apoptosis and does not or at least not significantly induce2 5 apoptosis in normal cells. Even more preferably, a proteinaceous substance according to the invention, or functional equivalent and/or fragment thereof, includes a nuclear location signal and/or a nuclear export signal as, for example, shown in FIG. 2.

[0017] Proteinaceous substance, herein also called TAP protein, is defined as a substance including a peptide, optionally having been modified by, for example glycosylation, myristilation, phosphorylation, the addition of lipids, by homologous or heterologous di- or multimerisation, or any other(post-translational) modifications known in the art.

[0018] TTV-derived protein or proteinaceous substance herein is defined as a protein, for example, encoded by strains of the recently discovered novel human single-stranded circular DNA virus TTV (Charlton et al., 1998; Miyata et al., 1999).

[0019] Thus far, TTV and TTV-like viruses have not been correlated to any known disease. However, TTV contains also a single-stranded circular DNA which relates it to CAV, from which Apoptin is derived. TTV has a similar genomic organization like CAV, however, none of the predicted open reading frames of TTV were proven to be transcribed and translated in TTV-infected cells (Miyata et al., 1999). In particular, the herein described TTV open reading frame has not been shown to be transcribed and translated in uluo, and no such TTV protein has until now been identified, let alone that a function has been assigned to it, at least not a function related to apoptotic activity.

[0020] A functional equivalent and/or a functional fragment thereof is a derivative and/or a fragment having the same kind of activity (capable of providing apoptosis) possibly in different amounts. In a preferred embodiment, the invention provides an isolated or recombinant nucleic acid or functional equivalent and/or functional fragment thereof encoding and/or capable of expression of a TTV-derived proteinaceous substance capable of providing apoptosis. In particular, the invention provides an isolated or recombinant nucleic acid or functional equivalent and/or functional fragment thereof from which a proteinaceous substance according to the invention can be transcribed2 5 and translated.

[0021] In another embodiment, the invention provides an isolated or recombinant nucleic acid or functional equivalent and/or fragment thereof encoding a TTV-derived proteinaceous substance capable of providing apoptosis capable of hybridizing to a nucleic acid molecule encoding a TTV-derived proteinaceous substance capable of providing apoptosis as shown in FIG. 1, in particular encoding a novel protein capable of providing apoptosis or functional equivalent and/or functional fragment thereof called TTV-apoptosis protein, abbreviated as TAP.

[0022] In particular, the invention provides an isolated or recombinant nucleic acid or functional equivalent and/or fragment thereof encoding, and preferably capable of expressing a TAP substance capable of providing apoptosis being at least 60% homologous, preferably at least 70%, more preferably at least 80%, even more preferably at least 90%, most preferably at least 95% homologous to a nucleic acid molecule, or to a functional equivalent and/or functional fragment thereof, encoding a TAP proteinaceous substance as shown in FIG 1.

[0023] Furthermore, the invention provides a vector including a nucleic acid encoding a proteinaceous substance according to the invention. Examples of such a vector are given in the detailed description given herein; such as vector is pCMV-TAP, a plasmid expressing a TAP product, and so on.

[0024] In yet another embodiment, the invention provides a vector including a nucleic acid encoding a proteinaceous substance according to the invention, the vector including a gene-delivery vehicle, making the invention very useful in gene therapy. By equipping a gene delivery vehicle with a nucleic acid according to the invention, and by targeting the vehicle to a cell or cells that behave over-proliferating and/or have shown decreased death rates, the gene delivery vehicle provides the cell or cells with the necessary means of apoptosis, providing far reaching therapeutic possibilities.

[0025] Furthermore, the invention provides a transformed host cell including a2 5 (recombinant) nucleic acid encoding a proteinaceous substance or a vector according to the invention. Examples include transformed or transfected bacterial cells as described in the detailed description herein. Preferred is a host cell according the invention which is a transformed eukaryotic cell, such as mammalian cells transformed or transfected with a nucleic acid or vector according to the invention. The cells are in general capable to express or to produce a proteinaceous substance capable of providing apoptosis.

[0026] The invention furthermore provides an isolated or recombinant TAP proteinaceous substance capable of inducing apoptosis. Expression of such TAP substances in cells, induces the apoptotic process. It can do so alone, or in the presence of other apoptosis inducing substances such as Apoptin, and especially so independent of p53 and/or insensitive to anti-apoptosis proteins such as Bcl-2 and/or in cases wherein functional caspase-3 is lacking, showing that also in those cases where (functional) p53 is absent and/or active Bcl-2 is present and/or functional caspase-3 is lacking apoptosis can be induced by a substance according to the invention.

[0027] In particular, the invention provides a proteinaceous substance according to the invention encoded by a nucleic acid according to the invention, for example including at least a part of an amino acid sequence as shown in FIG. 2 or a functional equivalent and/or functional fragment thereof capable of providing apoptosis alone or in combination with other apoptosis inducing substances such as Apoptin.

