WO2002040499A1 - A method for generating genetically altered antigens - Google Patents

A method for generating genetically altered antigens Download PDF

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Publication number
WO2002040499A1
WO2002040499A1 PCT/US2000/031135 US0031135W WO0240499A1 WO 2002040499 A1 WO2002040499 A1 WO 2002040499A1 US 0031135 W US0031135 W US 0031135W WO 0240499 A1 WO0240499 A1 WO 0240499A1
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gene
cell
antigen
mismatch repair
cells
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PCT/US2000/031135
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French (fr)
Inventor
Nicholas C. Nicolaides
Luigi Grasso
Philip M. Sass
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Morphotek Inc.
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Priority to PCT/US2000/031135 priority Critical patent/WO2002040499A1/en
Priority to AU2001216030A priority patent/AU2001216030A1/en
Priority to CA2429134A priority patent/CA2429134C/en
Priority to EP00978578A priority patent/EP1363930B1/en
Priority to DK00978578T priority patent/DK1363930T3/en
Priority to DE60030172T priority patent/DE60030172T2/en
Priority to AT00978578T priority patent/ATE336505T1/en
Priority to JP2002543507A priority patent/JP2005509399A/en
Publication of WO2002040499A1 publication Critical patent/WO2002040499A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/10—Antimycotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P33/00—Antiparasitic agents
    • A61P33/02—Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P33/00—Antiparasitic agents
    • A61P33/10—Anthelmintics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • the invention is related to the area of genetic alterations of antigens as potent vaccines. In particular it is related to the field of mutagenesis.
  • vaccines to build immunity against foreign and/or endogenous polypeptides provides an effective and selective strategy for treating the underlying cause of disease.
  • killed viruses such as the polio mellims and the Hepatitis B virus (John TJ. (2000) New Engl. J. Med. 14:806-807).
  • Standard methods for generating vaccines against candidate pathogenic organisms or molecules are known by those skilled in the art.
  • Vaccines for human use are developed in animal models to survey for the ability of killed or defective whole agents such as parasites, viruses or recombinant polypeptides to cause immunity against infection of the pathogenic agent (Boyce T.G. et al. (2000) Vaccine 19:217-226).
  • mice or rats are injected with a purified antigen in the presence of adjuvant to generate an immune response (Boyce T.G. et al. (2000) Vaccine 19:217-226).
  • antigens are capable of eliciting a strong immune response when injected into a host organism (Hoshino Y. and A.Z. Kapikian (2000) J. Health Popul. Nutr.18:5-14; Orenstein W. A. et al. (2000) Am. J. Public Health 90:1521-525; Lechmann M. and TJ. Liang (2000) Semin. Liver Dis. 20:211-226).
  • a method for generating diverse sequences within a polypeptide would be useful for the creation of more potent therapeutic agents. Moreover, the generation of randomly altered nucleotides and encoded polypeptide residues throughout an entire antigen molecule may result in new reagents that are: 1) more antigenic; 2) more immunogenic; and 3) have beneficial pharmacokinetic properties.
  • the invention described herein is directed to the use of random genetic mutation of a polypeptide in vivo by blocking the endogenous mismatch repair (MMR) activity of a host cell yielding structurally altered antigens that can be screened for antigenicity and immunogenicity in comparison to the wild type molecule.
  • MMR mismatch repair
  • the use of mammalian cell- based high throughput screens as taught by this application will facilitate identification of randomly altered antigens that may serve as effective vaccines.
  • the invention describes methods for repeated in vivo genetic alterations and selection for antigens with enhanced immunogenicity and pharmacokinetic profiles.
  • a potential problem in generating potent vaccine antigens against endogenous to the mammalian host is the source of antigen production.
  • recombinant polypeptides that are naturally produced by mammalian cells are generated recombinantly using insect, yeast or bacterial expression systems. These sources typically produce large amounts of proteins that are distinct from the mammalian-produced polypeptides, and may differ from the natural protein due to altered folding or altered post-translational modifications such as hyperglycosylation.
  • the invention described herein is directed to the creation of genetically altered mammalian cell hosts that produce structurally altered polypeptides as vaccine agents via the blockade of MMR.
  • the present invention facilitates the generation of highly antigenic polypeptides as vaccines.
  • the advantages of the present invention are further described in the examples and figures described herein.
  • the present invention provides methods for generating genetically altered antigens in vivo, whereby the antigen possesses desired biochemical property(s), such as, but not limited to, increased antigenicity and immunogenicity.
  • desired biochemical property(s) such as, but not limited to, increased antigenicity and immunogenicity.
  • One method for identifying antigens with increased antigenicity is through the screening of mismatch repair ("MMR") defective cell clones that produce desired antigens.
  • MMR mismatch repair
  • the invention also provides methods for rendering cells expressing a target antigen hypermutable.
  • the cells include, but are not limited to rodent, primate, human, plant, yeast or bacterial cells.
  • the antigens can be generated from endogenous genes or from introduced fransgenes.
  • the invention also provides methods for generating genetically altered cell lines that express antigenic polypeptides.
  • the invention provides methods for generating genetically altered cell lines that produce immunogenic polypeptides.
  • the invention provides methods for producing an antigen expression cassette for high throughput screening of altered polypeptides in vivo.
  • the invention provides methods of mutating a gene of interest in a mismatch repair defective cell.
  • the invention provides methods of creating genetically altered antigens in vivo by blocking the MMR activity of the cell host.
  • Still other embodiments of the invention provide methods of creating genetically altered polypeptides in vivo by transfecting genes encoding for an antigen in a MMR defective cell host.
  • the invention also embraces methods of creating antigens with increased immunogencity due to genetic alterations within the antigen-encoding gene by blocking endogenous MMR of the cell host.
  • the invention provides methods of creating a library of randomly altered antigens from mammalian cells by blockade of MMR of the cell host. In other embodiments, the invention provides methods of creating antigens with enhanced pharmacokinetic profiles due to genetic changes within the encoding gene by blocking endogenous MMR of the cell host.
  • the invention also provides methods of creating genetically altered antigens in MMR defective cells as vaccine agents.
  • the invention provides methods for high throughput screening of antigens produced by MMR defective cells.
  • a method for making MMR defective cell lines expressing a target antigen will be provided.
  • a polynucleotide encoding a dominant negative allele of an MMR gene is introduced into a target antigen- producing cell.
  • the cell becomes hypermutable as a result of the introduction of the gene.
  • an isolated hypermutable cell producing antigenic peptides is provided.
  • the cell is defective for mismatch repair and exhibits an enhanced rate of hypermutation.
  • the cell produces a polypeptide from a mutated gene encoding for the polypeptide.
  • a method for introducing a mutation into an endogenous gene encoding for a target polypeptide.
  • a polynucleotide encoding a dominant negative allele of a MMR gene is introduced into a cell.
  • the cell becomes hypermutable as a result of the introduction and expression of the MMR gene allele.
  • the cell further comprises a gene of interest.
  • the cell is grown and tested to determine whether the gene encoding for a polypeptide of interest harbors a mutation.
  • a method for producing a cell- based screening assay to identify antigenic proteins as vaccines.
  • a polynucleotide encoding a dominant negative allele of a MMR gene is introduced into a cell expressing a secreted antigen.
  • the cell becomes hypermutable as a result of the introduction of the gene.
  • the cell is grown and conditioned medium from the cell is tested for the expression of antigenic polypeptides.
  • a gene, or set of genes encoding for polypeptides or a combination therein are introduced into a mammalian cell host that is defective in MMR.
  • the cell is grown and clones are analyzed for antigens with enhanced antigenicity.
  • a method is provided for producing a cell- based screening assay to identify antigenic proteins as vaccines.
  • a polynucleotide encoding a secreted antigen is introduced into a naturally MMR defective cell.
  • the gene is hypermutable as a result of the introduction of MMR deficiency.
  • the cell is grown and conditioned medium from the cell is tested for the expression of antigenic polypeptides.
  • a method for restoring genetic stability in a cell containing a polynucleotide encoding for a dominant negative allele of a MMR gene.
  • the expression of the dominant negative MMR gene is suppressed and the cell restores its genetic stability including but not limited to genetic stability within the antigen-encoding genes.
  • a method for restoring genetic stability in a cell containing a polynucleotide encoding a dominant negative allele of an MMR gene and a newly selected phenotype.
  • the expression of the dominant negative mismatch repair gene is suppressed and the cell restores its genetic stability and the new phenotype is stable.
  • Figure l In situ ⁇ -galactosidase staining of TKPMS134/pCAR-OF or TKvect/pCAR-OF cells to assay for MMR defective cells containing genetically altered ⁇ - galactosidase genes. Arrows indicate Blue ( ⁇ -galactosidase positive) cells.
  • Figure 2 Schematic representation of sequence alterations of the D ⁇ -galactosidase gene produced by MMR defective host cells
  • FIG. 3 Schematic representation of sec-hist secretion proteins for screening of structurally altered antigenic polypeptides and the sec-hist expression cassette (SEQ JD NO: 17).
  • Panel A Schematic representation of sec-hist protein;
  • Panel B Sequence of sec- hist expression cassette.
  • the italic bold sequence represents a Hindlll site for subcloning; the double underlined sequence on the 5' end represents leader sequence from the human IL-2; the underlined sequence on the 3' end represents the poly histidine sequence followed by 2 termination codons; sequence in capital letters represents sequence from the polylinker region of pUC18; the polylinker contains the following restriction enzymes for cloning cDNAs: SacI-Sac ⁇ -Notl-Xbal-Spel-BarnHI-Smal-Pstl-EcoRI.
  • Figure 4 Schematic diagram for high throughput screening of conditioned medium from TK clones for the identification of antigenic sec-hist polypeptides.
  • Assays employ an in vitro antigenicity test using splenocytes from na ⁇ ' ve mice (non-primed) and antigen-exvosed (primed) mice. Clones exhibiting positive CM are then genetically analyzed to confirm structural alterations within the sec-hist sequence, followed by protein purification and retesting of purified proteins. Purified proteins with the best stimulatory activity are then screened in vivo for immunogenicity. The screening assay can be repeated for several rounds to add additional alterations within the antigen (long arrow).
  • the inventors have discovered a method for developing hypermutable cells producing therapeutic antigens by taking advantage of the conserved mismatch repair (MMR) process of host cells.
  • MMR conserved mismatch repair
  • Dominant negative alleles of such genes when introduced into cells or transgenic animals, increase the rate of spontaneous mutations by reducing the effectiveness of DNA repair and thereby render the cells or animals hypermutable.
  • Hypermutable cells or animals can then be utilized to develop new mutations in a gene or genes of interest.
  • Blocking MMR in cells producing antigens can enhance the rate of mutation within the gene encoding for the antigen that can be screened to identify clones producing structurally altered polypeptides with enhanced antigenicitiy and immunogenicity.
  • the methods are useful for the production of antigens that have increased antigenicity and/or immunogenicity.
  • antigens may be used as immunogens to elicit immune responses in animals against these antigens.
  • the antigens may be derived from, for example, pathogenic organisms or cancer cells such that an immune response is directed against the pathogenic organism or cancer cell and exerts an effect on the organism or cancer cell.
  • the effect may be, for example, to prevent, inhibit or terminate the growth of the pathogenic organism or cancer cell when an immunogenic amount of the antigen is administered to an animal.
  • the pathogenic organisms from which antigens may be derived include bacteria, fungi, parasitic protozoa, helminths, and viruses.
  • Non-limiting examples include species of the following genera: Staphylococcus , Streptococcus, Bacillus, Bordetella, Clostridium, Escherichia, Haemophilus, Helicobacter, Klebsiella, Listeria, Salmonella, Vibrio, Yersinia, Neisseria, Treponema, Borrelia, Corynebacterium, Mycobacterium, Mycoplasma, Chlamydia, Acremonium, Aspergillus, Blastomyces, Candida, Acanthamoeba, Ascaris, Babesia, Cryptosporidium, Echinococcus, Entamoeba, Giardia, Necator, Ancylostoma, Unicinaria, Leishmania, Onchocerca, Plasmodium, Schistosoma, Strong
  • Non-limiting examples of viruses include adenoviras, arborviruses, coronavirus, cytomegalo virus, entero viruses, Epstein- Barr virus, hepatitis viruses, herpes viruses, immunodeficiency viruses (e.g. , HIV, FIV SIN), papilloma viruses, T-cell leukemia viruses, influenza viruses, mumps viruses, parainfluenzae viruses, parvoviruses, poxviruses, Rabies virus, respiratory syncytial virus, rhino viruses, rotaviruses, Rubella viruses, and varicella-zoster viruses.
  • immunodeficiency viruses e.g. , HIV, FIV SIN
  • papilloma viruses papilloma viruses
  • T-cell leukemia viruses influenza viruses
  • mumps viruses parainfluenzae viruses
  • parvoviruses poxviruses
  • Rabies virus respiratory syncytial virus
  • rhino viruses rotaviruses
  • Rubella viruses
  • the antigens derived from the pathogenic organisms may be antigens known to elicit an immune response, for which an enhanced immune response is desired, or the antigen may be one that is known to generate a weak response for which an enhanced response is desired. It is also possible that some antigens that did not previously elicit an immune response will become antigenic as a result of the methods of the invention and the phenomenon of hypermutability of cells which contain dominant negative alleles of mismatch repair genes.
  • the antigens produced by the method of the invention are novel immunogens that may be admimstered in an appropriate pharmaceutical carrier, such as an adjuvant, for administration to animals as a vaccine.
  • the antigens of the invention may be administered to animals in immunogenic amounts such that an antibody and/or a cell-mediated immune response is elicited.
  • the administration of the antigens of the invention may be administered as a single dose, or, preferably as a plurality of doses to effect a boosted immune response.
  • the route of administration may be any accepted route of im ⁇ iunization including, for example, oral, intrmuscular, intrperitoneal, subcutaneous, intradermal, intranasal, or transdermal. Doses for humans can readily be extrapolated from animal studies as taught by
  • an immunogenic amount of the antigens of the invention will be in the range of about 5 to about 100 g.
  • the antigens of the present invention may be administered as single antigens or may be administered as combinations of antigens.
  • the antigen combinations may be antigens of the same pathogenic organism, or may be antigens of different pathogenic organisms, such that immune responses are elicited to more than one pathogenic organism.
  • the antigens of the present invention are hypermutated by the methods of the invention which take advantage of the mismatch repair system.
  • MMR also called mismatch proofreading
  • a MMR gene is a gene that encodes for one of the proteins of such a mismatch repair complex.
  • a MMR complex is believed to detect distortions of the DNA helix resulting from non-complementary pairing of nucleotide bases. The non-complementary base on the newer DNA strand is excised, and the excised base is replaced with the appropriate base, which is complementary to the older DNA strand. In this way, cells eliminate many mutations that occur as a result of mistakes in DNA replication.
  • Dominant negative alleles cause a MMR defective phenotype even in the presence of a wild-type allele in the same cell.
  • An example of a dominant negative allele of a MMR gene is the human gene hPMS2-134, which carries a truncating mutation at codon 134. The mutation causes the product of this gene to abnormally terminate at the position of the 134th amino acid, resulting in a shortened polypeptide containing the N-terminal 133 amino acids. Such a mutation causes an increase in the rate of mutations, which accumulate in cells after DNA replication. Expression of a dominant negative allele of a mismatch repair gene results in impairment of mismatch repair activity, even in the presence of the wild-type allele. Any allele that produces such effect can be used in this invention.
  • Dominant negative alleles of a MMR gene can be obtained from the cells of humans, animals, yeast, bacteria, or other organisms (Prolla T.A. et al. (1994) Science 264: 1091-1093; Strand M. et al. (1993) Nature 365:274-276; Su, S.S. et al. (1988) J. Biol. Chem. 263:6829-6835).
  • Such alleles can be identified by screening cells for defective MMR activity. Cells from animals or humans with cancer can be screened for defective mismatch repair. Cells from colon cancer patients may be particularly useful. Genomic DNA, cDNA, or mRNA from any cell encoding a MMR protein can be analyzed for variations from the wild type sequence.
  • Dominant negative alleles of a MMR gene can also be created artificially, for example, by producing variants of the hPMS2-134 allele or other MMR genes.
  • Various techniques of site-directed mutagenesis can be used. The suitability of such alleles, whether natural or artificial, for use in generating hypermutable cells or animals can be evaluated by testing the mismatch repair activity caused by the allele in the presence of one or more wild-type alleles, to determine if it is a dominant negative allele.
  • a cell or an animal into which a dominant negative allele of a mismatch repair gene has been infroduced will become hypermutable.
  • the degree of elevation of the spontaneous mutation rate can be at least 2- fold, 5-fold, 10-fold, 20-fold, 50-fold, 100-fold, 200-fold, 500-fold, or 1000-fold that of the normal cell or animal.
  • chemical mutagens such as but limited to methane sulfonate, dimethyl sulfonate, O6-methyl benzadine, MNU, ENU, etc. can be used in MMR defective cells to increase the rates an additional 10 to 100 fold that of the MMR deficiency itself.
  • a polynucleotide encoding for a dominant negative form of a MMR protein is infroduced into a cell.
  • the gene can be any dominant negative allele encoding a protein, which is part of a MMR complex, for example, PMS2, PMS1, MLHI, or MSH2.
  • the dominant negative allele can be naturally occurring or made in the laboratory.
  • the polynucleotide can be in the form of genomic DNA, cDNA, RNA, or a chemically synthesized polynucleotide.
  • the polynucleotide can be cloned into an expression vector containing a constitutively active promoter segment [such as but not limited to CMV, S V40, Elongation Factor (EF) or LTR sequences] or to inducible promoter sequences such as the steroid inducible pIND vector (InVifrogen), tetracycline, or MMTV, where the expression of the dominant negative MMR gene can be regulated.
  • a constitutively active promoter segment such as but not limited to CMV, S V40, Elongation Factor (EF) or LTR sequences
  • inducible promoter sequences such as the steroid inducible pIND vector (InVifrogen), tetracycline, or MMTV, where the expression of the dominant negative MMR gene can be regulated.
  • the polynucleotide can be introduced into the cell by transfection.
  • a gene, a set of genes or a chimeric gene encoding for whole or parts of a therapeutic antigen can be transfected into MMR deficient cell hosts, the cell is grown and screened for clones containing genetically altered genes encoding for antigens with new biochemical features including but not limited to increased antigenicity.