[0028] The invention also provides an isolated or synthetic antibody specifically recognizing a proteinaceous substance or functional equivalent and/or functional fragment thereof according to the invention. Such an antibody is for example obtainable by immunizing an experimental animal with a TAP PROTEINACEOUS substance or an immunogenic fragment and/or equivalent thereof and harvesting polyclonal antibodies from the immunized animal, or obtainable by other methods known in the art such as by producing monoclonal antibodies, or (single chain) antibodies or binding proteins2 5 expressed from recombinant nucleic acid derived from a nucleic acid library, for example obtainable via phage display techniques.

[0029] With such an antibody, the invention also provides a proteinaceous substance specifically recognizable by such an antibody according to the invention, for example obtainable via immunoprecipitation, Western Blotting, or other immunological techniques known in the art.

[0030] Furthermore, the invention provides use of a nucleic acid, vector, host cell, or proteinaceous substance according to the invention for the induction of apoptosis. In particular, such use is also provided further including use of a nucleic acid encoding Apoptin or a functional equivalent and/or functional fragment thereof or use of Apoptin or a functional equivalent and/or functional fragment thereof. Combining these apoptosis-inducing substances increases the percentage of apoptosis in treated tumor cells (see for example FIG. 4).

[0031] In particular, such use is provided wherein the apoptosis is p53-independent and/or BcI-2 insensitive and/or caspase-3 independent.

[0032] Such use as provided by the invention is particularly useful from a therapeutic viewpoint. The invention provides herewith a pharmaceutical composition including a nucleic acid, vector, host cell, or proteinaceous substance according to the invention. In addition, such a pharmaceutical composition according to the invention is provided further including a nucleic acid is encoding Apoptin or a functional equivalent or fragment thereof or Apoptin or a functional equivalent or fragment thereof. Such a pharmaceutical composition is in particular provided for the induction of apoptosis, for example wherein the apoptosis is p53-independent and/or Bcl-2 insensitive and/or caspase-3 independent, for the treatment of a disease where enhanced cell proliferation or decreased cell death is observed, as is in general the case when the disease includes cancer or auto-immune disease.

[0033] Herewith, the invention provides a method for treating an individual carrying a disease where enhanced cell proliferation or decreased cell death is observed including treating the individual with a pharmaceutical composition2 S according to the invention. Also, use of a nucleic acid, vector, host cell, or proteinaceous substance according to the invention is provided for the preparation of a pharmaceutical composition for the treatment of a disease where enhanced cell proliferation or decreased cell death is observed, as is in general the case when the disease includes cancer or auto-immune disease.

[0034] The invention further discloses the apoptotic activity of a proteinaceous substance according to the invention (also called TTV-apoptosis inducing protein or TAP; the terms may be used interchangeable herein) in tumor versus normal cells; the proteinaceous substance fails to induce apoptosis in normal fibroblast and hepatocytes and can therefor be used for depletion ofifically tumor cells. So TAP, just like Apoptin, is a very potent anti-tumor specific agent. Expression of TAP can be used for the induction of apoptosis in specifically (human) tumor cells. TAP, again 'ust like Apoptin, does not or at least not significantly induce apoptosis in normal cells, indicating that the toxicity of TAP-treatment will be low.

[0035] TAP can be (transiently) expressed in tumors by means of DNA transfection.

[0036] Expression of TAP in (tumor) cells may take place by infecting cells with(retro) viral vectors that contain a coding sequence for a proteinaceous substance according to the invention, capable of providing apoptosis, alone or in combination with other apoptosis-inducing substances, such as Apoptin.

[0037] Administration to cells of non-viral components (e.g. liposomes or transferrin-derived vectors) containing a proteinaceous substance according to the invention and/or a nucleic acid according to the invention is a further possibility for the expression/presence of a proteinaceous substance according to the invention and induction of apoptosis in tumor cells. Such a non-viral component according to the invention may further include Apoptin and/or coding sequences for Apoptin.

[0038] Furthermore, we have provided evidence that TAP, like Apoptin, does not need functional p53, cannot be blocked by inhibitors of the p53 apoptotic pathway, as, for example the Bcl-2 proteins and does not need functional caspase 2 5 Together with the fact that TAP induces apoptosis in different tumor cell, as disclosed herein, all these data imply that TAP can induce apoptosis indifferent tumor cells and is a very potent inducer of apoptosis in tumor cells, which can overcome blocks of anti-apoptotic activity in tumor cells. Therefore, TAP is a potent anti-tumor agent for a broad variety of tumor(s) (cells).

[0039] Thus, the invention provides a vehicle delivering a tumoricidal substance or a gene encoding a tumoricidal substance mainly, but not exclusively to a tumor cell, characterized in that the tumoricidal substance is TAP. In addition, such a vehicle according to the invention may further include Apoptin or a nucleic acid encoding Apoptin or a functional fragment thereof In the prior art many 1vehicles for delivering cytotoxic agents or precursors thereof have been disclosed. A major problem in delivering cytotoxic agents is that they are harmful to all cells and not ust the tumor cells. Therefore many different ways of targeting the cytotoxic substance to the tumor cells have been investigated.

[0040] Although many targeting moieties are nowadays known, essentially all of them suffer from the drawback of not being completely specific for the tumor target. Therefore the use of this cytotoxic substance has so far not met with great success. Experiments as disclosed herein for TAP have shown that this is not the case for TAP and as already disclosed before this is also the case for Apoptin. TAP and/or Apoptin only have a significant effect in tumor cells and is not in normal cells, at least not significantly. Thus, even if the targeting moiety or any other means of delivery of TAP and/or Apoptin is not very specific, this will result in hardly any toxicity to normal tissue. Thus the invention provides a conjugate for targeted tumor therapy including a targeting moiety having binding affinity for a molecule associated mainly, but not exclusively with the surface of a tumor cell and further including TAP. In addition such a conjugate according to the invention may further include Apoptin.

[0041] A targeting moiety is well defined in the art as a molecule with a specific binding activity for a target molecule. It should preferably be capable of2 5 internalization. The target molecule may be an antigen or an epitope, in which the targeting moiety is an antibody or a fragment or a derivative thereof. The target molecule may be a receptor in which case the targeting moiety is a ligand for the receptor (for example EGF and its receptor). These are just examples of suitable combinations. The bond between the targeting moiety and TAP has only one requirement in that it should allow the functions of both partners to operate. The same requirement is applicable for Apoptin if the invention further includes Apoptin. Thus, it may be a chemical (labile) bond, it may be a fusion protein. The conjugate may even be a liposome covered with targeting moieties and filled with TAP and optionally Apoptin (or gene(s)encoding such a protein). The invention also includes a vehicle delivering a gene encoding TAP to a tumor cell, using gene therapy. Such a vehicle according to the invention may also further include Apoptin or its encoding gene. Gene therapy has many well known methods to deliver genes to cells using viruses such as adenovirus or retrovirus. The person skilled in the art will know how to select the right vehicle. TAP and Apoptin only functions to induce apoptosis in transformed cells, it or its and/or they or theirs gene(s) can be used as a safety measure in other gene therapy regimens than tumor therapy, such as those rectifying deficiencies from inheritable diseases. It is then provided in a gene delivery vehicle together with the gene of interest and the cell in which the gene of interest becomes malignant then it will be1susceptible to the action of TAP. Thus the invention provides a vehicle for delivering a nucleic acid of interest to a target cell, the vehicle further including a nucleic acid according to the invention. Such a vehicle according to the invention may further include Apoptin.

[0042] The invention further provides TAP for use in a method of eliminating cells of a target cell population whereby the method is mainly, but not entirely specific for the cells of the target population, whereby TAP is the cytotoxic agent, as well as TAP for use in a method of eliminating cells of a target cells of a target cell population whereby the cells of the population are not sensitive to other apoptosis inducing agents.

[0043] The latter is possible because TAP and Apoptin cannot be inhibited by the mechanism inhibiting the other apoptosis inducing substances.

[0044] The last two mentioned methods according to the invention may further include Apoptin The expressions “mainly but not exclusively” and “mainly but not entirely” (e.g., “primarily”) reflect the finding that TAP (and optionally Apoptin) is/are only active in tumor cells and not, at least not significantly in normal cells and it is therefore no longer necessary to provide a targeting means which is exclusively found on tumor cells.

[0045] The invention will be explained in more detail in the “Detailed Description” portion, which is illustrative and not limiting to the invention.

BRIEF DESCRIPTION OF THE FIGURES

[0046] FIG. 1 shows the DNA sequence encoding TAP protein which has apoptotic activity in (human) tumor cells.

[0047] FIG. 2 shows an amino-acid sequence of TAP protein. The NES domain is located on the TAP protein in between amino acids 27 and 39. The NLS domain is situated in the TAP protein from position 62 and 68.

[0048] FIG. 3 shows the scheme of the used oligomers to construct pMN-TAP. Besides the TAP sequence the oligomers contain a myc-tag and BamH1restriction-enzyme site, which are required for binding to the myc-tag-specific antibody 9E IO and enabling cloning in a BamHI restriction-enzyme site, respectively.

[0049] FIG. 4 shows the apoptotic activity of TAP protein and/or Apoptin in various human tumor cell lines. DoHH-2: human lymphoma-derived cell line over-expressing Bcl-2; HepG2. human hepatoma-derived cell line expressing wild-type p53; Saos-2: human osteosarcoma-derived cells lacking functional p53; H1299: human lung carcinoma cells; Hep3B:human hepatoma cells lacking functional p53; MCF-7:human breast tumor cells lacking caspase-3 activity;U8:human squamous cell carcinoma cells lacking functional p53; U20S:human osteosarcoma cells which are functionally competent for p53 function.

DETAILED DESCRIPTION

[0050] The invention provides a method for inducing apoptosis through interference with the function of this newly discovered apoptosis-related TAP protein or functional equivalents or fragments thereof and/or the induction of apoptosis by means of (over)expression of TAP or related gene or functional equivalents thereof. The invention also provides an anti-tumor therapy based on the interference with the function of TAP-like proteins and/or its (over)expression.