  • MMR defective cells may be of human, primates, mammals, rodent, plant, yeast or of the prokaryotic kingdom.
  • Transfection is any process whereby a polynucleotide is introduced into a cell.
  • the process of transfection can be carried out in a living animal, e.g., using a vector for gene therapy, or it can be carried out in vitro, e.g. , using a suspension of one or more isolated cells in culture.
  • the cell can be any type of eukaryotic cell, including, for example, cells isolated from humans or other primates, mammals or other vertebrates, invertebrates, and single celled organisms such as protozoa, yeast, or bacteria.
  • transfection will be carried out using a suspension of cells, or a single cell, but other methods can also be applied as long as a sufficient fraction of the treated cells or tissue incorporates the polynucleotide so as to allow transfected cells to be grown and utilized.
  • the protein product of the polynucleotide may be transiently or stably expressed in the cell.
  • Techniques for transfection are well known. Available techniques for introducing polynucleotides include but are not limited to electroporation, transduction, cell fusion, the use of calcium chloride, and packaging of the polynucleotide together with lipid for fusion with the cells of interest.
  • An isolated cell is a cell obtained from a tissue of humans or animals by mechanically separating out individual cells and transferring them to a suitable cell culture medium, either with or without pretreatment of the tissue with enzymes, e.g., collagenase or trypsin. Such isolated cells are typically cultured in the absence of other types of cells.
  • Cells selected for the introduction of a dominant negative allele of a mismatch repair gene may be derived from a eukaryotic organism in the form of a primary cell culture or an immortalized cell line, or may be derived from suspensions of single-celled organisms.
  • a polynucleotide encoding for a dominant negative form of a MMR protein can be introduced into the genome of an animal by producing a transgenic animal.
  • the animal can be any species for which suitable techniques are available to produce transgenic animals.
  • transgenic animals can be prepared from domestic livestock, e.g., bovine, swine, sheep, goats, horses, etc.; from animals used for the production of recombinant proteins, e.g., bovine, swine, or goats that express a recombinant polypeptide in their milk; or experimental animals for research or product testing, e.g., mice, rats, guinea pigs, hamsters, rabbits, etc.
  • Cell lines that are determined to be MMR defective can then be used as a source for producing genetically altered genes encoding for therapeutic antigens in vitro by introducing whole, intact genes and/or chimeric genes encoding for a therapeutic antigen(s) into MMR defective cells from any tissue of the MMR defective animal.
  • transfected cell line or a colony of transgenic animals Once a transfected cell line or a colony of transgenic animals has been produced, it can be used to generate new mutations in one or more gene(s) of interest.
  • a gene of interest can be any gene naturally possessed by the cell line or transgenic animal or introduced into the cell line or transgenic animal.
  • An advantage of using such cells or animals to induce mutations is that the cell or animal need not be exposed to mutagenic chemicals or radiation, which may have secondary harmful effects, both on the object of the exposure and on the workers.
  • chemical mutagens may be used in combination with MMR deficiency, which renders such mutagens less toxic due to an undetermined mechamsm.
  • Hypermutable animals can then be bred and selected for those producing genetically variable cells that may be isolated and cloned to identify new cell lines that are useful for producing structurally altered polypeptides.
  • the dominant negative MMR gene allele can be removed by directly knocking out the allele by technologies used by those skilled in the art or by breeding to mates lacking the dominant negative allele to select for offspring with a desired trait and a stable genome.
  • Another alternative is to use a CRE-LOX expression system, whereby the dominant negative allele is spliced from the animal genome once an animal containing a genetically diverse protein profile has been established.
  • inducible vectors such as the steroicLinduced pLND (InVitrogen) or pMAM (Clonetech) vectors which express exogenous genes in the presence of corticosteroids.
  • Mutations can be detected by analyzing for alterations in the genotype of the cells or animals, for example by examining the sequence of genomic DNA, cDNA, messenger RNA, or amino acids associated with the gene of interest. Mutations can also be detected by screening for the production of antigenicity.
  • a mutant polypeptide can be detected by identifying alterations in electrophoretic mobility, spectroscopic properties, or other physical or structural characteristics of a protein encoded by a mutant gene.
  • One can also screen for altered function of the protein in situ, in isolated form, or in model systems.
  • One can screen for alteration of any property of the cell or animal associated with the function of the gene of interest, such as but not limited to antigenicity.
  • a high throughput mammalian cell- based assay is presented.
  • a MMR defective cell line is transfected with a secretion cassette containing a leader sequence for secretion at the N-terminus fused to the target antigen.
  • Cells are grown and clones are plated by limiting dilution into microtitre plates and conditioned medium are screened for antigenic peptides.
  • the advantage of such an approach is that the antigen is more similar to the natural polypeptide than it would be if produced by bacterial, yeast or baculovims systems which tend to cause misfolding and/or distorted post-translational modifications.
  • mismatch repair proteins and nucleic acid sequences include the following:
  • PMS2 human cDNA
  • MSH2 (human cDNA) (SEQ JD NO: 12) ggcgggaaac agcttagtgg gtgtggggtc gcgcattttc ttcaaccagg aggtgaggag 60 gtttcgacat ggcggtgcag ccgaaggaga cgctgcagtt ggagagcgcggcgaggtcg 120 gcttcgtgcg cttcttcag ggcatgccgg agaagccgac caccacagtg cgccttttcg 180 accggggcga cttctatacg gcgcacggcg aggacgcgct gct gccc cgggaggtgt 240 ⁇ > > Ni Ni Ni Ni
  • hPMS2-134 human cDNA (SEQ ID NO: 16) cgaggcggat cgggtgttgc atccatggag cgagctgaga gctcgagtac agaacctgct 60 aaggccatca aacctattga tcggaagtca gtccatcaga tttgctctgg gcaggtggta 120 ctgagtctaa gcactgcggt aaaggagtta gtagaaaaca gtctggatgc tggtgccact 180 aatattgatc taaagcttaa ggactatgga gtggatctta tgaagtttc agacaatgga 240 tgtggggtag aagaagaaaaa cttcgaaggc t
  • EXAMPLE 1 Stable expression of dominant negative MMR genes in cells results in widespread mutations of a reporter gene and its encoded polypeptide.
  • MMR deficient cells can lead to the generation of genetic alterations throughout the entire genome of a host organisms offspring, yielding a population of genetically altered offspring or siblings that may produce biochemicals with altered properties.
  • This patent application teaches of the use of dominant negative MMR genes in antigen-producing cells, including but not limited to rodent, human, primate, yeast, insect, and prokaryotic cells producing proteins that may serve as therapeutic antigens for vaccination.
  • MI microsatellite instability
  • a method used to detect MMR deficiency in eukaryotic cells is to employ a reporter gene that has a polynucleotide repeat inserted within the coding region that disrupts its reading frame due to a frame shift.
  • the reporter gene will acquire random mutations (i.e. insertions and/or deletions) within the polynucelotide repeat yielding clones that contain a functional reporter gene.
  • TK Syrian Hamster fibroblasts
  • pCAR-OF a mammalian expression construct containing a defective ⁇ -galactosidase gene
  • the pCAR-OF vector consists of a ⁇ -galactosidase gene containing a 29-basepair poly-CA tract inserted at the 5' end of its coding region, which causes the wild-type reading frame to shift out-of-irame.
  • This chimeric gene is cloned into the pCEP4, which contains the constitutively cytomegalovirus (CMN) promoter upstream of the cloning site and also contains the hygromycin-resistance (HYG) gene that allows for selection of cells containing this vector.
  • CPN constitutively cytomegalovirus
  • HOG hygromycin-resistance
  • the pCAR-OF reporter cannot generate ⁇ -galactosidase activity unless a frame-restoring mutation (i.e., insertion or deletion) arises following transfection into a host.
  • pCAR-JJF contains a ⁇ -galactosidase in which a 27-bp poly-CA repeat was cloned into the same site as the pCAR-OF gene, but it is biologically active because the removal of a single repeat restores the open reading frame and produces a functional chimeric ⁇ -galactosidase polypeptide (not shown).
  • the pCAR vectors also contain the neomycin resistance gene as selectable marker. In these proof-of-concept studies, TKPMS 134 and TKvect cells were transfected with the pCAR-OF reporter vector and selected for 17 days in neomycin plus hygromycin selection medium.
  • TKvect 65 +/- 9 0 0/65 0%
  • TKPMS134/pCAR-OF clones that were pooled and expanded also showed a number of cells that contained a functional ⁇ -galactosidase gene. No ⁇ -galactosidase positive cells were observed in TKvect cells transfected with the pCAR-OF vector. These data are shown in Figure 1 where the dark staining in panel B represent ⁇ -galactosidase positive cells present in the TKPMS 134/pCAR-OF cultures while none are found in the TKvect cells grown under similar conditions (panel A).
  • RT-PCR reverse transcriptase polymerase chain reaction
  • Sequence analysis of ⁇ - galactosidase message from TKvect cells found no structural alterations in the input gene sequence. Analysis of the ⁇ -galactosidase message from TKPMS134 cells found several changes within the coding sequences of the gene. These sequence alterations included insertion and deletions of the poly-CA tract in the amino terminus as expected. Other alterations included insertions of sequences outside of the poly-CA repeat as well as a series of single base alterations (transversions and transitions) contained throughout the length of the gene.
  • 100,000 cells are harvested and fixed in 1% gluteraldehyde, washed in phosphate buffered saline solution and incubated in 1 ml of X-gal substrate solution [0.15 M NaCl, 1 mM MgCl 2 , 3.3 mM K 4 Fe(CN) 6 , 3.3 mM K 3 Fe(CN) 6 , 0.2%
  • a fusion gene cassette was engineered that encodes for a secreted polypeptide containing a six polyhistidine domain at the C-terminus, which is useful for purification.
  • This gene cassette is referred to as sec-hist.
  • This gene was constructed by PCR using DNA from the pUC18 plasmid as template.
  • the sense primers contained nucleotide sequences corresponding to the leader sequence of human interleukin-2 (ref 32), which has been found to produce robust amounts of secreted polypeptides from TK cells (personal observation). This domain was introduced at the 5' end of the pUC18 polylinker.
  • Antisense primers containing nucleotide sequences encoding for 6 histidines were used to position these residues at the 3' end of the pUC18 polylinker. The nucleotide sequence of these primers are listed below.
  • SENSE Primer S'aflg-cttccatgtacaggatgcaactcctgtcttgcattgcactaagtcttgcacttgtcacaaacagtgcaCAAAAGCTG GAGCTC-3' (SEQ JD NO:l)
  • the italic sequence represents a Hindlll site for subcloning.
  • the underlined sequence represents leader sequence from the human IL-2. Sequence in capital letters represents sequence from the start of the polylinker region of pUC18.
  • the italic sequence represents a Hindlll site for subcloning.
  • the underlined sequence represents 6 codons encoding for histidine residues followed by 2 termination codons. Sequence in capital letters represents sequence to the 3' end of the pUC18 polylinker.
  • Amplified products were obtained using buffer conditions as previously described . Amplification reactions were carried out at 94°C for 30 sec, 52°C for 2 min, and 72°C for 2 min for 25 cycles. Products were run on 1% agarose gels containing ethidium bromide, and products of the expected molecular weight were excised and purified by Gene Clean (BiolOl). Products were then cloned into T-tailed vectors (InVitrogen) as suggested by the manufacturer. Recombinant clones were analyzed by restriction analysis and by DNA sequencing. Several clones contained fragments with the expected genomic sequence. The parental clone is referred to as TAsec-hist.
  • FIG. 3 A A schematic diagram of the sec-hist fusion protein is shown in Figure 3 A
  • the TAsec-hist plasmid is digested with Hindlll to release the sec-hist insert.
  • the insert was cloned into the unique Hindlll site of the pCEP4 mammalian expression vector, which also contains the Hygromycin resistance gene as selectable marker. Recombinant clones were analyzed by restriction digest and sequencing to assure the authenticity of the construct. Inserts can now be designed via PCR or direct cloning using the restricition sites contained within the polylinker (see Figure 3B).
  • Recombinant pCEPsec-hist plasmid will then be transfected into TK cells as previously described using cationic lipids.
  • Cells will be cotransfected along with the pEFPMS134, which is a mammalian expression vector containing the PMS 134 dominant negative MMR gene allele under control of the constitutive elongation factor (EF) promoter.
  • EF constitutive elongation factor
  • This vector contains the neomycin resistance gene and allows for double selection of TK cells for both the sec-hist and pEFPMS134 vectors.
  • TK cells will also be cotransfected with the sec-hist and pEF empty vector as a control.
  • ELISA will be performed on conditioned medium (CM) from TK cells transfected with pCEP4sec-hist to screen for high producers of the sec-hist polypeptide.
  • ELISAs are carried out as follows. Twohundred microliter aliquots of conditioned medium are taken from pCEP4sec-hist transfected and control cells. Aliquots are placed into 1.5ml eppendorf tubes and centrifuged at 14,000Xg for 3 minutes to pellet cell debris. Supernates are then collected and 50 ⁇ ls are placed into triplicate wells of a 96-well polystyrene microtiter plate (Nunc).
  • Plates are incubated at room temperature for 4 hours, washed twice with 200 ⁇ ls of IX Phosphate Buffered Saline (PBS) solution, pH 7.0 (Life Technologies), and blocked with 100 ⁇ ls of 5%milk in IX PBS for 1 hour. Plates are then incubated with a monoclonal anti-HIS antibody (diluted 1 : 1000 in IX PBS) (Santa Cruz) for 2 hours at room temperature and then washed twice with 200 ⁇ ls of IX PBS, and probed with an anti-mouse-horse radish peroxidase (HRP) conjugated secondary antibody diluted 1 :3000 in PBS.
  • PBS IX Phosphate Buffered Saline
  • HRP anti-mouse-horse radish peroxidase
  • CM or 50,000 cells from each culture is directly lysed in 2X lysis buffer (60 mM Tris, pH 6.8, 2% SDS, 10% glycerol, 0.1 M 2-mercaptoethanol, 0.001% bromophenol blue) and samples are boiled for 5 minutes. Lysate proteins are separated by electrophoresis on 4-20% Tris glycine gels (Novex) and then electroblotted onto Immobilon-P (Millipore) in 48 mM Tris base, 40 mM glycine, 0.0375% SDS, 20% methanol and blocked overnight at 4°C in Tris-buffered saline plus 0.05% Tween-20 and 5% condensed milk.
  • 2X lysis buffer 60 mM Tris, pH 6.8, 2% SDS, 10% glycerol, 0.1 M 2-mercaptoethanol, 0.001% bromophenol blue
  • Filters are then probed with an antibody generated against the PMS 134 or the polyHIS tag (Santa Cruz), followed by a secondary HRP-co ⁇ jugated antibody. After incubation with the secondary antibody, blots are developed using chemiluminescence (Pierce) and exposed to film to determine PMS 134 and sec-hist expression. Clones exhibiting expression of both genes will then be used in experiments described above.
  • a potential technical problem may exist in expressing the sec-hist protein due to toxicity that it may have on the growth of TK cells. If the production of no or low amounts of sec-hist polypeptide is found to occur in the above analysis, a Hindlll sec-hist fragment from the TAsec-hist plasmid will be subcloned into the unique Hindlll site of the pIND/N5 steroid inducible vector (Invitrogen). This vector has been found to produce robust protein expression in TK cells upon in steroid induction. This application teaches the use of employing an inducible vector containing the sec-hist expression cassette to express polypeptides in TK cells that may be toxic under constitutively expressed conditions.
  • Cells that are found to co-express the PMS 134 and the sec-hist genes or the control cell expressing the pEF empty vector and the sec-hist gene are cultured under high growth conditions in media containing neomycin, hygromycin and vitamins, which has been shown to increase the doubling time of TK cells and enhance the genetic alteration of ⁇ - galactosidase reporter plasmids in vivo (data not shown). Briefly, cells are grown in vitamin enriched medium for 20 doublings ( ⁇ 17 days), a time at which it has been found that 20-40% of clones contain sequence alterations within a particular genetic locus. After selection, cells will be subcloned in 96-well microtiter plates by limiting dilutions.
  • Clones will be grown for 5 days in the presence of neomycin/hygromycin-free medium containing heat inactivated serum to remove complement for in vitro antigenic assays that will be performed using murine lymphocytes as described in section below.
  • the sec-hist expression vector cassette can also be transfected into cell lines that are "naturally" defective for MMR such as the human cell lines derived from colon cancer tumors such as but not limited to HCT116 and DLD-1.
  • the vector can be in the constitutive backbone pCEP4 or under control of the steroid-inducible vectors pIND or pMAM.
  • EXAMPLE 3 Screening strategy to identify cell clones producing highly antigenic polypeptides.
  • the lymphocyte stimulatory activity of sec-hist polypeptides will be measured by adding CM of TKsec-hist cells with or without the PMS 134 to lymphocytes derived from naive or whole antigen exposed Balb/C mice. Briefly, 2 mice will be infected with whole antigen in the presence of Freund's Complete Adjuvant by subcutaneous injection in the tail with a 100- ⁇ l 1/1 mixture of complete Freund's adjuvant (CFA) (Difco). Two subcutaneous boosts will be performed with the same quantity of antigen, mixed 1/1 with incomplete Freund's adjuvant (Difco), after 2 and 4 weeks. Two control mice will receive adjuvant alone. Mice are sacrificed 5 days after the second boost (at day 33).
  • CFA complete Freund's adjuvant
  • PBMCs Peripheral blood mononuclear cells
  • splenocytes from whole blood and splenocytes from spleens of will be harvested following the previously described procedures (Nicolaides, N.C. et al. (1997) Proc. Natl. Acad. Sci. USA 94:13175-13180).
  • splenocyte assays whole spleens are pressed through sterile wire mesh into RPMI medium (Life Technology). Next, cells are washed twice in RPMI and incubated for 10 minutes in RBC lysis buffer. Cells are then washed again and resuspended at 1 X IO 5 cells/ml in RPMI-1640 medium plus 10% heat inactivated fetal bovine serum.
  • PBMC isolation whole blood is isolated by eye puncture and collected into vacutainer tubes containing EDTA. An equal volume of PBS (Mg 2+ /Ca 2+ -free) is added to whole blood. PBMCs are isolated by centrifugation over Ficoll-Paque gradients (Pharmacia Biotech 17-1440-02).