[0051] The invention provides a therapy for cancer, auto-immune diseases or related diseases which is based on TAP-like proteins alone or in combination with Apoptin and/or Apoptin-like compounds. DNA cloning the various cloning steps have been carried out according to the methods described by Maniatis et al., 1982.

[0052] For drug selections Luria Broth (LB) plates for E. coli were supplemented with ampicillin (50 microgram per ml).

[0053] Sequence analysis: The clones containing the sequences encoding TAP proteins were sequenced using dideoxy NTPs according to the Sanger-method, which was performed by BaseClear, Leiden, The Netherlands. The used sequencing primer was a 20-mer of the DNA-sequence 5′-ggatccctagcaggtctgcg-3′.

[0054] Primary rat hepatocytes Primary rat hepatocytes were isolated from collagenase-perfused livers as standard and cultured in Williams E medium (Gibco Life Technologies, Grand Island, N.Y., USA) supplemented with insulin (2 mU/ml) and dexamethasone (1 mM). The cells were grown on collagen-coated culture slides(Micronic, Lelystad, The Netherlands).

[0055] Transfection methods Plasmid DNA was purified by QIAGEN-column chromatography according to the instructions of the manufacturer (Westburg BV, Leusden, The Netherlands). The various mammalian cell lines were grown in the appropriate culture medium supplemented with penicillin and streptomycin (GIBCO/BRL).

[0056] The cells were transfected by calcium-phosphate precipitation as described (Graham and Van der Eb, 1973) or transfected with Fugene, according the instructions provided by the manufacturer (Roche, Almere, The Netherlands).

[0057] Micro-injection of plasmid DNA encoding TAP and control genes.1 5 Cells were micro-injected in the cytoplasm with plasmid pCMV-TAP(cloning as described herein), pCMV-LacZ or pCMV-Apoptin (Danen-Van Oorschot et al., 1997) at a concentration of 50 ng per ul using an Eppendorf micro-injector with the injection pressure of 0.5 psi. The cells were co-injected with Dextran-rhodamine (MW: 70 kDa; Molecular probes, Leiden, The Netherlands) to be able to later identify injected cells. The cells were incubated at 37′C after injection until the cells were fixed.

[0058] Immunofluorescence assays Cells were fixed with 80% acetone and used for immunofluorescence tests with mye-tagged- and/or Apoptin-specific monoclonal antibodies with fluorescein-isothiocyanate (Noteborn et al., 1998).

[0059] Apoptosis assays The apoptotic cells were initially determined by means of DAPI staining (Telford et al., 1992). DAPI stains intact cellular DNA strongly and regularly, whereas it stains apoptotic DNA weakly and/or irregularly.

[0060] The TUNEL assay was carried out as described by Pietersen et al., 1999 with the use of an in-situ cell death detection kit (Roche, Almere, The Netherlands).

[0061] Western-blot analysis The cells were harvested after transfection and lysed in 2×sample buffer [100 mM TrisHCI (pH 6.8), 4% SDS, 20% glycerol, 0.2% bromophenol blue, 2.5%beta-mercaptoethanol]. Proteins were fractionated on 15% SDS-polyacrylamide gels and electroblotted onto Immobilon-P membranes(Millipore). Parts of the blots were then incubated with Mab 9E10 (1:5000) to myc-tag to detect TAP. Positive signals were visualized by enhanced chemiluminescence according to the manufacture's protocol (Amersham, The Netherlands).

[0062] Results and discussion Construction of a plasmid containing the TAP gene.

[0063] To examine whether TAP protein harbors apoptotic activity we have to make a DNA construct containing the complete TAP DNA sequences, which are shown in FIG. 1. In addition, the stop codon has been also indicated. The presented TAP DNA sequence synthesizes a putative protein of 105 aminoids (FIG. 2). Furthermore, at the N-terminal end of the TAP gene, a Myc-aci tag (amino acids: EQKLISEEDL) has been linked which is in frame with the TAP gene product. This Myc-tag enables the recognition of the TAP proteins by means of the Myc-tag-specific 9E10 antibody.

[0064] The DNA construct containing the TAP DNA sequences, Myc-tag DNA sequences and BamHI restriction-enzyme sites has been made by using a panel of DNA oligomers as shown in FIG. 3. All steps for making the required approximately 0.36 kb DNA fragment was carried by The Midland certified Reagent Co., Midland, Tex., USA.

[0065] In principle the synthesized DNA oligomers were synthesized and purified by preparative polyacrylamide gel electrophoresis and 5′-phosphorylated to permit ligation. Subsequently, the various Oligomers were annealed and then ligated en masse in a thermostable ligation reaction. The long internal overlaps annealed stably and are efficiently ligated, whereas the cohesive termini tend to remain disassociated. As a consequence, the ligation product could be directly purified by preparative low-melting-point agarose gel electrophoresis using the freeze-squeeze method. The appropriated approximately 0.36 kb DNA fragment was made visible in the gel with long wavelength UV light. Next, the DNA band was excised and purified and ligated in BamH1-linearized pUC19 plasmid DNA, which was treated with calfintestine alkaline phosphatase. The final product was analyzed by BamH1digestion for containing an approximately 0.36 kb DNA fragment and sequence analysis. The plasmid DNA containing the myc-tagged TAP DNA sequences has been called “pMN-TAP”.