  • Purified cells are seeded at 1 X IO 5 cells/ml in RPMI 1640 containing 10% heat-inactivated fetal bovine serum (Life Technologies, Inc.) and lOO ⁇ ls are plated in 96 well flat bottom microtiter plates and incubated at 37 °C in 5% CO 2 .
  • PBMCs and splenocytes from primed and non- primed mice are incubated with 10% conditioned medium (CM) from TKsec-hist cells with or without the PMS 134 gene.
  • CM conditioned medium
  • 5 ⁇ g/ml of concavahnA (ConA) is used as a positive control for splenocyte culture assays, while 5 ⁇ g/ml phorbol 12-myristate 13-acetate and 1 ⁇ g/ml phytohemagglutinin (Sigma) are used as a positive control for PBMC cultures.
  • CM from parental TK cells grown in the presence of RPMI with 10% heat inactivated medium will be used as negative control.
  • CM from TK cells Previous studies using CM from TK cells have found no stimulatory activity to be produced on PBMCs or splenocytes (N. Nicolaides, personal observation). Cultures are incubated at 37 °C in 5% CO 2 for 6 days and scored for antigenic activity as determined by proliferation assay. Proliferation is assayed using a modified protocol of the acid phosphatase assay as described (Grasso, L. et al. (1998) J Biol. Chem. 273:24016-24024). Briefly, 50 ⁇ ls of a buffer containing 0.1 Msodium acetate (pH 5.5), 0.1% Triton X-100, and 10 mM -nitrophenyl phosphate (Sigma
  • 104 phosphatase substrate is added directly to each well containing 0.2 ml of growth medium and incubated for 1.5 h at room temperature. Reactions are terminated by the addition of 0.05 N sodium hydroxide and quantified by absorbance at 410 nm using a BioRad plate reader. Data is represented as a stimulation index (SI), which is the proliferation of experimental data points divided by the mean of 10 aliquots of CM from TK parental cells. All experiments will be performed in at least triplicate.
  • SI stimulation index
  • TKsec-hist clones co-expressing the PMS 134 protein will be found to have an enhanced antigenicity on PBMCs and/or splenocytes due to conformational changes that will occur within the coding region of the target antigen. These changes may form secondary domains that serve as T and/or B cell epitopes and in turn are responsible for stimulating their respective activation. Clones that reproducibly produce enhanced antigenic activation will be sequenced to confirm and identify that a structural alteration(s) has indeed occurred within the coding region of the gene. Sequence data may also shed additional light into the importance of critical domains within this candidate vaccine polypeptide for additional rounds of alteration that may lead to the creation of a super-antigen that may serve as a potent vaccine.
  • RNA extraction and reverse transcription will be carried out using the Trizol method as previously described (Nicolaides, N.C. et al. (1997) Proc. Natl. Acad. Sci. USA 94:13175-13180; Grasso, L. et al. (1998) J. Biol. Chem. 273:24016-24024). Reverse transcription will be carried out using Superscript II (Life Technology) as previously described (Nicolaides, N.C et al. (1998) Mol. Cell. Biol. 18:1635-1641).
  • cDNAs will be amplified to isolate the sec-hist transcript using the sense primer: 5'-catgtacaggatgcaactcctg-3' (SEQ JD NO:3), which is located at the IL-2 leader sequence site (see Figure 3), and the antisense primer: 5'-tactagtggtgatggtgatggtg-3' (SEQ ID NO:4), which is located at the C-terminal polyhis site.
  • Amplification is carried out at 94°C for 30 sec, 52°C for 2 min, 72°C for 2 min for 30 cycles. Reactions are analyzed on agarose gels.
  • samples will be cleaned using the QIAquick PCR template kit (Qiagen) to remove PCR amplimers and sequenced using the following primers that cover the entire coding region of the sec- hist gene. Clones are then sequenced using primers specific to the gene encoding the antigen.
  • Qiagen QIAquick PCR template kit
  • Clones producing genetically altered sec-hist polypeptides will then be expanded into T-75 flasks to a density that will enable for the sufficient production of secreted sec- hist polypeptide in the CM.
  • Conditioned medium containing the sec-hist polypeptide is then collected, and centrifuged at 3,500Xg for 10 minutes to remove cellular debris.
  • CM is then loaded onto a 10ml- HiTrap Nickel column following the manufacturer's protocol (Pharmacia). After absorption and washing, the column is treated with 200 mM imidazole to elute the fusion protein. Recovered polypeptides are then analyzed by SDS-PAGE using 4-12% NuPAGE gels (Novex) and silver stained following the manufacturer's protocol (Novex).
  • sec-hist alleles may be generated by clones producing enhanced antigenic polypeptides, which contain a nonsense or frame-shift mutation, therefore forming polypeptides lacking a polyHIS C-terminus. If a nonsense or frameshift mutation does occur in clones producing polypeptides with increased antigenicity, then the new allele is reengineered via PCR to contain a polyHIS tag at the C-terminus, and this new fusion protein will be rescreened as above. Purified polypeptides will be rescreened at a final concentration of 10 ⁇ g/ml in the in vitro assays described above to confirm that the antigenic activity is indeed coming from the sec-hist protein.
  • TK cells producing altered antigens with enhanced activity on both PBMCs and splenocytes will then be tested along with the non-altered sec-hist protein in vivo in Balb/C mice for the ability to illicit an immune response in the absence of adjuvant.
  • EXAMPLE 4 Screening strategy to identify cell clones producing highly immunogenic antigens. To test the immunogenic potential that the altered polypeptides identified from
  • mice will be injected with the 6 most antigenic polypeptides and the wild type sec-hist polypeptide produced from TKEFempty/sec-hist cells in the absence of adjuvant. Briefly, mice will be immunized with 30 ⁇ gs of purified sec-hist protein in sterile phosphate buffered saline (PBS) without adjuvant by subcutaneous injection in the tail. One group of mice will receive a lOO ⁇ ls of a mixture of polypeptides diluted 1/1 in complete Freund's adjuvant (CFA) (Difco) as a positive control.
  • CFA complete Freund's adjuvant
  • mice Two subcutaneous boosts will be performed with the same quantity of antigen, and the mouse receiving the polypeptide mixture with adjuvant will be boosted with a 1/1 mixture with incomplete Freund's adjuvant (Difco), at 2 and 4 weeks after the initial injection. Mice will be bled 5 and 15 days after the second boost (at day 33) to measure for antigen titers. Control mice will receive PBS alone. Before the start of immunization, a prebleed will be obtained from each mouse.
  • Difco incomplete Freund's adjuvant
  • Immune responses will be measured by screening for whole Ig and sec-hist specific antibody titers by ELISA following the protocol described above.
  • 96-well plates will be coated with a 50uls of a solution containing 5 ⁇ g/ml each antigen used for vaccination in PBS. Plates will then be probed with serial dilutions of prebleeds, 5 day and 15 day bleeds. Detection of antibodies will be done using a sheep anti-mouse-HRP conjugated secondary antibody followed by incubation with TMB substrate as described above.
  • mice immunized with altered sec-hist protein that is able to cross react with the native sec-hist protein will be demonstrated with the generation of antisera from mice immunized with altered sec-hist protein that is able to cross react with the native sec-hist protein. If no titers are found in the samples without adjuvant, mice will be administrated antigen in complete Freund's Adjuvant and titers analyzed 14 days later, followed by immunization in Incomplete Freund's at day 17 if no titers are found and analyzed at day 31.
  • a potential problem that may occur with the outlined strategy is that antibody titers may be generated against the sec-polyhistidine fusion domain.
  • the antigen lacking the polyhistidine domain will be generated by in vitro transcription-translation (TNT) in the presence of radiolabelled methionine.
  • TNT in vitro transcription-translation
  • a template containing the sec-hist polypeptide will also be made and the encoded protein used as a control. Templates for the TNT reactions will be generated by PCR as described (Nicolaides, N.C. et al. (1998) Mol. Cell. Biol.18:1635- 1641). Briefly, the TAsec-hist plasmid will be used as template to amplify gene segments that encode for the untqagged antigen or the sec-hist tagged protein.
  • Translated polypeptides are first analyzed by SDS-PAGE gel electrophoresis and autoradiography to ensure that the polypeptide with the expected molecular weight are synthesized. Proteins are then immunoprecipitated using antiserum from vaccinated mice to determine if these antibodies recognize authentic antigen sequences. Briefly, immunoprecipitations are performed on in vttro-translated proteins by mixing the translation reaction mixtures with lOO ⁇ ls of mouse antiserum or 1 ⁇ gof a HIS-specific monoclonal antibody (MAB) (Santa Cruz) in 400 ⁇ ls of EBC buffer (50 mM Tris [pH 7.5], 0.1 M NaCl, 0.5% Nonidet P-40). After incubation for 1 h at 4°C, protein A-
  • Sepharose (Sigma) is added to a final concentration of 10% and the reaction mixtures are incubated at 4°C for 1 h. Proteins bound to protein A are washed five times in EBC and separated by electrophoresis on 4-20% Tris-glycine gradient gels, which are then dried and autoradiographed. If antisera are able to react with authentic sequences lacking HIS residues, the data from these studies will be continued in further preclinical animal studies. Discussion
  • the initial steps of MMR are dependent on two protein complexes, called MutS ⁇ and MutL ⁇ .
  • the use of dominant negative MMR alleles are able to perturb the formation of these complexes with downstream biochemicals involved in the excision and polymerization of nucleotides comprising the "corrected" nucleotides. Examples from this application show the ability of a truncated MMR allele (PMS 134 is capable of blocking MMR resulting in a hypermutable cell line that gains genetic alterations throughout its entire genome per cell division. Once a cell line is produced that contains genetic alterations within genes encoding for an antigen, it is desirable to restore the genomic integrity of the cell host.
  • inducible vectors whereby dominant negative MMR genes are cloned into such vectors, introduced into antigen- producing cells and the cells are cultured in the presence of inducer molecules and/or conditions.
  • Inducible vectors include but are not limited to chemical regulated promoters such as the steroid inducible MMTV, tetracycline regulated promoters, temperature sensitive MMR gene alleles, and temperature sensitive promoters.
  • This application also teaches us that any method used to block MMR can be performed to generate hypermutablility in an antigen-producing cell that can lead to genetically altered proteins with enhanced biochemical features such as but not limited to increased antigenicity, increased immunogenicity, and enhanced pharmacokinetic profiles.
  • the blockade of MMR in such cells can be through the use of dominant negative MMR gene alleles from any species including bacteria, yeast, protozoa, insects, rodents, primates, mammalian cells, and man.
  • Blockade of MMR can also be generated through the use of antisense RNA or deoxynucleotides directed to any of the genes involved in the MMR biochemical pathway.
  • Blockade of MMR can be through the use of polypeptides that interfere with subunits of the MMR complex including but not limited to antibodies.
  • the blockade of MMR may be through the use chemicals such as but not limited to nonhydrolyzable ATP analogs, which have been shown to block MMR (Galio, L. et al. (1999) Nucl. Acids Res. 27:2325-2331 ; Spampinato, C and P. Modrich (2000) J Biol Chem. 275:9863-9869).

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Abstract

Dominant negative alleles of human mismatch repair genes can be used to generate hypermutable cells and organisms. By introducing these genes into cells and transgenic animals, new cell lines animal varieties with novel and useful properties can be prepared more efficiently than by relying on the natural rate of mutation. These methods are useful for generating genetic diversity within genes encoding for therapeutic antigens to produce altered polypeptides with enhanced antigenic and immunogenic activity. Moreover, these methods are useful for generating effective vaccines.

Description

A METHOD FOR GENERATING GENETICALLY ALTERED ANTIGENS
TECHNICAL FIELD OF THE INVENTION
The invention is related to the area of genetic alterations of antigens as potent vaccines. In particular it is related to the field of mutagenesis.
BACKGROUND OF THE INVENTION
The use of vaccines to build immunity against foreign and/or endogenous polypeptides provides an effective and selective strategy for treating the underlying cause of disease. In particular is the use of killed viruses such as the polio mellims and the Hepatitis B virus (John TJ. (2000) New Engl. J. Med. 14:806-807). Standard methods for generating vaccines against candidate pathogenic organisms or molecules are known by those skilled in the art. Vaccines for human use are developed in animal models to survey for the ability of killed or defective whole agents such as parasites, viruses or recombinant polypeptides to cause immunity against infection of the pathogenic agent (Boyce T.G. et al. (2000) Vaccine 19:217-226). Briefly, rodents such as mice or rats are injected with a purified antigen in the presence of adjuvant to generate an immune response (Boyce T.G. et al. (2000) Vaccine 19:217-226). Unfortunately, not all antigens are capable of eliciting a strong immune response when injected into a host organism (Hoshino Y. and A.Z. Kapikian (2000) J. Health Popul. Nutr.18:5-14; Orenstein W. A. et al. (2000) Am. J. Public Health 90:1521-525; Lechmann M. and TJ. Liang (2000) Semin. Liver Dis. 20:211-226). While the reasons for the lack of immune response are not clear, some factors, such as the lack of T-cell epitopes which are important for stimulating cellular-mediated immune responses, may be absent within a given antigen (Ausiello CM. et al. (1999) Infect. Immun.61:4064- 4071; Brosstoff S. (1995) Adv. Exp. Med. Biol. 383:249-254). In the case of parasitic infections, the development of effective vaccines has been hampered by the presence of many different developmental stages that occur within an infected host and that a diverse array of aϊlelic forms occurs within genes encoding for prominent surface antigens (MALARIA OBSTACLES AND OPPORTUNITIES, Oaks , S . C . et al. , Eds . , National Academy Press, p 1, 1991; Anders, R.F. "Vaccines Against Asexual Blood Stages of Plasmodiumfalciparum" NEW GENERATION VACCINES, 2nd Ed., Anders, R.F., pp. 1035- 1055, 1997). It is believed by many skilled in the art that the generation of highly antigenic polypeptides may overcome these limitations and produce a protective immune response to pathogens (McLeod R. et al. (1995) Curr. Opin. Immunol.") 1. -539-552).
A method for generating diverse sequences within a polypeptide would be useful for the creation of more potent therapeutic agents. Moreover, the generation of randomly altered nucleotides and encoded polypeptide residues throughout an entire antigen molecule may result in new reagents that are: 1) more antigenic; 2) more immunogenic; and 3) have beneficial pharmacokinetic properties.
SUMMARY OF THE INVENTION
The invention described herein is directed to the use of random genetic mutation of a polypeptide in vivo by blocking the endogenous mismatch repair (MMR) activity of a host cell yielding structurally altered antigens that can be screened for antigenicity and immunogenicity in comparison to the wild type molecule. The use of mammalian cell- based high throughput screens as taught by this application will facilitate identification of randomly altered antigens that may serve as effective vaccines. Moreover, the invention describes methods for repeated in vivo genetic alterations and selection for antigens with enhanced immunogenicity and pharmacokinetic profiles.
The ability to develop and screen genetically altered mammalian cells that secrete structurally altered polypeptides in a high throughput manner provides a valuable method for creating vaccines for therapeutic development. A potential problem in generating potent vaccine antigens against endogenous to the mammalian host is the source of antigen production. In many instances recombinant polypeptides that are naturally produced by mammalian cells are generated recombinantly using insect, yeast or bacterial expression systems. These sources typically produce large amounts of proteins that are distinct from the mammalian-produced polypeptides, and may differ from the natural protein due to altered folding or altered post-translational modifications such as hyperglycosylation. The invention described herein is directed to the creation of genetically altered mammalian cell hosts that produce structurally altered polypeptides as vaccine agents via the blockade of MMR. The present invention facilitates the generation of highly antigenic polypeptides as vaccines. The advantages of the present invention are further described in the examples and figures described herein.
The present invention provides methods for generating genetically altered antigens in vivo, whereby the antigen possesses desired biochemical property(s), such as, but not limited to, increased antigenicity and immunogenicity. One method for identifying antigens with increased antigenicity is through the screening of mismatch repair ("MMR") defective cell clones that produce desired antigens.
The invention also provides methods for rendering cells expressing a target antigen hypermutable. The cells include, but are not limited to rodent, primate, human, plant, yeast or bacterial cells. The antigens can be generated from endogenous genes or from introduced fransgenes.
The invention also provides methods for generating genetically altered cell lines that express antigenic polypeptides. In some embodiments, the invention provides methods for generating genetically altered cell lines that produce immunogenic polypeptides. , h other embodiments, the invention provides methods for producing an antigen expression cassette for high throughput screening of altered polypeptides in vivo.
In other embodiments, the invention provides methods of mutating a gene of interest in a mismatch repair defective cell.
In some embodiments, the invention provides methods of creating genetically altered antigens in vivo by blocking the MMR activity of the cell host.
Still other embodiments of the invention provide methods of creating genetically altered polypeptides in vivo by transfecting genes encoding for an antigen in a MMR defective cell host.
The invention also embraces methods of creating antigens with increased immunogencity due to genetic alterations within the antigen-encoding gene by blocking endogenous MMR of the cell host.
In some embodiments, the invention provides methods of creating a library of randomly altered antigens from mammalian cells by blockade of MMR of the cell host. In other embodiments, the invention provides methods of creating antigens with enhanced pharmacokinetic profiles due to genetic changes within the encoding gene by blocking endogenous MMR of the cell host.
The invention also provides methods of creating genetically altered antigens in MMR defective cells as vaccine agents.
In some embodiments, the invention provides methods for high throughput screening of antigens produced by MMR defective cells.
These and other objects of the invention are provided by one or more of the embodiments described below, hi one embodiment of the invention, a method for making MMR defective cell lines expressing a target antigen will be provided. A polynucleotide encoding a dominant negative allele of an MMR gene is introduced into a target antigen- producing cell. The cell becomes hypermutable as a result of the introduction of the gene.
In another embodiment of the invention, an isolated hypermutable cell producing antigenic peptides is provided. The cell is defective for mismatch repair and exhibits an enhanced rate of hypermutation. The cell produces a polypeptide from a mutated gene encoding for the polypeptide.
In another embodiment of the invention, a method is provided for introducing a mutation into an endogenous gene encoding for a target polypeptide. A polynucleotide encoding a dominant negative allele of a MMR gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction and expression of the MMR gene allele. The cell further comprises a gene of interest. The cell is grown and tested to determine whether the gene encoding for a polypeptide of interest harbors a mutation.
In another embodiment of the invention, a method is provided for producing a cell- based screening assay to identify antigenic proteins as vaccines. A polynucleotide encoding a dominant negative allele of a MMR gene is introduced into a cell expressing a secreted antigen. The cell becomes hypermutable as a result of the introduction of the gene. The cell is grown and conditioned medium from the cell is tested for the expression of antigenic polypeptides.
In another embodiment of the invention, a gene, or set of genes encoding for polypeptides or a combination therein, are introduced into a mammalian cell host that is defective in MMR. The cell is grown and clones are analyzed for antigens with enhanced antigenicity. In another embodiment of the invention, a method is provided for producing a cell- based screening assay to identify antigenic proteins as vaccines. A polynucleotide encoding a secreted antigen is introduced into a naturally MMR defective cell. The gene is hypermutable as a result of the introduction of MMR deficiency. The cell is grown and conditioned medium from the cell is tested for the expression of antigenic polypeptides.
In another embodiment of the invention, a method will be provided for restoring genetic stability in a cell containing a polynucleotide encoding for a dominant negative allele of a MMR gene. The expression of the dominant negative MMR gene is suppressed and the cell restores its genetic stability including but not limited to genetic stability within the antigen-encoding genes.
In another embodiment of the invention, a method will be provided for restoring genetic stability in a cell containing a polynucleotide encoding a dominant negative allele of an MMR gene and a newly selected phenotype. The expression of the dominant negative mismatch repair gene is suppressed and the cell restores its genetic stability and the new phenotype is stable.
These and other embodiments of the invention provide the art with methods that can generate enhanced mutability in cells and animals as well as providing cells and animals harboring potentially useful mutations for the large-scale production of highly antigenic polypeptides as potent vaccines.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure l: In situ β-galactosidase staining of TKPMS134/pCAR-OF or TKvect/pCAR-OF cells to assay for MMR defective cells containing genetically altered β- galactosidase genes. Arrows indicate Blue (β-galactosidase positive) cells. Figure 2: Schematic representation of sequence alterations of the D β-galactosidase gene produced by MMR defective host cells
Figure 3: Schematic representation of sec-hist secretion proteins for screening of structurally altered antigenic polypeptides and the sec-hist expression cassette (SEQ JD NO: 17). Panel A: Schematic representation of sec-hist protein; Panel B: Sequence of sec- hist expression cassette. In Panel B, the italic bold sequence represents a Hindlll site for subcloning; the double underlined sequence on the 5' end represents leader sequence from the human IL-2; the underlined sequence on the 3' end represents the poly histidine sequence followed by 2 termination codons; sequence in capital letters represents sequence from the polylinker region of pUC18; the polylinker contains the following restriction enzymes for cloning cDNAs: SacI-Sacπ-Notl-Xbal-Spel-BarnHI-Smal-Pstl-EcoRI. Figure 4: Schematic diagram for high throughput screening of conditioned medium from TK clones for the identification of antigenic sec-hist polypeptides. Assays employ an in vitro antigenicity test using splenocytes from naϊ've mice (non-primed) and antigen-exvosed (primed) mice. Clones exhibiting positive CM are then genetically analyzed to confirm structural alterations within the sec-hist sequence, followed by protein purification and retesting of purified proteins. Purified proteins with the best stimulatory activity are then screened in vivo for immunogenicity. The screening assay can be repeated for several rounds to add additional alterations within the antigen (long arrow).
The inventors have discovered a method for developing hypermutable cells producing therapeutic antigens by taking advantage of the conserved mismatch repair (MMR) process of host cells. Dominant negative alleles of such genes, when introduced into cells or transgenic animals, increase the rate of spontaneous mutations by reducing the effectiveness of DNA repair and thereby render the cells or animals hypermutable. Hypermutable cells or animals can then be utilized to develop new mutations in a gene or genes of interest. Blocking MMR in cells producing antigens (including, but not limited to, mammalian cells, plant cells, yeast cells, and prokaryotic cells) can enhance the rate of mutation within the gene encoding for the antigen that can be screened to identify clones producing structurally altered polypeptides with enhanced antigenicitiy and immunogenicity.
In one aspect of the invention, the methods are useful for the production of antigens that have increased antigenicity and/or immunogenicity. Such antigens may be used as immunogens to elicit immune responses in animals against these antigens.
The antigens may be derived from, for example, pathogenic organisms or cancer cells such that an immune response is directed against the pathogenic organism or cancer cell and exerts an effect on the organism or cancer cell. The effect may be, for example, to prevent, inhibit or terminate the growth of the pathogenic organism or cancer cell when an immunogenic amount of the antigen is administered to an animal.
The pathogenic organisms from which antigens may be derived include bacteria, fungi, parasitic protozoa, helminths, and viruses. Non-limiting examples include species of the following genera: Staphylococcus , Streptococcus, Bacillus, Bordetella, Clostridium, Escherichia, Haemophilus, Helicobacter, Klebsiella, Listeria, Salmonella, Vibrio, Yersinia, Neisseria, Treponema, Borrelia, Corynebacterium, Mycobacterium, Mycoplasma, Chlamydia, Acremonium, Aspergillus, Blastomyces, Candida, Acanthamoeba, Ascaris, Babesia, Cryptosporidium, Echinococcus, Entamoeba, Giardia, Necator, Ancylostoma, Unicinaria, Leishmania, Onchocerca, Plasmodium, Schistosoma, Strongyloides , Taenia, Toxoplasma, Trichinella, Trichomonas, Trichuris, Trypanosoma, Dirofilaria, Brugia, Wuchereria, and Eimeria. Non-limiting examples of viruses include adenoviras, arborviruses, coronavirus, cytomegalo virus, entero viruses, Epstein- Barr virus, hepatitis viruses, herpes viruses, immunodeficiency viruses (e.g. , HIV, FIV SIN), papilloma viruses, T-cell leukemia viruses, influenza viruses, mumps viruses, parainfluenzae viruses, parvoviruses, poxviruses, Rabies virus, respiratory syncytial virus, rhino viruses, rotaviruses, Rubella viruses, and varicella-zoster viruses.
The antigens derived from the pathogenic organisms, for example, may be antigens known to elicit an immune response, for which an enhanced immune response is desired, or the antigen may be one that is known to generate a weak response for which an enhanced response is desired. It is also possible that some antigens that did not previously elicit an immune response will become antigenic as a result of the methods of the invention and the phenomenon of hypermutability of cells which contain dominant negative alleles of mismatch repair genes.
The antigens produced by the method of the invention are novel immunogens that may be admimstered in an appropriate pharmaceutical carrier, such as an adjuvant, for administration to animals as a vaccine. The antigens of the invention may be administered to animals in immunogenic amounts such that an antibody and/or a cell-mediated immune response is elicited. The administration of the antigens of the invention may be administered as a single dose, or, preferably as a plurality of doses to effect a boosted immune response. The route of administration may be any accepted route of imήiunization including, for example, oral, intrmuscular, intrperitoneal, subcutaneous, intradermal, intranasal, or transdermal. Doses for humans can readily be extrapolated from animal studies as taught by
Katocs et al. , Chapter 27 of REMINGTON'S PHARMACEUTICAL SCIENCES, 18th Edition, Gennaro (Ed.) Mack Publishing Co., Easton, PA, 1990. Immunogenic dosages can be adjusted by one skilled in the art, and may vary depending on several factors, including the age, health, physical condition, weight, type and extent of the disease or disorder of the recipient, frequency of treatment, the nature of concurrent therapy, if required, and the nature and scope of the desired effect(s) (Nies et al, Chapter 3, GOODMAN & GILMAN'S THE PHARMACOLOGICAL BASIS OF THERAPEUTICS, 9th Ed. , Hardman et al. , Eds., McGraw-Hill, New York, NY, 1996). Typically, an immunogenic amount of the antigens of the invention will be in the range of about 5 to about 100 g.
The antigens of the present invention may be administered as single antigens or may be administered as combinations of antigens. As a non-limiting example, the antigen combinations may be antigens of the same pathogenic organism, or may be antigens of different pathogenic organisms, such that immune responses are elicited to more than one pathogenic organism.
The antigens of the present invention are hypermutated by the methods of the invention which take advantage of the mismatch repair system. The process of MMR, also called mismatch proofreading, is carried out by protein complexes in cells ranging from bacteria to mammalian cells. A MMR gene is a gene that encodes for one of the proteins of such a mismatch repair complex. Although not wanting to be bound by any particular theory of mechanism of action, a MMR complex is believed to detect distortions of the DNA helix resulting from non-complementary pairing of nucleotide bases. The non-complementary base on the newer DNA strand is excised, and the excised base is replaced with the appropriate base, which is complementary to the older DNA strand. In this way, cells eliminate many mutations that occur as a result of mistakes in DNA replication.
Dominant negative alleles cause a MMR defective phenotype even in the presence of a wild-type allele in the same cell. An example of a dominant negative allele of a MMR gene is the human gene hPMS2-134, which carries a truncating mutation at codon 134. The mutation causes the product of this gene to abnormally terminate at the position of the 134th amino acid, resulting in a shortened polypeptide containing the N-terminal 133 amino acids. Such a mutation causes an increase in the rate of mutations, which accumulate in cells after DNA replication. Expression of a dominant negative allele of a mismatch repair gene results in impairment of mismatch repair activity, even in the presence of the wild-type allele. Any allele that produces such effect can be used in this invention.
Dominant negative alleles of a MMR gene can be obtained from the cells of humans, animals, yeast, bacteria, or other organisms (Prolla T.A. et al. (1994) Science 264: 1091-1093; Strand M. et al. (1993) Nature 365:274-276; Su, S.S. et al. (1988) J. Biol. Chem. 263:6829-6835). Such alleles can be identified by screening cells for defective MMR activity. Cells from animals or humans with cancer can be screened for defective mismatch repair. Cells from colon cancer patients may be particularly useful. Genomic DNA, cDNA, or mRNA from any cell encoding a MMR protein can be analyzed for variations from the wild type sequence. Dominant negative alleles of a MMR gene can also be created artificially, for example, by producing variants of the hPMS2-134 allele or other MMR genes. Various techniques of site-directed mutagenesis can be used. The suitability of such alleles, whether natural or artificial, for use in generating hypermutable cells or animals can be evaluated by testing the mismatch repair activity caused by the allele in the presence of one or more wild-type alleles, to determine if it is a dominant negative allele.
A cell or an animal into which a dominant negative allele of a mismatch repair gene has been infroduced will become hypermutable. This means that the spontaneous mutation rate of such cells or animals is elevated compared to cells or animals without such alleles. The degree of elevation of the spontaneous mutation rate can be at least 2- fold, 5-fold, 10-fold, 20-fold, 50-fold, 100-fold, 200-fold, 500-fold, or 1000-fold that of the normal cell or animal. The use of chemical mutagens such as but limited to methane sulfonate, dimethyl sulfonate, O6-methyl benzadine, MNU, ENU, etc. can be used in MMR defective cells to increase the rates an additional 10 to 100 fold that of the MMR deficiency itself.
According to one aspect of the invention, a polynucleotide encoding for a dominant negative form of a MMR protein is infroduced into a cell. The gene can be any dominant negative allele encoding a protein, which is part of a MMR complex, for example, PMS2, PMS1, MLHI, or MSH2. The dominant negative allele can be naturally occurring or made in the laboratory. The polynucleotide can be in the form of genomic DNA, cDNA, RNA, or a chemically synthesized polynucleotide. The polynucleotide can be cloned into an expression vector containing a constitutively active promoter segment [such as but not limited to CMV, S V40, Elongation Factor (EF) or LTR sequences] or to inducible promoter sequences such as the steroid inducible pIND vector (InVifrogen), tetracycline, or MMTV, where the expression of the dominant negative MMR gene can be regulated. The polynucleotide can be introduced into the cell by transfection.
According to another aspect of the invention, a gene, a set of genes or a chimeric gene encoding for whole or parts of a therapeutic antigen can be transfected into MMR deficient cell hosts, the cell is grown and screened for clones containing genetically altered genes encoding for antigens with new biochemical features including but not limited to increased antigenicity. MMR defective cells may be of human, primates, mammals, rodent, plant, yeast or of the prokaryotic kingdom.
Transfection is any process whereby a polynucleotide is introduced into a cell. The process of transfection can be carried out in a living animal, e.g., using a vector for gene therapy, or it can be carried out in vitro, e.g. , using a suspension of one or more isolated cells in culture. The cell can be any type of eukaryotic cell, including, for example, cells isolated from humans or other primates, mammals or other vertebrates, invertebrates, and single celled organisms such as protozoa, yeast, or bacteria.
In general, transfection will be carried out using a suspension of cells, or a single cell, but other methods can also be applied as long as a sufficient fraction of the treated cells or tissue incorporates the polynucleotide so as to allow transfected cells to be grown and utilized. The protein product of the polynucleotide may be transiently or stably expressed in the cell. Techniques for transfection are well known. Available techniques for introducing polynucleotides include but are not limited to electroporation, transduction, cell fusion, the use of calcium chloride, and packaging of the polynucleotide together with lipid for fusion with the cells of interest. Once a cell has been transfected with the dominant negative MMR gene, the cell can be grown and reproduced in culture. If tlie transfection is stable, such that the gene is expressed at a consistent level for many cell generations, then a cell line results. An isolated cell is a cell obtained from a tissue of humans or animals by mechanically separating out individual cells and transferring them to a suitable cell culture medium, either with or without pretreatment of the tissue with enzymes, e.g., collagenase or trypsin. Such isolated cells are typically cultured in the absence of other types of cells. Cells selected for the introduction of a dominant negative allele of a mismatch repair gene may be derived from a eukaryotic organism in the form of a primary cell culture or an immortalized cell line, or may be derived from suspensions of single-celled organisms. A polynucleotide encoding for a dominant negative form of a MMR protein can be introduced into the genome of an animal by producing a transgenic animal. The animal can be any species for which suitable techniques are available to produce transgenic animals. For example, transgenic animals can be prepared from domestic livestock, e.g., bovine, swine, sheep, goats, horses, etc.; from animals used for the production of recombinant proteins, e.g., bovine, swine, or goats that express a recombinant polypeptide in their milk; or experimental animals for research or product testing, e.g., mice, rats, guinea pigs, hamsters, rabbits, etc. Cell lines that are determined to be MMR defective can then be used as a source for producing genetically altered genes encoding for therapeutic antigens in vitro by introducing whole, intact genes and/or chimeric genes encoding for a therapeutic antigen(s) into MMR defective cells from any tissue of the MMR defective animal.
Once a transfected cell line or a colony of transgenic animals has been produced, it can be used to generate new mutations in one or more gene(s) of interest. A gene of interest can be any gene naturally possessed by the cell line or transgenic animal or introduced into the cell line or transgenic animal. An advantage of using such cells or animals to induce mutations is that the cell or animal need not be exposed to mutagenic chemicals or radiation, which may have secondary harmful effects, both on the object of the exposure and on the workers. However, chemical mutagens may be used in combination with MMR deficiency, which renders such mutagens less toxic due to an undetermined mechamsm. Hypermutable animals can then be bred and selected for those producing genetically variable cells that may be isolated and cloned to identify new cell lines that are useful for producing structurally altered polypeptides. Once an altered polypeptide is identified, the dominant negative MMR gene allele can be removed by directly knocking out the allele by technologies used by those skilled in the art or by breeding to mates lacking the dominant negative allele to select for offspring with a desired trait and a stable genome. Another alternative is to use a CRE-LOX expression system, whereby the dominant negative allele is spliced from the animal genome once an animal containing a genetically diverse protein profile has been established. Yet another alternative is the use of inducible vectors such as the steroicLinduced pLND (InVitrogen) or pMAM (Clonetech) vectors which express exogenous genes in the presence of corticosteroids. Mutations can be detected by analyzing for alterations in the genotype of the cells or animals, for example by examining the sequence of genomic DNA, cDNA, messenger RNA, or amino acids associated with the gene of interest. Mutations can also be detected by screening for the production of antigenicity. A mutant polypeptide can be detected by identifying alterations in electrophoretic mobility, spectroscopic properties, or other physical or structural characteristics of a protein encoded by a mutant gene. One can also screen for altered function of the protein in situ, in isolated form, or in model systems. One can screen for alteration of any property of the cell or animal associated with the function of the gene of interest, such as but not limited to antigenicity.
According to another aspect of the invention, a high throughput mammalian cell- based assay is presented. A MMR defective cell line is transfected with a secretion cassette containing a leader sequence for secretion at the N-terminus fused to the target antigen. Cells are grown and clones are plated by limiting dilution into microtitre plates and conditioned medium are screened for antigenic peptides. The advantage of such an approach is that the antigen is more similar to the natural polypeptide than it would be if produced by bacterial, yeast or baculovims systems which tend to cause misfolding and/or distorted post-translational modifications.