[0066] Construction of an expression vector for the identification of TAP protein in human and other mammalian cells.

[0067] To study whether the cloned myc-tagged TAP gene encode protein products, we have carried out the following experiments.

[0068] The DNA plasmid pcDNA3.1 (Invitrogen, Groningen, The Netherlands)contains the cytomegalovirus (CW promoter enabling high levels of expression of foreign genes in transformed human and other mammalian cells, such as Saos-2 and Cos cells.

[0069] The pcDNA3.1 construct expressing Myc-tagged TAP DNA was constructed as follows. The pMN-TAP clone was digested with the restriction enzyme BamH1 and the requested approximately 0.36 kb DNA insert was isolated. The expression vector pcDNA3.1 digested with BamH1 and treated with calf intestine alkaline phosphatase and ligated to the isolated myc-tagged TAP DNA insert. By restriction-enzyme digestions and sequence analysis, the pcDNA3.1 construct containing the myc-tagged TAP DNA in the correct orientation was identified. The final construct containing the TAP sequences is called pCMV-TAP.

[0070] The synthesis of the Myc-tagged TAP protein was analyzed by transfection of Cos cells with plasmid pCMV-TAP. As negative control, COS cells were mock-transfected. Two days after transfection, the cells were lysed and Western-blot analysis was carried out using the Myc-tag-specific antibody9E10.

[0071] The Cos cells transfected with pCMV-TAP were proven to synthesize a specific Myc.-tag ed TAP product with the expected size of approximately 12@gkDa. As expected, the lysates of the mock-transfected Cos cells did not contain a protein product reacting with the Myc-tag-specific antibodies.

[0072] These results indicate that we have been able to construct a plasmid that is able to produce a protein product derived from the putative TAP open reading frame.

[0073] Over-expression of the novel TAP protein in human hepatoma HepG2cells induces the apoptotic process. Next, we have examined whether TAP carries apoptotic activity. First, we have analyzed the cellular localization of the novel TAP protein in human hepatoma-derived HepG2 cells, which are synthesizing functional tumor suppressor protein p53 (Pietersen et al., 1999). To that end, the HepG2 cells were transfected with plasmid pCW-TAP encoding the myc-tagged TAP PROTEIN, as described by Danen-van Oorschot (1997). As a negative control, HepG2 cells were transfected with a plasmid encoding myc-tagged lacZ.

[0074] Two days after transfection, the cells were fixed. By indirect immunofluorescence using the myc-tag-specific antibodies 9E10 and DAPI, which stains the nuclear DNA, it was shown that the TAP protein was present in the cytoplasm of the cell.

[0075] Finally, we examined whether (over)-expression of our novel TAP PROTEIN results in induction of apoptosis. To that end, we have analyzed the TAP-positive cells for DAPI-staining. Four days after transfection, almost all TAP-positive cells were aberrantly stained with DAPI, which is indicative for induction of apoptosis (Telford, 1992, Danen-van Oorschot, 1997). At this time point, TAP was localized in the nuclear structures of the transfected HepG2cells. The nuclear DNA of the cells expressing LacZ was not aberrantly stained with DAPI. Therefore, the obtained results (FIG. 4) indicate that TAP can induce apoptosis in human tumor cells.

[0076] Over-expression of the novel TAP protein in human osteosarcomaU20S cells expressing wild-type p53 versus human osteosarcoma Saos-2 and hepatoma Hep3B cells lacking functional p53.

[0077] During tumor development, most of the tumors will lack functional tumor suppressor p53. Tumor cells lacking functional p53 are in general poor responders to (chemo)therapeutic agents. In the above described experiment, we have shown that TAP can induce apoptosis in cells containing functional tumor suppressor protein p53. Therefore, it is also of importance to prove whether TAP can induce apoptosis in human tumor cells in the absence of functional p53.

[0078] To that end, we have transfected human osteosarcoma-derived Saos-2cells and human hepatoma-derived Hep3B cells synthesizing no tumor suppressor p53 (Zhuang et al. 1995a, 1995b) with plasmid pCMV-TAP-encoding myc-tagged TAP protein, U20S cells expressing wild-type p53 were used as a control in this experiment. As control, the three different cell lines were transfected with the plasmid pCNIV-LacZ encoding myc-tagged LacZ.

[0079] Four or five days after transfection, the cells were fixed and analyzed for myc-tagged TAP expression by means of immunofluorescence using the myc-tag specific antibody 9E10 and apoptotic activity by DAPI staining. In parallel, transfected Saos-2, U20S and Hep3B cells were fixed and examined for induction of apoptosis by means of a TUNEL assay (Pietersen et al., 1999).

[0080] An equal significant amount of Saos-2 and U20S cells were stained aberrantly with DAPI whereas the cells containing myc-tagged LacZ were not, which is indicative for induction of TAP-specific apoptosis to a similar level in p53-minus Saos-2 versus p53-positive U20S cells. In addition, Saos-2 and U20Scell cultures transfected with pCNW-TAP showed a significant higher amount of TUNEL-positive cells than Saos-2 cell cultures transfected with pCMV-LacZ.