Examples of mismatch repair proteins and nucleic acid sequences include the following:
PMS2 (mouse) (SEQ ID NO:5)
MEQTEGVSTE CAKAIKPIDG KSVHQICSGQ VILSLSTAVK ELIENSVDAG ATTIDLRLKD 60
YGVDLIEVSD NGCGVEEENF EGLALKHHTS KIQEFADLTQ VETFGFRGEA LSSLCALSDV 120
TISTCHGSAS VGTRLVFDHN GKITQKTPYP RPKGTTVSVQ HLFYTLPVRY KEFQRNIKKE 180
YSKMVQVLQA YCIISAGVRV SCTNQLGQGK RHAVVCTSGT SGMKENIGSV FGQKQLQSLI 240 PFVQLPPSDA VCEEYGLSTS GRHKTFSTFR ASFHSARTAP GGVQQTGSFS SSIRGPVTQQ 300
RSLSLSMRFY HMYNRHQYPF WLNVSVDSE CVDINVTPDK RQILLQEEK LLAVLKTSLI 360
GMFDSDANKL NVNQQPLLDV EGNLVKLHTA ELEKPVPGKQ DNSPSLKSTA DEKRVASISR 420
LREAFSLHPT KE1KSRGPET AELTRSFPSE KRGVLSSYPS DVISYRGLRG SQDKLVSPTD 480
SPGDCMDREK IEKDSGLSST SAGSEEEFST PEVASSFSSD YNVSSLEDRP SQETINCGDL 540 DCRPPGTGQS LKPEDHGYQC KALPLARLSP TNAKRFKTEE RPSNVNISQR LPGPQSTSAA 600 EVDVAIK NK RIVLLEFSLS SLAKR KQLQ H KAQNKHEL SYRKFRAKIC PGENQAAEDE 660 RKEISKSMF AEMEILGQFN GFIVTKLKE DLFLVDQHAA DEKYNFEMLQ QHTVLQAQRL 720
ITPQTLNLTA VNEAVLIENL EIFRKNGFDF VIDEDAPVTE RAKLISLPTS KNWTFGPQDI 780
DELIFMLSDS PGVMCRPSRV RQMFASRACR KSVMIGTALN ASEMKKLITH MGEMDHPWNC 840 PHGRPTMRHV ANLDVISQN 859
PMS2 (mouse cDNA) (SEQ JD NO:6) gaattccggt gaaggtcctg aagaatttcc agattcctga gtatcattgg aggagacaga 60 taacctgtcg tcaggtaacg atggtgtata tgcaacagaa atgggtgttc ctggagacgc 120 gtcttttccc gagagcggca ccgcaactct cccgcggtga ctgtgactgg aggagtcctg 180 catccatgga gcaaaccgaa ggcgtgagta cagaatgtgc taaggccatc aagcctattg 240 atgggaagtc agtccatcaa atttgttctg ggcaggtgat actcagttta agcaccgctg 300 tgaaggagtt gatagaaaat agtgtagatg ctggtgctac tactattgat ctaaggctta 360 aagactatgg ggtggacctc attgaagttt cagacaatgg atgtggggta gaagaagaaa 420 actttgaagg tctagctctg aaacatcaca catctaagat tcaagagttt gccgacctca 480 cgcaggttga aactttcggc tttcgggggg aagctctgag ctctctgtgt gcactaagtg 540 atgtcactat atctacctgc cacgggtctg caagcgttgg gactcgactg gtgtttgacc 600 ataatgggaa aatcacccag aaaactccct acccccgacc taaaggaacc acagtcagtg 660 tgcagcactt attttataca ctacccgtgc gttacaaaga gtttcagagg aacattaaaa 720 aggagtattc caaaatggtg caggtcttac aggcgtactg tatcatctca gcaggcgtcc 780 gtgtaagctg cactaatcag ctcggacagg ggaagcggca cgctgtggtg tgcacaagcg 840 gcacgtctgg catgaaggaa aatatcgggt ctgtgtttgg ccagaagcag ttgcaaagcc 900 tcattccttt tgttcagctg ccccctagtg acgctgtgtg tgaagagtac ggcctgagca 960 cttcaggacg ccacaaaacc ttttctacgt ttcgggcttc atttcacagt gcacgcacgg 1020 cgccgggagg agtgcaacag acaggcagtt tttcttcatc aatcagaggc cctgtgaccc 1080 agcaaaggtc tctaagcttg tcaatgaggt tttatcacat gtataaccgg catcagtacc 1140 catttgtcgt ccttaacgtt tccgttgact cagaatgtgt ggatattaat gtaactccag 1200 ataaaaggca aattctacta caagaagaga agctattgct ggccgtttta aagacctcct 1260 tgataggaat gtttgacagt gatgcaaaca agcttaatgt caaccagcag ccactgctag 1320 atgttgaagg taacttagta aagctgcata ctgcagaact agaaaagcct gtgccaggaa 1380 agcaagataa ctctccttca ctgaagagca cagcagacga gaaaagggta gcatccatct 1440 ccaggctgag agaggccttt tctcttcatc ctactaaaga gatcaagtct aggggtccag 1500 agactgctga actgacacgg agttttccaa gtgagaaaag gggcgtgtta tcctcttatc 1560 cttcagacgt catctcttac agaggcctcc gtggctcgca ggacaaattg gtgagtccca 1620 cggacagccc tggtgactgt atggacagag agaaaataga aaaagactca gggctcagca 1680 gcacctcagc tggctctgag gaagagttca gcaccccaga agtggccagt agctttagca 1740 gtgactataa cgtgagctcc ctagaagaca gaccttctca ggaaaccata aactgtggtg 1800 acctggactg ccgtcctcca ggtacaggac agtccttgaa gccagaagac catggatatc 1860 aatgcaaagc tctacctcta gctcgtctgt cacccacaaa tgccaagcgc ttcaagacag 1920 aggaaagacc ctcaaatgtc aacatttctc aaagattgcc tggtcctcag agcacctcag 1980 cagctgaggt cgatgtagcc ataaaaatga ataagagaat cgtgctcctc gagttctctc 2040 tgagttctct agctaagcga atgaagcagt tacagcacct aaaggcgcag aacaaacatg 2100 aactgagtta cagaaaattt agggccaaga tttgccctgg agaaaaccaa gcagcagaag 2160 atgaactcag aaaagagatt agtaaatcga tgtttgcaga gatggagatc ttgggtcagt 2220 ttaacctggg atttatagta accaaactga aagaggacct cttcctggtg gaccagcatg 2280 ctgcggatga gaagtacaac tttgagatgc tgcagcagca cacggtgctc caggcgcaga 2340 ggctcatcac accccagact ctgaacttaa ctgctgtcaa tgaagctgta ctgatagaaa 2400 atctggaaat attcagaaag aatggctttg actttgtcat tgatgaggat gctccagtca 2460 ctgaaagggc taaattgatt tccttaccaa ctagtaaaaa ctggaccttt ggaccccaag 2520 atatagatga actgatcttt atgttaagtg acagccctgg ggtcatgtgc cggccctcac 2580 gagtcagaca gatgtttgct tccagagcct gtcggaagtc agtgatgatt ggaacggcgc 2640 tcaatgcgag cgagatgaag aagctcatca cccacatggg tgagatggac cacccctgga 2700 actgccccca cggcaggcca accatgaggc acgttgccaa tctggatgtc atctctcaga 2760 actgacacac cccttgtagc atagagttta ttacagattg ttcggtttgc aaagagaagg 2820 ttttaagtaa tctgattatc gttgtacaaa aattagcatg ctgctttaat gtactggatc 2880 catttaaaag cagtgttaag gcaggcatga tggagtgttc ctctagctca gctacttggg 2940 tgatccggtg ggagctcatg tgagcccagg actttgagac cactccgagc cacattcatg 3000 agactcaatt caaggacaaa aaaaaaaaga tatttttgaa gccttttaaa aaaaaa 3056
PMS2 (human) (SEQ ID NO:7)
MERAESSSTE PAKAIKPIDR KSVHQICSGQ WLSLSTAVK ELVENSLDAG ATNIDLKLKD 60 YGVD IEVSD NGCGVEEENF EGLTLKHHTS KIQEFADLTQ VETFGFRGEA LSSLCALSDV 120 TISTCHASAK VGTRLMFDHN GKIIQ TPYP RPRGTTVSVQ QLFSTLPVRH KEFQRNIKKE 180 YAKMVQVLHA YCIISAGIRV SCTNQLGQGK RQPWCTGGS PSIKENIGSV FGQKQLQSLI 240 PFVQLPPSDS VCEEYGLSCS DALHNLFYIS GFISQCTHGV GRSSTDRQFF FINRRPCDPA 300 KVCRLVNEVY HMYNRHQYPF VVLNISVDSE CVDINVTPDK RQILLQEEKL LLAVLKTSLI 360 GMFDSDVNKL NVSQQPLLDV EGNLIKMHAA DLEKPMVEKQ DQSPSLRTGE EKKDVSISRL 420 REAFSLRHTT ENKPHSPKTP EPRRSPLGQK RGMLSSSTSG AISDKGVLRP QKEAVSSSHG 480 PSDPTDRAEV E DSGHGSTS VDSEGFSIPD TGSHCSSEYA ASSPGDRGSQ EHVDSQEKAP 540 ETDDSFSDVD CHSNQEDTGC KFRVLPQPTN LATPNTKRFK KEEILSSSDI CQKLVNTQDM 600 SASQVDVAVK INKKWPLDF SMSSLAKRIK QLHHEAQQSE GEQNYRKFRA KICPGENQAA 660 EDELRKEISK TMFAEMEIIG QFNLGFIITK LNEDIFIVDQ HATDEKYNFE MLQQHTVLQG 720 QRLIAPQTLN LTAVNEAVLI ENLEIFRKNG FDFVIDENAP VTERAKLISL PTSKN TFGP 780 QDVDELIFML SDSPGV CRP SRVKQMFASR ACRKSVMIGT ALNTSEMKKL ITHMGEMDHP 840 WNCPHGRPTM RHIANLGVIS QN 862
PMS2 (human cDNA) (SEQ ID NO:8) cgaggcggat cgggtgttgc atccatggag cgagctgaga gctcgagtac agaacctgct 60 aaggccatca aacctattga tcggaagtca gtccatcaga tttgctctgg gcaggtggta 120 ctgagtctaa gcactgcggt aaaggagtta gtagaaaaca gtctggatgc tggtgccact 180 aatattgatc taaagcttaa ggactatgga gtggatctta ttgaagtttc agacaatgga 240 tgtggggtag aagaagaaaa cttcgaaggc ttaactctga aacatcacac atctaagatt 300 caagagtttg ccgacctaac tcaggttgaa acttttggct ttcgggggga agctctgagc 360 tcactttgtg cactgagcga tgtcaccatt tctacctgcc acgcatcggc gaaggttgga 420 actcgactga tgtttgatca caatgggaaa attatccaga aaacccccta cccccgcccc 480 agagggacca cagtcagcgt gcagcagtta ttttccacac tacctgtgcg ccataaggaa 540 tttcaaagga atattaagaa ggagtatgcc aaaatggtcc aggtcttaca tgcatactgt 600 atcatttcag caggcatccg tgtaagttgc accaatcagc ttggacaagg aaaacgacag 660 ^ > L Ni tsi 1— ' - '
Ol Ul i o Ui
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TJ « F < N s rt r+ rt rt ιq >Q iQ rt Ω βJ BJ rt uQ BJ BJ Ω Ω rt uq PJ β) rt PJ u uq Ω BJ rt PJ Ω i-3 o « Ir1 to IO rt rt Ω Ω ιQ Ω rt rt rt iQ iQ rt rt rt uq uq Ω PJ uq rt o uq uq uq BJ BJ rt rt rt Ω rt cu uq r
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D S3 SO o TJ jjd
< co H S3 HI 1 fu Ω tq BJ rt sQ BJ Cu BJ Ω BJ u3 iQ uq uq uq Ω rt rt uq uq rt Ω uq Ω Ω rt BJ Ω Ω Ω rt Ω uq
(U Ω Ω CU ιQ Ω id BJ rt B BJ rt PJ uq BJ rt rt BJ BJ Ω uq uq rt Ω PJ rt o rt PJ uq uq PJ BJ r
2 TI < H < R PJ rt BJ Ω ιQ ιQ "3 Ω Ω rt Ω Ω PJ PJ BJ rt BJ Ω uq rt Ω uq uq rt Ω uq Ω uq rt BJ uq PJ Ω uq PJ
Ir1 H "d tr1 SO g Ω sQ Ω ιQ ιQ tQ rt uq uq BJ rt βJ iQ uq uq PJ BJ uq Ω BJ Ω BJ rt PJ rt J Ω BJ uq Ω Ω rt uq rt r ι-3 co CO s Ir1 P O O BJ rt BJ rt rt Q Cu PJ Ω rt rt PJ Ω rt BJ Ω pi DJ uq βJ uq Ω uq 0 rt Ω BJ rt BJ Ω uq uq rt uq
TJ Ir1 S3 IO « tr1 rt rt ιQ ιQ ιQ Ω rt Ω Ω uq BJ BJ uq rt BJ BJ uq Ω Ω rt rt Ω Ω uq BJ uq rt Ω rt Ω rt uq Ω α CO a O
W « Ki C
TJ O 77Λ OJ rt ιQ BJ PJ BJ BJ sQ uq u3 BJ Q BJ Ω Ω BJ BJ uq uq PJ uq rt BJ Ω cu uq Ω PJ u Ω rt J rt Ω
« ι-3 O rt u3 rt rt rt Ω BJ Ω rt rt BJ PJ BJ Ω O BJ BJ uq uq Ω uq Ω rt rt rt Ω Ω BJ uq Ω rt BJ Ω
CD J co ι-3 CO W rt rt rt ιQ ι£3 ιQ Ω PJ rt ιQ PJ BJ rt uq Ω rt uq rt uq Ω Ω Ω Ω BJ rt BJ uq Ω rt uq rt uq uq PJ BJ
IO H < S3 CO IO O rt rt cQ sQ BJ rt rt vQ Ω uq PJ Ω Ω Ω Ω Ω BJ uq BJ βJ BJ rt uq Ω rt Ω rt uq Ω BJ uq
< 50 H tr1 « H Cu Cu rt BJ rt ιQ rt BJ rt rt rt rt PJ BJ rt BJ uq Ω uq uq Ω BJ Ω PJ rt Ω Ω BJ PJ uq uq uq tr> CO S! O H H Θ 0) rt Ω Ω rt Ω Ω rt rt Ω sQ Ω BJ BJ uq uq rt Ω PJ uq Ω rt rt uq Ω PJ uq rt Cu rt Ω rt Ω Ω r
Ir1 ^ IO a HI fu sQ BJ Ω ιQ Ω u3 "3 Ω Ω uq PJ u PJ uq uq rt uq uq rt BJ Ω rt BJ BJ CU uq rt uq Ω Ω uq rt Ω uq lO H « O O O 2 fu rt rt BJ sQ iQ Ω rt BJ BJ rt Ω uq βJ PJ rt uq Ω Ω BJ Ω Ω uq BJ BJ rt BJ Ω Ω uq uq rt uq a *l CO ι-3 S3 p PJ rt rt O u3 ιQ BJ rt ιQ iQ Ω rt rt Ω Ω rt cu uq rt rt Ω BJ rt PJ uq rt uq rt BJ BJ β) rt Ω BJ
« H SO •-3 M Cu rt rt Ω BJ Ω Ω Ω BJ iQ Ω ιQ uq uq rt CU BJ rt Ω uq rt uq uq Ω Ω Ω uq PJ BJ rt uq uq rt PJ
PJ 2 < < α O Ό cu rt Ω Ω Ω Ω Ω Ω rt ιΩ BJ iQ Ω rt rt PJ uq Ω Ω Ω uq uq Ω rt PJ rt rt P) rt Ω rt Ω rt uq
CO O O ι-3 Ir1 < s— ^ BJ ιQ rt Ω rt rt Ω PJ BJ U2 iQ rt Ω BJ rt uq BJ rt rt uq Ω BJ rt U uq uq rt BJ Cu rt rt uq rt Ω
< SO o If M r+ Ω rt sQ rt O U3 iQ Ω Ω Ω uq uq rt rt βJ PJ uq uq uq Ω uq uq Ω uq uq uq BJ uq BJ uq uq Ω Ω iz< TJ S3 t"1 a w PJ BJ BJ ιQ Ω Ω PJ rt PJ BJ BJ PJ PJ uq Ω Ω fu PJ Ω rt Ω Ω BJ uq PJ uq uq rt OJ uq Ω Ω
M SO t1
S < tS Ω BJ ιQ ^q rt Ω iQ Ω BJ iQ rt u3 uq rt PJ BJ BJ cu Ω uq Ω Ω PJ rt cu uq rt uq rt rt Ω 3 fe tr1 i-3 t"1 PJ uQ BJ BJ Ω Ω iQ J BJ PJ ιQ rt uq uq PJ uq uq rt PJ uq Ω uq Ω uq PJ Ω uq uq uq rt PJ t"1 IO 3^ < 1 Hi l-l Ω PJ PJ BJ rt ιQ PJ Ω PJ iQ Ω rt PJ rt Ω rt Ω uq uq rt Ω PJ BJ uq rt PJ rt rt uq Ω rt uq
H « t-i M BJ Ω Ω Ω rt PJ Ω rt rt "3 Ω rt rt cu uq Ω BJ rt rt Ω rt rt Ω BJ uq BJ rt uq rt Ω uq rt rt Ω
2 O g a O a n- BJ rt rt CU iQ vQ iQ Ω Ω BJ J uq Ω PJ rt uq Ω uq rt rt uq rt uq rt BJ rt BJ Ω rt Ω uq PJ t"1 H O t-1 CO Ω ιq uq ιQ BJ rt rt BJ rt rt Ω PJ BJ uq Ω J uq CU Ω Ω BJ Ω uq Ω Ω BJ rt rt rt uq uq rt rt r
S ir> < TJ S t-l BJ BJ BJ rt Ω Ω Ω PJ uq Ω iQ Ω uq rt rt BJ PJ Ω Ω rt Ω rt BJ Ω Ω Ω rt rt rt Ω rt uq rt BJ ι-3 « t-< < Ώ α Ω ι Ω Ω BJ PJ iQ uq J iQ Ω Ω rt Ω BJ uq uq Ω uq Ω uq rt Ω rt uq rt P) fu rt Ω Ω BJ
HI l→ Ώ so M > BJ rt Ω Ω Ω BJ PJ "3 BJ rt BJ rt rt BJ Ω J rt rt Ω BJ Ω BJ uq rt Ω rt rt BJ uq Ω BJ PJ
O H 1-3 « o Ω Ω up Ω BJ iQ rt iQ BJ PJ Ω sQ PJ rt rt uq rt r Ω BJ uq rt Ω uq rt rt rt uq Ω BJ PJ rt uq uq pa IO t"1 to Ω rt rt Ω BJ Ω ^ iQ BJ iQ ιQ vQ BJ rt rt uq Ω rt rt uq uq BJ BJ BJ rt rt BJ BJ Ω BJ Ω PJ BJ Ω uq
O S3 " <n ι-3 Ω rt CU BJ ιQ BJ PJ Ω rt Ω up uq BJ rt rt rt rt Ω uq uq Ω uq Ω Ω rt uq rt rt rt Ω PJ rt
13 S3 S O O BJ Ω id rt Ω iQ BJ rt BJ iQ J Ω PJ rt rt uq rt uq uq uq BJ Ω rt PJ BJ rt BJ rt Ω PJ rt uq PJ
Ki a O H rf BJ rt ιQ IQ BJ Ω 0J rt Ω CU rt PJ PJ uq uq rt Ω rt uq rt uq uq Ω Ω rt BJ uq Ω rt uq uq Ω Ω PJ
TJ 2! a ι-3 o α n- Ω Ω sQ BJ rt rt BJ rt Ω BJ rt BJ uq Ω PJ Ω Ω rt rt BJ uq Ω rt rt BJ βJ Ω rt PJ rt Ω BJ ω t"1 s π < r rt BJ PJ vQ iQ sQ CU rt rt uq rt uq rt rt Ω rt rt Ω Ω Ω Ω rt rt PJ BJ rt βJ rt uq Ω rt Ω rt ι-3 « is H s*: BJ BJ Ω BJ BJ rt BJ Ω BJ Ω rt BJ uq β) BJ uq Ω rt BJ PJ βJ uq Ω Ω PJ BJ uq uq uq PJ BJ rt Ω
3 o O t-" BJ BJ rt ua rt rt rt rt iQ BJ BJ rt PJ BJ rt uq BJ 0 uq uq uq rt rt uq uq rt rt rt BJ uq rt Ω rt co t"1 •*d O H H PJ Ω vQ U3 ιQ rt Ω "3 fu uq rt PJ uq uq BJ PJ rt uq BJ uq Ω BJ Ω rt uq uq Ω uq rt rt PJ rt rt Ω
« IO « < a CU Ω rt Ω u tQ rt BJ J BJ BJ BJ rt Ω uq rt Ω uq uq BJ uq Ω uq Ω PJ Ω BJ uq uq uq Ω rt BJ uq
K M Ki σ tr1 Ki tQ rt BJ o BJ Ω rt rt BJ Ω PJ rt rt rt uq Ω Ω Ω BJ uq rt Ω rt uq PJ Ω βJ PJ βJ BJ uq uq
3 co S3 w o rt- rt rt BJ ιQ Ω Ω rt iQ rt Ω BJ BJ rt BJ rt rt BJ rt Ω Ω uq uq Ω rt rt Ω rt uq uq Ω rt Ω a ι-3 O H ι-3 "J ιQ rr u3 BJ BJ rt rt PJ Ω rt PJ BJ BJ uq uq β) uq rt Ω uq BJ Ω PJ uq uq u rt uq rt BJ uq rt
« O M w HI σ PJ rt u3 Ω BJ Ω rt Ω PJ rt rt Ω uq uq rt rt PJ Ω rt Ω Ω uq fu Ω uq Ω cu Ω rt rt rt BJ Ω ι-3 t-1 H « d ^ rf rt BJ O PJ Ω iQ O rt Ω Ω Ω rt uq BJ uq Ω rt uq uq βJ uq uq β) BJ uq uq βJ Ω rt Ω Ω rt α Ki O H HI H Ω rt BJ Ω BJ Ω rt iQ BJ uq CU Cu uq BJ J βJ PJ uq Ω uq uq Ω PJ uq uq Ω Ω uq rt rt rt rt uq
< TJ IO M rt rt rt rt ιβ rt rt u3 BJ PJ PJ Ω BJ PJ rt BJ BJ rt Ω Ω cu Ω rt rt (U PJ rt Ω Ω rt ω < H σ < rt- rt PJ uq ιQ U up "3 Ω o Ω uq PJ PJ uq BJ rt rt o uq Ω uq rt PJ uq U rt Ω Ω Ω uq t ^ Ki t-1 D SO u3 rt BJ PJ PJ iQ PJ Ω rt rt PJ Ω BJ cu Ω rt Ω rt uq PJ uq Ω PJ uq uq uq BJ rt rt Ω rt uq uq rt
P-^ T) t-1 t-1 a D BJ rt rt ιQ rt Ω ιp Ω rt rt rt rt Ω BJ rt uq rt uq Ω BJ uq PJ cu rt uq PJ rt uq rt rt α tr1 co s fj a up rt rt CU Ω Ω Ω DJ rt BJ iQ ιQ uq uq uq rt rt Ω Ω uq uq uq uq uq cu rt rt uq Ω Ω rt rt uq rt
H « o co CO o BJ BJ ιQ Ω BJ rt uq βJ uq BJ Ω J βJ rt BJ Ω uq Ω Ω uq BJ uq PJ cu rt uq rf uq BJ βJ rr rt uq
< H ^ ^d ι-3 w BJ BJ "3 BJ Ω uq PJ Ω J Ω rt BJ rt rt r BJ BJ Ω J BJ uq BJ uq BJ cu rt rt rt rt rt rt rt uq uq t-1 D tr" o O Ώ Ω BJ rt Ω Ω Ω Ω rt rt rt ιQ rt uq rt BJ rt BJ rt rt Ω uq BJ rt Ω BJ uq Ω uq rt uq Ω Ω rt uq u> ω to ι-> H1 ISO t t > M to to t to to to t to to t -1 t-> I-1 h-1 H> h-" t-> H1 h-1 H1 H1 -1 so 00 ~j σi o CO tO σ> -J -J -J σi ω t t I-1 I-1 o so so CO CO -J CS C ( l ω ω to t I-1 o O σs o CO to o o o o O o -J σi o 00 N3 σi o CO t σi o CO to Λ o O to as O J^ CO to as o CO to o o o o o l-1 o o o O O o o O o o o o o o o o o O σ o o O O o o o o o o o
SKTAETDVLF NKVESSGKNY SNVDTSVIPF QNDMHNDESG KNTDDCLNHQ ISIGDFGYGH 420 CSSEISNIDK NTKNAFQDIS MSNVS ENSQ TEYSKTCFIS SVKHTQSENG NKDHIDESGE 480 NEEEAGLENS SEISADEWSR GNILKNSVGE NIEPVKILVP EKSLPCKVSN NNYPIPEQMN 540 LNEDSCNKKS NVIDNKSGKV TAYDLLSNRV IKKPMSASAL FVQDHRPQFL IENPKTSLED 600 ATLQIEEL K TLSEEEKLKY EEKATKDLER YNSQMKRA1E QESQMSLKDG RKKIKPTSA 660 NLAQKHKLKT SLSNQPKLDE LLQSQIEKRR SQNIKMVQIP FSMK LKINF KKQNKVDLEE 720 KDEPCLIHNL RFPDA LMTS KTEVMLLNPY RVEEALLFKR LLENHKLPAE PLEKPIMLTE 780 SLFNGSHYLD VLYKMTADDQ RYSGSTYLSD PRLTANGFKI KLIPGVSITE NYLEIEGMAN 840 CLPFYGVADL KEILNAILNR NAKEVYECRP RKVISYLEGE AVRLSRQLP YLSKEDIQDI 900 IYRMKHQFGN EIKECVHGRP FFHHLTY PE TT 932
PMS1 (human) (SEQ JD NO:10) ggcacgagtg gctgcttgcg gctagtggat ggtaattgcc tgcctcgcgc tagcagcaag 60 ctgctctgtt aaaagcgaaa atgaaacaat tgcctgcggc aacagttcga ctcctttcaa 120 gttctcagat catcacttcg gtggtcagtg ttgtaaaaga gcttattgaa aactccttgg 180 atgctggtgc cacaagcgta gatgttaaac tggagaacta tggatttgat aaaattgagg 240 tgcgagataa cggggagggt atcaaggctg ttgatgcacc tgtaatggca atgaagtact 300 acacctcaaa aataaatagt catgaagatc ttgaaaattt gacaacttac ggttttcgtg 360 gagaagcctt ggggtcaatt tgttgtatag ctgaggtttt aattacaaca agaacggctg 420 ctgataattt tagcacccag tatgttttag atggcagtgg ccacatactt tctcagaaac 480 cttcacatct tggtcaaggt acaactgtaa ctgctttaag attatttaag aatctacctg 540 taagaaagca gttttactca actgcaaaaa aatgtaaaga tgaaataaaa aagatccaag 600 atctcctcat gagctttggt atccttaaac ctgacttaag gattgtcttt gtacataaca 660 aggcagttat ttggcagaaa agcagagtat cagatcacaa gatggctctc atgtcagttc 720 tggggactgc tgttatgaac aatatggaat cctttcagta ccactctgaa gaatctcaga 780 tttatctcag tggatttctt ccaaagtgtg atgcagacca ctctttcact agtctttcaa 840 caccagaaag aagtttcatc ttcataaaca gtcgaccagt acatcaaaaa gatatcttaa 900 agttaatccg acatcattac aatctgaaat gcctaaagga atctactcgt ttgtatcctg 960 ttttctttct gaaaatcgat gttcctacag ctgatgttga tgtaaattta acaccagata 1020 aaagccaagt attattacaa aataaggaat ctgttttaat tgctcttgaa aatctgatga 1080 cgacttgtta tggaccatta cctagtacaa attcttatga aaataataaa acagatgttt 1140 ccgcagctga catcgttctt agtaaaacag cagaaacaga tgtgcttttt aataaagtgg 1200 aatcatctgg aaagaattat tcaaatgttg atacttcagt cattccattc caaaatgata 1260 tgcataatga tgaatctgga aaaaacactg atgattgttt aaatcaccag ataagtattg 1320 gtgactttgg ttatggtcat tgtagtagtg aaatttctaa cattgataaa aacactaaga 1380 atgcatttca ggacatttca atgagtaatg tatcatggga gaactctcag acggaatata 1440 gtaaaacttg ttttataagt tccgttaagc acacccagtc agaaaatggc aataaagacc 1500 atatagatga gagtggggaa aatgaggaag aagcaggtct tgaaaactct tcggaaattt 1560 ctgcagatga gtggagcagg ggaaatatac ttaaaaattc agtgggagag aatattgaac 1620 ctgtgaaaat tttagtgcct gaaaaaagtt taccatgtaa agtaagtaat aataattatc 1680 caatccctga acaaatgaat cttaatgaag attcatgtaa caaaaaatca aatgtaatag 1740 ataataaatc tggaaaagtt acagcttatg atttacttag caatcgagta atcaagaaac 1800 ccatgtcagc aagtgctctt tttgttcaag atcatcgtcc tcagtttctc atagaaaatc 1860 ctaagactag tttagaggat gcaacactac aaattgaaga actgtggaag acattgagtg 1920 aagaggaaaa actgaaatat gaagagaagg ctactaaaga cttggaacga tacaatagtc 1980 aaatgaagag agccattgaa caggagtcac aaatgtcact aaaagatggc agaaaaaaga 2040 taaaacccac cagcgcatgg aatttggccc agaagcacaa gttaaaaacc tcattatcta 2100 atcaaccaaa acttgatgaa ctccttcagt cccaaattga aaaaagaagg agtcaaaata 2160 ttaaaatggt acagatcccc ttttctatga aaaacttaaa aataaatttt aagaaacaaa 2220 acaaagttga cttagaagag aaggatgaac cttgcttgat ccacaatctc aggtttcctg 2280 atgcatggct aatgacatcc aaaacagagg taatgttatt aaatccatat agagtagaag 2340 aagccctgct atttaaaaga cttcttgaga atcataaact tcctgcagag ccactggaaa 2400 agccaattat gttaacagag agtcttttta atggatctca ttatttagac gttttatata 2460 aaatgacagc agatgaccaa agatacagtg gatcaactta cctgtctgat cctcgtctta 2520 cagcgaatgg tttcaagata aaattgatac caggagtttc aattactgaa aattacttgg 2580 aaatagaagg aatggctaat tgtctcccat tctatggagt agcagattta aaagaaattc 2640 ttaatgctat attaaacaga aatgcaaagg aagtttatga atgtagacct cgcaaagtga 2700 taagttattt agagggagaa gcagtgcgtc tatccagaca attacccatg tacttatcaa 2760 aagaggacat ccaagacatt atctacagaa tgaagcacca gtttggaaat gaaattaaag 2820 agtgtgttca tggtcgccca ttttttcatc atttaaccta tcttccagaa actacatgat 2880 taaatatgtt taagaagatt agttaccatt gaaattggtt ctgtcataaa acagcatgag 2940 tctggtttta aattatcttt gtattatgtg tcacatggtt attttttaaa tgaggattca 3000 ctgacttgtt tttatattga aaaaagttcc acgtattgta gaaaacgtaa ataaactaat 3060 aac 3063
MSH2 (human) (SEQIDNO:l1)
MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT 60
QGVIKYMGPA GAKNLQS VL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKEND YLA 120 YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD 180
NDQFSNLEAL LIQIGPKECV LPGGETAGD GKLRQIIQRG GILITERKKA DFSTKDIYQD 240
LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM 300
KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQ IKQPL MDKNRIEERL 360
NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA 420 LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE 480
LREI NDLEK KMQST ISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS 540
TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE P QTLNDVLA 600
QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD 660
KQMFHIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCΞSA EVSIVDCILA RVGAGDSQLK 720 GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAAISEYI ATKIGAFCMF 780
ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV 840
IECAKQKALE LEEFQYIGES QGYDXMEPAA KKCY EREQG EKIIQEF SK VKQMPFTEMS 900
EENITIKLKQ LKAEVIAKNN SFVNEIISRI KVTT 934
MSH2 (human cDNA) (SEQ JD NO: 12) ggcgggaaac agcttagtgg gtgtggggtc gcgcattttc ttcaaccagg aggtgaggag 60 gtttcgacat ggcggtgcag ccgaaggaga cgctgcagtt ggagagcgcg gccgaggtcg 120 gcttcgtgcg cttctttcag ggcatgccgg agaagccgac caccacagtg cgccttttcg 180 accggggcga cttctatacg gcgcacggcg aggacgcgct gctggccgcc cgggaggtgt 240 ^ > > Ni Ni
O ft o IΛ O \ O uq uq Ω uq Ω rt rt Ω uq rt rt Ω rt Ω cu fu uq fl) rt rt fl) fl) rt rt uq uq uq uq rt Ω rt rt uq rt uq uq rt rt Ω uq rt Ω fl) rt uq cu fl) uq uq rt Ω uq Ω rt rt- rt Ω cu Ω uq Ω uq uq rt rt fl) Ω rt rt rt rt uq uq Ω Ω uq uq Ω uq rt Ω Ω Ω fl) rt Ω fl) fl) rt cu uq rt fu rt uq Ω rt Ω rt cu rt rt rt Ω uq Ω Ω fl) uq cu fl) rt Ω uq uq Ω uq rt uq rt rt uq rt rt uq uq cu rt rt rt rt rt rt rt rt uq rt cu cu rt- rt Ω uq cu rt rt 0) rt uq uq uq rt uq rt uq uq Ω rt rt uq Ω uq uq uq uq uq uq uq uq fl) Ω uq rt rt cu fu rt uq uq uq uq uq Ω uq uq uq Ω
Ω uq Ω rt uq rt rt rt Ω uq Ω rt Ω uq uq Ω rt rt Ω fl) rt rt uq Ω rt rt fl) uq rt cu Ω rt rt Ω rt rt uq fl) rt rt rt Ω u rt rt BJ rt rt rt [u Ω uq rt rt Ω fl) uq D) Ω uq fl) Ω fl) rt rtuq rt rt rt- Ω uq uq Ω uq Ω uq uq uq uq Ω rt Ω Ω cu uq i rt rt uq fl) Ω rt Ω cu Ω fl) rt Ω uq rt uq BJ rt uq DJ Ω uq rt rt BJ Ω uq uq uq uq rt Ω uq rt Ω rt rt cu rt Ω Ω rt rt uq rt fl) rt rt uq
Ω Ω rt uq P> rt uq rt rt rt fl) rt rt uq rt rt rt rt BJ uq Ω rt rt uq rt rt uq rt uq uq uq rt uq rt uq uq uq Ω uq Ω Ω uq uq uq rt uq Ω uq uq Ω Ω rt uq uq rt uq uq uq uq rt uq uq rt fl) uq uq rt Ω rt rt rt Ω rt Ω rt rt rt cu uq fl) uq rt rt uq rt fl) rt fl) uq Ω rt fl) uq rt fl) uq rt Ω Ω rt Ω uq rt uq rt Ω uq Ω rt uq rt fl) fl) rt rt Ω uq rt uq Ω rt rt uq rt fl) uq uq rt rt uq Ω uq rt rt rt uq uq uq uq rt uq rt Ω uq uq Ω fl) uq Ω uq rt uq uq Ω Ω uq Ω uq uq uq rt uq rt rt uq cu Ω Ω Ω a Ω uq rt Ω rt rt rt rt uq rt Ω uq rt uq fl) rt Ω Ω fl) rt rt
Cu Ω rt rt rt rt rt Ω Ω uq uq u Ω rt rt rtrt rt rt uq rt rt fl) uq Ω rt rt rt rt uq uq cu uq rt rt rt rt- uq uq uq uq Ω uq rt rt rt uq rt uq uq Ω uq cu uq Ω Ω rt rt uq Ω Ω rt Ω rt uq rt uq rt rt cu p) rt rt Ω Ω rt uq rt Ω rt rt rt rt rt Ω rt Ω rt uq uq rt uq uq rt rt- Ω rt rt uq rt uq Ω Ω rt rt Ω rt rt rt rt uq uq rt uq Ω rt rt rt rt Ω Ω rt Ω rt rt rt Ω uq uq rt Ω uq uq Ω Ω uq Ω rt uq rt Ω uq Ω Ω Ω uq rt uq Ω Ω rt uq rt Ω uq rt fl) rt uq rt Ω uq rt rt uq uq rt fl) uq rt rt Ω cu rt
Ω rt fl) uq rt Ω rt rt rt rt u rt rt Ω rt rt rt Ω Ω Ω uq Ω Ω rt rt Ω cu Ω fl) rt Ω rt uq Ω rr Ω rt rt Ω uq Ω uq rt rt uq uq uq Ω rt Ω rt uq rt Ω rt uq uq Ω rt rt rt rt- rt uq uq Ω rt uq uq uq uq uq uq rt uq Ω uq uq Ω uq rt Ω uq rt uq fl) uq fl) uq uq uq uq rt rt rt rt rt Ω rt rt rt rt rt Cu rt Ω Ω cu uq uq rt rt rt Ω rt Ω Ω rt uq uq uq
Ω uq uq uq rt Ω Ω uq Ω Ω rt uq Ω rt uq Ω Ω rt rt Ω cu fl) rt rt rt uq fl) rt fl) rt rt uq rt Ω Ω rt uq uq Ω rt uq rt Ω uq uq cu rt Ω uq uq rt cu Ω Ω uq uq uq uq uq uq uq Ω uq uq uq rt rt rt uq Ω rt Ω rt Ω uq rt rt u uq uq cu uq Ω fu rt rt rt rt Ω rt uq rt uq uq Ω rt rt Ω Ω rt rt uq Ω uq rt rt rt Ω Ω rt Ω Ω rt rt rt Ω Ω Ω rt uq rt Ω rt Ω rt rt rt rt rt rt rt uq rt rt Ω Ω uq uq uq uq uq cu uq rt rt uq uq rt rt rt Ω rt uq Ω uq fl) Ω rt uq uq rt uq Ω uq rt uq
Ω rt rt Ω Ω rt Ω rt rt Ω rt uq rt Ω uq uq rt rt Ω fl) u Ω uq Ω fl) uq Ω rt rt uq rt uq
BJ BJ uq Ω rt rt rt Ω uq rt rt rt rt rt uq Ω uq Ω Ω Ω rt Ω Cu uq Ω fl) uq fl) fl) fl) uq Ω uq Ω fl) rt uq
Ω rt uq Ω Ω uq uq rt uq rt uq uq uq Ω uq uq uq uq uq uq Ω Ω Ω Ω uq Ω rt uq ct rt fu uq uq uq rt uq Ω uq Ω Ω rt Ω rt rt Ω uq Ω Ω rtrt rt fl) uq Ω rt Ω rt Ω fl) cu cu Ω rt uq Ω rt- Ω
Ω cu uq rt uq Ω Ω uq Ω Ω rt rt rt uq uq uq rt rt uq Ω rt uq Ω rt rt rt rt- uq uq uq uq rt rt rt uq Ω Ω rt uq Ω uq rt uq Ω uq rt uq Ω uq Ω Ω Ω uq Ω uq uq Ω Ω uq Ω cu uq rt Ω rt rt rt rt rt Ω Ω rt uq rt rt uq rt rt rt rt u rt uq Ω rt rt rt Ω uq uq rt Ω uq rt uq uq Ω Ω rt Ω rt fl) uq uq fl) rt fl) rt rt Ω uq rt uq cu rt uq Ω uq rt uq uq
Ω uq Ω uq rt uq uq uq uq Ω fl) cu uq Ω uq rt fl) fl) Ω rt uq uq Ω rt uq uq uq Ω fl) rt uq l) uq uq rt rt rt Ω rt Ω Ω uq uq rt rt uq rt Ω rt fl) rt rt rt Ω rt f rt Ω cu uq rt uq rt Ω uq uq uq rt Ω cu rt rt rt uq rt cu rt uq uq Ω Cu uq rt Ω uq rt uq Ω uq Ω uq rt rt uq uq uq uq uq Ω rt uq uq Ω uq rt fl) fl) rt uq fl) Ω uq Ω rt fl) fl) uq rt Ω uq rt cu cu Ω Ω uq Ω rt uq rt Ω rt Ω rt Ω rt rt Ω rt rt fl) rt Ω Ω rt cu rt rt Ω rt Ω rt uq uq uq rt rt fl) rt uq uq rt rt uq Ω Ω uq rt uq rt uq uq rt uq rt rt- uq uq rt Ω cu uq Ω rt
CU uq Ω rt uq Ω Ω uq uq uq rt uq uq Ω Ω Ω rt rt Ω rt rt cu uq rt Ω Ω rt uq Ω
Ω Ω uq cu rt rt uq Ω uq uq uq rt Ω rt rt Ω rt rt uq uq rt Ω rt rt Ω rt rt- Ω fl) rt rt rt Ω uq rt uq uq uq rt uq rt rt rt uq Ω Ω rt uq uq uq uq uq uq uq rt rt rt Cu uq Ω uq uq Ω Ω uq rt uq
Cu uq fl) rt rt uq Ω fl) rt uq rt uq uq rt uq Ω Ω uq rt rt uq Ω rt Ω Ω rt fl) u uq uq cu uq Ω
Ω rt rt Ω rt rt rt Ω Ω Ω rt uq rt uq uq uq Ω rt rt Ω rt rt cu rt rt Ω uq rt uq Ω rt rt uq uq rt rt rt rt rt rt rt rt rt rt Ω uq Ω rt rt rt rt uq Ω uq rt Ω rt rt rt uq uq rt rt uq Ω Ω Ω rt Ω uq rt uq uq uq uq Ω uq rt uq uq uq Ω Ω u uq uq DJ Ω uq Ω uq Ω uq Ω uq rt Ω rt Ω uq Ω rt uq rt rt Ω rt Ω Ω rt Ω Ω uq Ω uq uq uq rt rt rt rt rt
Ω uq uq rt rt rt rt Ω rt uq fu Ω rt Ω Ω rt rt rt rt cu Ω rt Ω uq rt- uq fl) uq rt Ω rt rt uq