[0081] Furthermore, the TAP-positive Hep3B cells underwent also apoptosis as assayed both with the DAPI-staining method as well as with the TUNEL assay. The level of apoptosis induction was similar to the level of apoptosis found induction in HepG2 cells.

[0082] The results (FIG. 4), obtained with TAP synthesis in both HepG2 versus Hep3B and Saos-2 versus U20S cells, prove that TAP can induce apoptosis independent of p53. Therefore, tumors or tumorous cells having functional p53 or not can be treated with TAP-synthesizing vectors.

[0083] Over-expression of the novel TAP protein in human lymphoma DoHH-2 cells induces the apoptotic process.

[0084] Besides non-functional p53, over-expression of anti-apoptosis proteins such as Bcl-2 hamper conventional anti-cancer therapies. Therefore, we have also examined whether TAP can induce apoptosis in human tumor cells over-expressing Bcl-2 such as DoHH-2 cells (Zhuang et al., 1995). To that end, DoHH-2 cells were transfected with pCMV-TAP or pCMV-IacZ and analyzed as described for the HepG2 cells. Only the DoHH-2 cells synthesizing TAP protein were shown to be stained aberrantly with DAPI.

[0085] Therefore, we conclude that TAP also induces apoptosis in cells over-expressing Bel The results are shown in FIG. 4.

[0086] Co-expression of TAP and Apoptin induces apoptosis in human tumor cells in a very efficient way.

[0087] The CAV-derived protein Apoptin induces apoptosis upon nuclear localization as seems also to be the case for TAP-induced apoptosis. However, the TAP protein is present in a more diffused way in the cytoplasm in comparison to Apoptin. Furthermore, TAP seems to enter the nucleus shortly before the cells undergo apoptosis, whereas Apoptin does earlier (see above and below). In the following transfection experiments (carried out as described above), we have examined the rate of apoptosis induction in human tumor cells synthesizing both TAP and Apoptin in comparison with tumor cells synthesizing only TAP or Apoptin.

[0088] All 3 examined human tumor cell lines HepG2, Saos-2 and DoHH-2underwent a significant higher level of apoptosis after co-expression of Apoptin and TAP proteins in comparison with the cells expressing Apoptin or TAP separately. The results are shown in FIG. 4.

[0089] TAP induces apoptosis in cells lacking essential factors of the caspase-regulated apoptosis execution pathway.

[0090] Essential factors in the apoptotic machinery are the specific proteases called caspases (Danen-Van Oorschot et al., 2000 and references herein).

[0091] Apoptin was shown to be able to induce apoptosis in human breast-tumor-derived MCF-7 cells lacking the essential execution caspase-3 (Danen-Van Oorschot et al., 2000).

[0092] To test if this is also the case for TAP, we have transfected human MCF-7 cells with plasmid pCMV-TAP encoding myc-tagged TAP protein. As control, the cells were transfected with the plasmid pCMV-LacZ encoding the myc-tagged LacZ, as was the case for all above described experiments. Four or five days after transfection, the cells were fixed and analyzed for myc-tagged TAP expression by means of immunofluorescence using the myc-tag specific is antibody 9E10 and apoptotic activity by DAPI staining.

[0093] A significant amount of MCF-7 cells were stained aberrantly with DAPI whereas the cells containing LacZ were not, which is indicative for induction of TAP-specific apoptosis. The level of apoptosis was to a comparable level as inp53-minus Saos-2 cells or p53-positive U20S cells, which indicates that despite the fact that functional caspase-3 is absent in these human tumor cells, TAP is able to force these cells undergoing apoptosis.

[0094] TAP induces apoptosis in cell lines derived from human lung-tumor and squamous cell carcinomas.

[0095] Next, we have examined whether cell lines derived from human lung tumors and squamous cell carcinoma were sensitive to TAP-induced apoptosis.

[0096] To that end, we have transfected human lung-tumor H1299 cells (Friedlander et al., 1996) and human squamous cell carcinoma U8 cells (van Damme et al., 1997) with plasmid pCMV-TAP encoding myc-tagged TAP protein. As control, the cells were transfected with the plasmid pCAW-LacZ expressing the myc-tagged LacZ. Four or five days after transfection, the cells were fixed and analyzed for myc-tagged TAP expression by means of immunofluorescence using the myc-tag specific antibody 9E10 and apoptotic activity by DAPI staining.

[0097] A significant amount of H1299 and U8 cells were stained aberrantly with DAPI whereas the cells containing LacZ were not, which is indicative for induction of TAP-specific apoptosis.

[0098] In conclusion, we have provided evidence that expression of TAP proteins in various human tumorigenic cells results in induction of apoptosis.

[0099] Therapies based on induction of (p53-independent and/or Bcl-2 insensitive and/or caspase-3 independent) apoptosis are possible utilizing the TAP PROTEINS. Combined therapies can be carried out using TAP protein and other apoptosis-inducing proteins such as Apoptin. Another CAV-derived protein, which is known to induce apoptosis and also known to enhance Apoptin activity is VP2 (Noteborn et al., 1997).