Cu rt uq rt rt Ω uq Ω uq Ω rt rt¬ uq Ω uq rt fl) rt Ω rt rt cu Ω rt rt rt uq uq rt uq rt uq Ω Ω ft) rt rt rt Ω Ω Ω rt Ω Ω Ω Ω Ω rt uq rt Ω Ω rt uq rt rt Ω Ω rt rt Ω rt uq rt uq u rt rt Ω uq rt rt Ω Ω Ω Ω rt rt Ω uq rt rt rt¬ rt rt fl) rt rt Ω rt rt Ω fl) rt rt rt rt rt uq uq Ω uq uq rt rt rt rt rt uq uq uq uq uq Ω Ω uq Ω uq rt uq uq uq uq rt Ω rt Ω Ω uq rt Ω rt rt rt uq uq uq Ω rt Ω rt rt Ω Ω rt Ω rt rt rt uq rt rt rt rt uq uq uq uq
Ω rt fl) rt rt uq rt rt Ω uq rt rt rt Ω rt rt rt rt D) rt rt uq rt uq rt Ω rt rt uq fl) Ω rt uq uq rt
Ω uq uq uq BJ rt uq rt Ω uq rt uq fl) Ω uq uq rt Ω Ω rt uq uq uq uq uq Ω uq rt rt Ω uq rt Ω rt rt uq to t t t t t to to to to to to to t-1 (-> t-1 t-1 (-> co σs σs ω ω ω to to o so en ω t t o o as o >fc. to σs o to o to as o to σs o t o to as o to as t σs o to o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o
cagtaatgga atgaaggtaa tattgataag ctattgtctg taatagtttt atattgtttt 2940 atattaaccc tttttccata gtgttaactg tcagtgccca tgggctatca acttaataag 3000 atatttagta atattttact ttgaggacat tttcaaagat ttttattttg aaaaatgaga 3060 gctgtaactg aggactgttt gcaattgaca taggcaataa taagtgatgt gctgaatttt 3120 ataaataaaa tcatgtagtt tgtgg 3145
MLH1 (human) (SEQ JD NO:13)
MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ 60 IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA 120 DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV 180 GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF 240 KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP 300 QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV 360 KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS 420 SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE 480 MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEV REMLHNHSF VGCVNPQWAL 540 AQHQTKLYLL NTTKLSEELF YQILIYDFAN FGVLRLSEPA PLFDLAMLAL DSPESGWTEE 600 DGPKEGLAEY IVEFLKKKAE MLADYFSLEI DEEGNLIGLP LLIDNYVPPL EGLPIFILRL 660 ATEVN DEEK ECFESLSKEC AMFYSIRKQY ISEESTLSGQ QSEVPGSIPN S K TVEHIV 720 YKALRSHILP PKHFTEDGNI LQLANLPDLY KVFERC 756
MLH1 (human) (SEQ IDNO:14) cttggctctt ctggcgccaa aatgtcgttc gtggcagggg ttattcggcg gctggacgag 60 acagtggtga accgcatcgc ggcgggggaa gttatccagc ggccagctaa tgctatcaaa 120 gagatgattg agaactgttt agatgcaaaa tccacaagta ttcaagtgat tgttaaagag 180 ggaggcctga agttgattca gatccaagac aatggcaccg ggatcaggaa agaagatctg 240 gatattgtat gtgaaaggtt cactactagt aaactgcagt cctttgagga tttagccagt 300 atttctacct atggctttcg aggtgaggct ttggccagca taagccatgt ggctcatgtt 360 actattacaa cgaaaacagc tgatggaaag tgtgcataca gagcaagtta ctcagatgga 420 aaactgaaag cccctcctaa accatgtgct ggcaatcaag ggacccagat cacggtggag 480 gacctttttt acaacatagc cacgaggaga aaagctttaa aaaatccaag tgaagaatat 540 gggaaaattt tggaagttgt tggcaggtat tcagtacaca atgcaggcat tagtttctca 600 gttaaaaaac aaggagagac agtagctgat gttaggacac tacccaatgc ctcaaccgtg 660 gacaatattc gctccatctt tggaaatgct gttagtcgag aactgataga aattggatgt 720 gaggataaaa ccctagcctt caaaatgaat ggttacatat ccaatgcaaa ctactcagtg 780 aagaagtgca tcttcttact cttcatcaac catcgtctgg tagaatcaac ttccttgaga 840 aaagccatag aaacagtgta tgcagcctat ttgcccaaaa acacacaccc attcctgtac 900 ctcagtttag aaatcagtcc ccagaatgtg gatgttaatg tgcaccccac aaagcatgaa 960 gttcacttcc tgcacgagga gagcatcctg gagcgggtgc agcagcacat cgagagcaag 1020 ctcctgggct ccaattcctc caggatgtac ttcacccaga ctttgctacc aggacttgct 1080 ggcccctctg gggagatggt taaatccaca acaagtctga cctcgtcttc tacttctgga 1140 agtagtgata aggtctatgc ccaccagatg gttcgtacag attcccggga acagaagctt 1200 gatgcatttc tgcagcctct gagcaaaccc ctgtccagtc agccccaggc cattgtcaca 1260 gaggataaga cagatatttc tagtggcagg gctaggcagc aagatgagga gatgcttgaa 1320 ctcccagccc ctgctgaagt ggctgccaaa aatcagagct tggaggggga tacaacaaag 1380 gggacttcag aaatgtcaga gaagagagga cctacttcca gcaaccccag aaagagacat 1440 cgggaagatt ctgatgtgga aatggtggaa gatgattccc gaaaggaaat gactgcagct 1500 tgtacccccc ggagaaggat cattaacctc actagtgttt tgagtctcca ggaagaaatt 1560 aatgagcagg gacatgaggt tctccgggag atgttgcata accactcctt cgtgggctgt 1620 gtgaatcctc agtgggcctt ggcacagcat caaaccaagt tataccttct caacaccacc 1680 aagcttagtg aagaactgtt ctaccagata ctcatttatg attttgccaa ttttggtgtt 1740 ctcaggttat cggagccagc accgctcttt gaccttgcca tgcttgcctt agatagtcca 1800 gagagtggct ggacagagga agatggtccc aaagaaggac ttgctgaata cattgttgag 1860 tttctgaaga agaaggctga gatgcttgca gactatttct ctttggaaat tgatgaggaa 1920 gggaacctga ttggattacc ccttctgatt gacaactatg tgcccccttt ggagggactg 1980 cctatcttca ttcttcgact agccactgag gtgaattggg acgaagaaaa ggaatgtttt 2040 gaaagcctca gtaaagaatg cgctatgttc tattccatcc ggaagcagta catatctgag 2100 gagtcgaccc tctcaggcca gcagagtgaa gtgcctggct ccattccaaa ctcctggaag 2160 tggactgtgg aacacattgt ctataaagcc ttgcgctcac acattctgcc tcctaaacat 2220 ttcacagaag atggaaatat cctgcagctt gctaacctgc ctgatctata caaagtcttt 2280 gagaggtgtt aaatatggtt atttatgcac tgtgggatgt gttcttcttt ctctgtattc 2340 cgatacaaag tgttgtatca aagtgtgata tacaaagtgt accaacataa gtgttggtag 2400 cacttaagac ttatacttgc cttctgatag tattccttta tacacagtgg attgattata 2460 aataaataga tgtgtcttaa cata 2484
hPMS2-134 (human) (SEQ ID NO:15)
MERAESSSTE PAKAIKPIDR KSVHQICSGQ VVLSLSTAVK ELVENSLDAG ATNIDLKLKD 60
YGVDLIEVSD NGCGVEEENF EGLTLKHHTS KIQEFADLTQ VETFGFRGEA LSSLCALSDV 120 TISTCHASAK VGT 133
hPMS2-134 (human cDNA) (SEQ ID NO: 16) cgaggcggat cgggtgttgc atccatggag cgagctgaga gctcgagtac agaacctgct 60 aaggccatca aacctattga tcggaagtca gtccatcaga tttgctctgg gcaggtggta 120 ctgagtctaa gcactgcggt aaaggagtta gtagaaaaca gtctggatgc tggtgccact 180 aatattgatc taaagcttaa ggactatgga gtggatctta ttgaagtttc agacaatgga 240 tgtggggtag aagaagaaaa cttcgaaggc ttaactctga aacatcacac atctaagatt 300 caagagtttg ccgacctaac tcaggttgaa acttttggct ttcgggggga agctctgagc 360 tcactttgtg cactgagcga tgtcaccatt tctacctgcc acgcatcggc gaaggttgga 420 acttga 426
For further information on the background of the invention the following references may be consulted, each of which is incorporated herein by reference in its entirety: 1. John, TJ. (2000) The final stages of the global eradication of polio. New Engl. J. Med 14:806-807.
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The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples which are provided herein for purposes of illustration only, and are not intended to limit the scope of the invention. EXAMPLE 1: Stable expression of dominant negative MMR genes in cells results in widespread mutations of a reporter gene and its encoded polypeptide.
Expression of a dominant negative allele in an otherwise MMR proficient cell could render these host cells MMR deficient (Nicolaides, N.C. et al. (1998) Mol.Cell. Biol. .18: 1635-1641). The creation of MMR deficient cells can lead to the generation of genetic alterations throughout the entire genome of a host organisms offspring, yielding a population of genetically altered offspring or siblings that may produce biochemicals with altered properties. This patent application teaches of the use of dominant negative MMR genes in antigen-producing cells, including but not limited to rodent, human, primate, yeast, insect, and prokaryotic cells producing proteins that may serve as therapeutic antigens for vaccination. The cell expression systems described above that are used to produce antigens are well known by those skilled in the art of vaccine therapeutics. To demonstrate the ability to create MMR defective mammalian cells using dominant negative alleles of MMR genes, we first transfected a MMR proficient rodent cell line with an expression vector containing the human the previously published dominant negative PMS2 mutant referred herein as PMSl 34 (cell line referred to as TKPMS134), or with no insert (cell line referred to as TKvec). A fragment contaimng the PMSl 34 cDNA was cloned into the pEF expression vector which contains the constitutively active elongation factor promoter along with the neomycin resistance gene as selectable marker. The results showed that the PMSl 34 mutant could exert a robust dominant negative effect, resulting in biochemical and genetic manifestations of MMR deficiency. A brief description of the methods are provided below.
A hallmark of MMR deficiency is the generation of unstable microsatellite repeats in the genome of host cells. This phenotype is referred to as microsatellite instability (MI). MI consists of deletions and/or insertions within repetitive mono-, di- and/or tri nucleotide repetitive sequences throughout the entire genome of a host cell. Extensive genetic analysis eukaryotic cells have found that the only biochemical defect that is capable of producing MI is defective MMR. In light of this unique feature that defective MMR has on promoting MI, it is now used as a biochemical marker to survey for lack of MMR activity within host cells.
A method used to detect MMR deficiency in eukaryotic cells is to employ a reporter gene that has a polynucleotide repeat inserted within the coding region that disrupts its reading frame due to a frame shift. In the case where MMR is defective, the reporter gene will acquire random mutations (i.e. insertions and/or deletions) within the polynucelotide repeat yielding clones that contain a functional reporter gene. An example of the ability to alter desired genes via defective MMR comes from experiments using Syrian Hamster fibroblasts (TK) cells (described above), where a mammalian expression construct containing a defective β-galactosidase gene (referred to as pCAR-OF) was transfected into TKPMS 134 or TKvect cells as described above. The pCAR-OF vector consists of a β-galactosidase gene containing a 29-basepair poly-CA tract inserted at the 5' end of its coding region, which causes the wild-type reading frame to shift out-of-irame. This chimeric gene is cloned into the pCEP4, which contains the constitutively cytomegalovirus (CMN) promoter upstream of the cloning site and also contains the hygromycin-resistance (HYG) gene that allows for selection of cells containing this vector. The pCAR-OF reporter cannot generate β-galactosidase activity unless a frame-restoring mutation (i.e., insertion or deletion) arises following transfection into a host. Another reporter vector called pCAR-JJF contains a β-galactosidase in which a 27-bp poly-CA repeat was cloned into the same site as the pCAR-OF gene, but it is biologically active because the removal of a single repeat restores the open reading frame and produces a functional chimeric β-galactosidase polypeptide (not shown). The pCAR vectors also contain the neomycin resistance gene as selectable marker. In these proof-of-concept studies, TKPMS 134 and TKvect cells were transfected with the pCAR-OF reporter vector and selected for 17 days in neomycin plus hygromycin selection medium. After the 17th day, resistant colonies were stained for β-galactosidase production to determine the number of clones containing a genetically altered β-galactosidase gene. All conditions produced a relatively equal number of neomycin hygromycin resistant cells, however, only the cells expressing the PMS 134 dominant negative allele (TKPMS 134) contained a subset of clones that were positive for β-galactosidase activity (Table 1). This result was also observed using a similar experimental strategy with a MMR proficient human cell line (data not shown). Table 1 shows the data from these experiments, where cell colonies were stained in situ for β-galactosidase activity and scored for activity. Cells were scored positive if the colonies turned blue in the presence of X-gal substrate and scored negative if colonies remained white. Analysis of triplicate experiments showed a significant increase in the number of β-galactosidase positive cells in the TKPMS 134 cultures, while no β-galactosidase cells were seen in the control TKvect cells.
Table 1. Number of TKPMS134 and TKvect cells containing functional β- galactosidase gene as a result of MMR deficiency.