[0100] TAP induces apoptosis in a tumor-specific way.

[0101] An efficient anti-tumor therapy without obvious side effects is by far the preferable one. Therefore, we have examined whether TAP can induce apoptosis in normal human fibroblasts. In addition, we have also analyzed the TAP apoptosis activity in rat primary hepatocytes.

[0102] To that end, we have transfected human VH10 fibroblasts (Danen-Van Oorschot et al. 1997) with plasmid pCMV-TAP encoding myc-tagged TAP protein. As control, the cells were transfected with the plasmid pCMV-LacZ encoding myc-tagged LacZ or with pCMV-Apoptin encoding Apoptin (negative controls). Four or five days after transfection, the cells were fixed as described above. In parallel, human transformed NW18 fibroblasts (Danen-Van Oorschot al., 1997) were examined for TAP-induced apoptosis as described for the human normal fibroblasts.

[0103] By means of micro-injection of rat primary hepatocytes with plasmids pCMV-TAP, pCMV-Apoptin or PCMV-LacZ, we examined whether TAP was able to induce apoptosis in these normal rat hepatocytes. In parallel, human transformed HepG2 cells were microinjected with the above described43plasmids encoding myc-tagged TAP, Apoptin or myc-tagged LacZ protein, respectively. Six and 24 hours after micro-injection the cells were fixed.

[0104] The cells were analyzed for myc-tagged TAP or myc-tagged LacZ expression by means of immunofluorescence using the myc-tag specific antibody 9E10 or the Apoptin expression by using the Apoptin-specific antibody 111.3 and apoptotic activity by DAPI staining.

[0105] The human VH10 fibroblasts and rat hepatocytes containing TAP PROTEIN were stained aberrantly with DAPI to a background level as the cells containing LacZ or Apoptin, whereas the transformed/tumorigenic controls samples NW18 and HepG2 cells clearly showed high levels of apoptosis induction when synthesizing TAP or Apoptin but not when produce/contain LacZ. This data are indicating that TAP does not or at least not significantly induce apoptosis in the human and rodent normal cells.

[0106] Therefore, we conclude that TAP like Apoptin induces tumor-specifically apoptosis.

[0107] Production of polyclonal antibodies directed against TAP proteins.

[0108] For the production of polyclonal antibodies against TAP proteins three putative immunogenic peptides were synthesized.

[0109] N-terminus-THPLPVPSETCPSDG-C-terminus; N-terminus-CRLSRLRQRRPEIEH-C-terminus; N-terminus-CTQTMEAPLEDPKTQT-C-terminus; (EuroGentec SA, Seraing, Belgium). Subsequently, co-workers of EuroGentec injected two rabbits with the TAP-specific peptides according to standard procedures. The serum derived from the rabbits injected with the TAP peptides was shown to recognize specifically for in this report described TAP products by means of immunofluorescence and Western-blot assays. These results imply that we have generated specific antibodies, which can be used for detecting our novel TAP protein. Furthermore, this antibody forms the basis for a diagnostic test in detecting TAP in sera of TTV-infected individuals, which is indicative for a TTV strain with apoptotic activity.

[0110] Functional domains of TAP Although, TAP does not share overall sequence similarities with any known protein sequence and in particular with the CAV-derived apoptosis-inducing protein Apoptin, it also has apoptotic activity in human tumor cells.

[0111] TAP harbors putative sequences resembling a nuclear location signal or a nuclear export signal as indicated in FIG. 2. Furthermore, TAP has a relatively high percentage (>8%) of proline residues. Computer analysis revealed a significant structural homology among TAP and Apoptin, which might explain the similarity in their activity.

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Claims

1. An apoptosis-inducing proteinaceous substance encoded by an isolated or recombinant nucleic acid or functional equivalent and/or functional fragment thereof derivable from mammalian gyrovirus-like virus nucleic acid.

2. The apoptosis-inducing proteinaceous substance of claim 1 wherein said mammalian gyrovirus-like virus comprises a single-stranded circular DNA virus.

3. The apoptosis-inducing proteinaceous substance of claim 2 wherein said single-stranded circular DNA virus comprises a TTV-like virus.

4. The apoptosis-inducing proteinaceous substance of any one of claims 1 to 3 wherein said isolated or recombinant nucleic acid is at least 60 percent homologous to a TTV nucleic acid as shown in FIG. 1.

5. The apoptosis-inducing proteinaceous substance of any one of claims 1 to 4, further in combination with a second apoptosis-inducing substance.

6. The apoptosis-inducing proteinaceous substance of claim 5 wherein said second apoptosis-inducing substance comprises Apoptin or a functional fragment thereof.

7. The apoptosis-inducing proteinaceous substance of any one of claims 1 to 6 capable of providing apoptosis independent of p53.

8. The apoptosis-inducing proteinaceous substance of any one of claims 1 to 7 capable of providing tumor specific apoptosis.

9. The apoptosis-inducing proteinaceous substance of any one of claims 1 to 8 capable of providing apoptosis independent of caspase-3.

10. The apoptosis-inducing proteinaceous substance of any one of claims 1 to 9 further comprising a nuclear location signal and/or a nuclear export signal.

11. An isolated or recombinant nucleic acid or functional equivalent and/or functional fragment thereof from which the apoptosis-inducing proteinaceous substance of any one of claims 1 to 10 can be transcribed and translated.

12. A vector comprising the isolated or recombinant nucleic acid or functional equivalent and/or functional fragment thereof of claim 11.

13. The vector of claim 12 further comprising a gene-delivery vehicle.

14. A host cell comprising the isolated or recombinant nucleic acid or functional equivalent and/or functional fragment thereof claim 11 or the vector of claim 12 or claim 13.

15. The host cell of claim 14 wherein said host cell is a eukaryotic cell.

16. An isolated or synthetic antibody specifically recognizing the proteinaceous substance or functional equivalent and/or functional fragment thereof of any one of claims 1 to 10.

17. A proteinaceous substance specifically recognizable by isolated or synthetic antibody of claim 16.

18. A method of inducing apoptosis comprising using the nucleic acid of claim 11, the vector of claim 12 or 13, the host cell of claim 14 or 15, the apoptosis-inducing proteinaceous substance of any one of claims 1 to 10 or 17 to induce apoptosis.

19. The method according to claim 18 wherein said apoptosis is p53-independent.

20. The method according to claim 18 or 19 wherein said apoptosis is tumor-specific.

21. The method according to any one of claims 18 to 20 wherein said apoptosis is caspase-3 independent.

22. The method according to any one of claims 18 to 21 further comprising: using a nucleic acid encoding Apoptin or a functional equivalent and/or functional fragment thereof or using Apoptin or a functional equivalent and/or functional fragment thereof.

23. A pharmaceutical composition comprising the nucleic acid of claim 11, the vector of claim 12 or 13, the host cell of claim 14 or 15, or the proteinaceous substance of any one of claims 1 to 10 or 17.

24. The pharmaceutical composition of claim 23 further comprising a nucleic acid encoding Apoptin or a functional equivalent and/or functional fragment thereof.

25. The pharmaceutical composition of claim 23 or 24 for the induction of apoptosis.

26. The pharmaceutical composition of claim 25 wherein said apoptosis is p53-independent.

27. The pharmaceutical composition of claim 25 or 26 wherein said apoptosis is tumor-specific.

28. The pharmaceutical composition of any one of claims 25 to 27 wherein said apoptosis is caspase-3 independent.

29. The pharmaceutical composition of any one of claims 23 to 28 for the treatment of a disease where enhanced cell proliferation or decreased cell death is observed.

30. The pharmaceutical composition of claim 29 wherein said disease comprises cancer or auto-immune disease.

31. A method for treating a subject carrying a disease where enhanced cell proliferation or decreased cell death is observed, said method comprising treating said subject with a pharmaceutical composition of any one of claims 23 to 30.

32. A method of treating a metabolic state wherein enhanced cell or proliferation or decreased cell death in a subject is observed, said method comprising administering a pharmaceutical composition comprising: the nucleic acid of claim 11, the vector of claim 12 or 13, the host cell according to claim 14 or 15, and/or the apoptosis-inducing proteinaceous substance of any one of claims 1 to 10 or 17.

33. A vehicle for delivering a nucleic acid of interest to a target cell, said vehicle comprising the apoptosis-inducing proteinaceous substance of any one of claims 1 to 10 or 17.

34. The vehicle of claim 33 further comprising Apoptin or functional equivalent and/or functional fragment thereof.

35. A conjugate for targeted tumor therapy, said conjugate comprising: a targeting moiety having binding affinity for a molecule associated mainly, but not exclusively on the surface of a tumor cell, and the proteinaceous substance of any one of claims 1 to 10 or 17.

36. The conjugate of claim 35 further comprising Apoptin or a functional equivalent and/or functional fragment thereof.

37. A vehicle for delivering a tumoricidal substance or a gene encoding a tumoricidal substance to a molecule associated primarily with a tumor cell, said vehicle wherein the tumoricidal substance is the proteinaceous substance of any one of claims 1 to 10 or 17.

38. The vehicle according to claim 37 further comprising Apoptin or a gene-encoding Apoptin or a functional equivalent and/or functional fragment thereof.

39. A cytotoxic agent for use in a method of eliminating cells of a target cell population, wherein the method is primarily specific for the cells of the target population, wherein the proteinaceous substance of any one of claims 1 to 10 or 17 is the cytotoxic agent.

40. A method of eliminating cells of a target cell population wherein the cells of said population are not sensitive to other apoptosis inducing agents, said method comprising bringing said cells into contact with the apoptosis-inducing proteinaceous substance of any one of claims 1 to 10 or 17 or a functional equivalent and/or a functional fragment thereof for use in a method of eliminating cells of a target cell population wherein the cells of said population are not sensitive to other apoptosis inducing agents.

41. The cytotoxic agent of claim 39 together in combination with Apoptin or a functional equivalent and/or functional fragment thereof.