Cells White Colonies Blue Colonies % Clones with altered B-gal
TKvect 65 +/- 9 0 0/65 = 0%
TKPMS 134 40 +/- 12 28 +/- 4 28/68 = 41%
Table 1. β-galactosidase expression of HBvec, HBPMS2 and HB134 cells transfected with pCAR-OF reporter vectors. Cells were transfected with the pCAR-OF β-galactosidase reporter plasmid. Transfected cells were selected in hygromycin and G418, expanded and stained with X-gal solution to measure for β-galactosidase activity (blue colored cells). 3 plates each were analyzed by microscopy. The results below represent the mean +/- standard deviation of these experiments.
TKPMS134/pCAR-OF clones that were pooled and expanded also showed a number of cells that contained a functional β-galactosidase gene. No β-galactosidase positive cells were observed in TKvect cells transfected with the pCAR-OF vector. These data are shown in Figure 1 where the dark staining in panel B represent β-galactosidase positive cells present in the TKPMS 134/pCAR-OF cultures while none are found in the TKvect cells grown under similar conditions (panel A). These data demonstrate the ability of dominant negative alleles of MMR genes to generate in vivo gene alterations, which allows for the rapid screening of clones with altered polypeptides exhibiting new biochemical features. To confirm that alterations within the nucleotide sequences of the β-galactosidase gene was indeed responsible for the in vivo β-galactosidase activity present in TKPMS 134 clones, RNA was isolated from TKPMS 134/pCAR-OF and TKvect/pCAR-OF and the β- galactosidase mRNA primary structure was examined by reverse transcriptase polymerase chain reaction (RT-PCR) amplification and sequencing. Sequence analysis of β- galactosidase message from TKvect cells found no structural alterations in the input gene sequence. Analysis of the β-galactosidase message from TKPMS134 cells found several changes within the coding sequences of the gene. These sequence alterations included insertion and deletions of the poly-CA tract in the amino terminus as expected. Other alterations included insertions of sequences outside of the poly-CA repeat as well as a series of single base alterations (transversions and transitions) contained throughout the length of the gene.
In situ X-gal staining
For in situ analysis, 100,000 cells are harvested and fixed in 1% gluteraldehyde, washed in phosphate buffered saline solution and incubated in 1 ml of X-gal substrate solution [0.15 M NaCl, 1 mM MgCl2, 3.3 mM K4Fe(CN)6, 3.3 mM K3Fe(CN)6, 0.2%
X-Gal ] in 24 well plates for 2 hours at 37°C Reactions are stopped in 500 mM sodium bicarbonate solution and transferred to microscope slides for analysis. Three plates each are counted for blue (β-galactosidase positive cells) or white (β-galactosidase negative cells) to assess for MMR inactivation. Table 1 shows the results f om these studies. EXAMPLE 2: Generation of an expression cassette for screening of structurally altered polypeptides in MMR defective cells.
In order to produce recombinant proteins for screening of highly antigenic polypeptides, a fusion gene cassette was engineered that encodes for a secreted polypeptide containing a six polyhistidine domain at the C-terminus, which is useful for purification. This gene cassette is referred to as sec-hist. This gene was constructed by PCR using DNA from the pUC18 plasmid as template. The sense primers contained nucleotide sequences corresponding to the leader sequence of human interleukin-2 (ref 32), which has been found to produce robust amounts of secreted polypeptides from TK cells (personal observation). This domain was introduced at the 5' end of the pUC18 polylinker. Antisense primers containing nucleotide sequences encoding for 6 histidines were used to position these residues at the 3' end of the pUC18 polylinker. The nucleotide sequence of these primers are listed below.
SENSE Primer: S'aflg-cttccatgtacaggatgcaactcctgtcttgcattgcactaagtcttgcacttgtcacaaacagtgcaCAAAAGCTG GAGCTC-3' (SEQ JD NO:l) The italic sequence represents a Hindlll site for subcloning. The underlined sequence represents leader sequence from the human IL-2. Sequence in capital letters represents sequence from the start of the polylinker region of pUC18.
ANTISENSE Primer:
5 'ccggαtccctactagtggtgatggtgatggtgGCTTGATATCGAATTCCTG-S ' (SEQ JD NO:2)
The italic sequence represents a Hindlll site for subcloning. The underlined sequence represents 6 codons encoding for histidine residues followed by 2 termination codons. Sequence in capital letters represents sequence to the 3' end of the pUC18 polylinker.
Amplified products were obtained using buffer conditions as previously described . Amplification reactions were carried out at 94°C for 30 sec, 52°C for 2 min, and 72°C for 2 min for 25 cycles. Products were run on 1% agarose gels containing ethidium bromide, and products of the expected molecular weight were excised and purified by Gene Clean (BiolOl). Products were then cloned into T-tailed vectors (InVitrogen) as suggested by the manufacturer. Recombinant clones were analyzed by restriction analysis and by DNA sequencing. Several clones contained fragments with the expected genomic sequence. The parental clone is referred to as TAsec-hist.
A schematic diagram of the sec-hist fusion protein is shown in Figure 3 A In order to generate TK cells that secrete the sec-hist polypeptide, the TAsec-hist plasmid is digested with Hindlll to release the sec-hist insert. The insert was cloned into the unique Hindlll site of the pCEP4 mammalian expression vector, which also contains the Hygromycin resistance gene as selectable marker. Recombinant clones were analyzed by restriction digest and sequencing to assure the authenticity of the construct. Inserts can now be designed via PCR or direct cloning using the restricition sites contained within the polylinker (see Figure 3B).
Recombinant pCEPsec-hist plasmid will then be transfected into TK cells as previously described using cationic lipids. Cells will be cotransfected along with the pEFPMS134, which is a mammalian expression vector containing the PMS 134 dominant negative MMR gene allele under control of the constitutive elongation factor (EF) promoter. This vector contains the neomycin resistance gene and allows for double selection of TK cells for both the sec-hist and pEFPMS134 vectors. TK cells will also be cotransfected with the sec-hist and pEF empty vector as a control.
Cells are co-selected for 14 days in 0.6 mg/ml G418 and 0.8mg/ml hygromycin B (these concentrations have been previously determined for double transfection of TK cells). After 14 days, macroscopic colonies will be isolated and subcloned into 24 well dishes (Nunc) as 1 ml cultures. Clones will then be analyzed for secreted sec-hist protein using both ELISA and western blot analysis of conditioned supernatants from sec- hist/pEFPMS134, sec-hist/pEFempty vector, and parental TK cells. A monoclonal anti- HIS antibody (Santa Cruz), which has been successfully used for other western and ELISA studies, will be used for both assays. Analysis of PMS 134 expression will be determined by western blot using a PMS2-specific polyclonal antibody (Morphotek, personal communication).
ELISA will be performed on conditioned medium (CM) from TK cells transfected with pCEP4sec-hist to screen for high producers of the sec-hist polypeptide. ELISAs are carried out as follows. Twohundred microliter aliquots of conditioned medium are taken from pCEP4sec-hist transfected and control cells. Aliquots are placed into 1.5ml eppendorf tubes and centrifuged at 14,000Xg for 3 minutes to pellet cell debris. Supernates are then collected and 50 μls are placed into triplicate wells of a 96-well polystyrene microtiter plate (Nunc). Plates are incubated at room temperature for 4 hours, washed twice with 200 μls of IX Phosphate Buffered Saline (PBS) solution, pH 7.0 (Life Technologies), and blocked with 100 μls of 5%milk in IX PBS for 1 hour. Plates are then incubated with a monoclonal anti-HIS antibody (diluted 1 : 1000 in IX PBS) (Santa Cruz) for 2 hours at room temperature and then washed twice with 200 μls of IX PBS, and probed with an anti-mouse-horse radish peroxidase (HRP) conjugated secondary antibody diluted 1 :3000 in PBS. Plates are then incubated at room temperature for 1 hour, washed three times with 200 μls of IX PBS and incubated with TMB substrate (BioRad) for 15-30 minutes. After incubation is completed, reactions are stopped using 0.1N H2SO4 and plates are read using a BioRad microplate reader at 415nm. Clones are determined to be positive for secreted sec-hist if expected cells are found to produce a significant signal over control cells. Conditioned medium from positive cultures will then be analyzed by western blot using the anti-HIS antibody as probe to confirm ELISA data. Western blot analysis will be carried out as follows. Briefly, 50μls of CM or 50,000 cells from each culture is directly lysed in 2X lysis buffer (60 mM Tris, pH 6.8, 2% SDS, 10% glycerol, 0.1 M 2-mercaptoethanol, 0.001% bromophenol blue) and samples are boiled for 5 minutes. Lysate proteins are separated by electrophoresis on 4-20% Tris glycine gels (Novex) and then electroblotted onto Immobilon-P (Millipore) in 48 mM Tris base, 40 mM glycine, 0.0375% SDS, 20% methanol and blocked overnight at 4°C in Tris-buffered saline plus 0.05% Tween-20 and 5% condensed milk. Filters are then probed with an antibody generated against the PMS 134 or the polyHIS tag (Santa Cruz), followed by a secondary HRP-coηjugated antibody. After incubation with the secondary antibody, blots are developed using chemiluminescence (Pierce) and exposed to film to determine PMS 134 and sec-hist expression. Clones exhibiting expression of both genes will then be used in experiments described above.
A potential technical problem may exist in expressing the sec-hist protein due to toxicity that it may have on the growth of TK cells. If the production of no or low amounts of sec-hist polypeptide is found to occur in the above analysis, a Hindlll sec-hist fragment from the TAsec-hist plasmid will be subcloned into the unique Hindlll site of the pIND/N5 steroid inducible vector (Invitrogen). This vector has been found to produce robust protein expression in TK cells upon in steroid induction. This application teaches the use of employing an inducible vector containing the sec-hist expression cassette to express polypeptides in TK cells that may be toxic under constitutively expressed conditions.
Cells that are found to co-express the PMS 134 and the sec-hist genes or the control cell expressing the pEF empty vector and the sec-hist gene are cultured under high growth conditions in media containing neomycin, hygromycin and vitamins, which has been shown to increase the doubling time of TK cells and enhance the genetic alteration of β- galactosidase reporter plasmids in vivo (data not shown). Briefly, cells are grown in vitamin enriched medium for 20 doublings (~17 days), a time at which it has been found that 20-40% of clones contain sequence alterations within a particular genetic locus. After selection, cells will be subcloned in 96-well microtiter plates by limiting dilutions. Clones will be grown for 5 days in the presence of neomycin/hygromycin-free medium containing heat inactivated serum to remove complement for in vitro antigenic assays that will be performed using murine lymphocytes as described in section below. The sec-hist expression vector cassette can also be transfected into cell lines that are "naturally" defective for MMR such as the human cell lines derived from colon cancer tumors such as but not limited to HCT116 and DLD-1. The vector can be in the constitutive backbone pCEP4 or under control of the steroid-inducible vectors pIND or pMAM.
The techniques described above teach us the use of producing structurally altered antigens from mammalian cells to ensure proper folding or post-translation modifications of the polypeptide. This approach gives an advantage over others that employ the use of prokaryotic, yeast or baculovims produced antigens that have been found to produce weak antigenic responses due to misfolding or improper post-translational modifications.
EXAMPLE 3: Screening strategy to identify cell clones producing highly antigenic polypeptides.
In order to identify antigenic polypeptides produced by TKPMS 134 cell clones, the following in vitro assays will be performed.
First, the lymphocyte stimulatory activity of sec-hist polypeptides will be measured by adding CM of TKsec-hist cells with or without the PMS 134 to lymphocytes derived from naive or whole antigen exposed Balb/C mice. Briefly, 2 mice will be infected with whole antigen in the presence of Freund's Complete Adjuvant by subcutaneous injection in the tail with a 100-μl 1/1 mixture of complete Freund's adjuvant (CFA) (Difco). Two subcutaneous boosts will be performed with the same quantity of antigen, mixed 1/1 with incomplete Freund's adjuvant (Difco), after 2 and 4 weeks. Two control mice will receive adjuvant alone. Mice are sacrificed 5 days after the second boost (at day 33). Peripheral blood mononuclear cells (PBMCs) from whole blood and splenocytes from spleens of will be harvested following the previously described procedures (Nicolaides, N.C. et al. (1997) Proc. Natl. Acad. Sci. USA 94:13175-13180). For splenocyte assays, whole spleens are pressed through sterile wire mesh into RPMI medium (Life Technology). Next, cells are washed twice in RPMI and incubated for 10 minutes in RBC lysis buffer. Cells are then washed again and resuspended at 1 X IO5 cells/ml in RPMI-1640 medium plus 10% heat inactivated fetal bovine serum. One hundred microliters of cells are aliquoted into twenty 96-well titer flat bottom plates. For PBMC isolation, whole blood is isolated by eye puncture and collected into vacutainer tubes containing EDTA. An equal volume of PBS (Mg2+/Ca2+-free) is added to whole blood. PBMCs are isolated by centrifugation over Ficoll-Paque gradients (Pharmacia Biotech 17-1440-02). Purified cells are seeded at 1 X IO5 cells/ml in RPMI 1640 containing 10% heat-inactivated fetal bovine serum (Life Technologies, Inc.) and lOOμls are plated in 96 well flat bottom microtiter plates and incubated at 37 °C in 5% CO2.
To measure for T-cell activation, PBMCs and splenocytes from primed and non- primed mice are incubated with 10% conditioned medium (CM) from TKsec-hist cells with or without the PMS 134 gene. 5 μg/ml of concavahnA (ConA) is used as a positive control for splenocyte culture assays, while 5 μg/ml phorbol 12-myristate 13-acetate and 1 μg/ml phytohemagglutinin (Sigma) are used as a positive control for PBMC cultures. CM from parental TK cells grown in the presence of RPMI with 10% heat inactivated medium will be used as negative control. Previous studies using CM from TK cells have found no stimulatory activity to be produced on PBMCs or splenocytes (N. Nicolaides, personal observation). Cultures are incubated at 37 °C in 5% CO2 for 6 days and scored for antigenic activity as determined by proliferation assay. Proliferation is assayed using a modified protocol of the acid phosphatase assay as described (Grasso, L. et al. (1998) J Biol. Chem. 273:24016-24024). Briefly, 50 μls of a buffer containing 0.1 Msodium acetate (pH 5.5), 0.1% Triton X-100, and 10 mM -nitrophenyl phosphate (Sigma
104 phosphatase substrate) is added directly to each well containing 0.2 ml of growth medium and incubated for 1.5 h at room temperature. Reactions are terminated by the addition of 0.05 N sodium hydroxide and quantified by absorbance at 410 nm using a BioRad plate reader. Data is represented as a stimulation index (SI), which is the proliferation of experimental data points divided by the mean of 10 aliquots of CM from TK parental cells. All experiments will be performed in at least triplicate.
It is expected that several TKsec-hist clones co-expressing the PMS 134 protein will be found to have an enhanced antigenicity on PBMCs and/or splenocytes due to conformational changes that will occur within the coding region of the target antigen. These changes may form secondary domains that serve as T and/or B cell epitopes and in turn are responsible for stimulating their respective activation. Clones that reproducibly produce enhanced antigenic activation will be sequenced to confirm and identify that a structural alteration(s) has indeed occurred within the coding region of the gene. Sequence data may also shed additional light into the importance of critical domains within this candidate vaccine polypeptide for additional rounds of alteration that may lead to the creation of a super-antigen that may serve as a potent vaccine. Sequence analysis of clones will be performed as follows. First positive clones will be expanded from 96-well plates to 24-well plates. Confluent wells will be expanded and cells will be harvested for RNA extraction. RNA extraction and reverse transcription will be carried out using the Trizol method as previously described (Nicolaides, N.C. et al. (1997) Proc. Natl. Acad. Sci. USA 94:13175-13180; Grasso, L. et al. (1998) J. Biol. Chem. 273:24016-24024). Reverse transcription will be carried out using Superscript II (Life Technology) as previously described (Nicolaides, N.C et al. (1998) Mol. Cell. Biol. 18:1635-1641). cDNAs will be amplified to isolate the sec-hist transcript using the sense primer: 5'-catgtacaggatgcaactcctg-3' (SEQ JD NO:3), which is located at the IL-2 leader sequence site (see Figure 3), and the antisense primer: 5'-tactagtggtgatggtgatggtg-3' (SEQ ID NO:4), which is located at the C-terminal polyhis site. Amplification is carried out at 94°C for 30 sec, 52°C for 2 min, 72°C for 2 min for 30 cycles. Reactions are analyzed on agarose gels. If products of the expected molecular weight are generated then samples will be cleaned using the QIAquick PCR template kit (Qiagen) to remove PCR amplimers and sequenced using the following primers that cover the entire coding region of the sec- hist gene. Clones are then sequenced using primers specific to the gene encoding the antigen.
Clones producing genetically altered sec-hist polypeptides will then be expanded into T-75 flasks to a density that will enable for the sufficient production of secreted sec- hist polypeptide in the CM. Conditioned medium containing the sec-hist polypeptide is then collected, and centrifuged at 3,500Xg for 10 minutes to remove cellular debris. CM is then loaded onto a 10ml- HiTrap Nickel column following the manufacturer's protocol (Pharmacia). After absorption and washing, the column is treated with 200 mM imidazole to elute the fusion protein. Recovered polypeptides are then analyzed by SDS-PAGE using 4-12% NuPAGE gels (Novex) and silver stained following the manufacturer's protocol (Novex). Due to the random nature of defective MMR, the possibility exists that sec-hist alleles may be generated by clones producing enhanced antigenic polypeptides, which contain a nonsense or frame-shift mutation, therefore forming polypeptides lacking a polyHIS C-terminus. If a nonsense or frameshift mutation does occur in clones producing polypeptides with increased antigenicity, then the new allele is reengineered via PCR to contain a polyHIS tag at the C-terminus, and this new fusion protein will be rescreened as above. Purified polypeptides will be rescreened at a final concentration of 10 μg/ml in the in vitro assays described above to confirm that the antigenic activity is indeed coming from the sec-hist protein. TK cells producing altered antigens with enhanced activity on both PBMCs and splenocytes will then be tested along with the non-altered sec-hist protein in vivo in Balb/C mice for the ability to illicit an immune response in the absence of adjuvant.
A schematic diagram outlining the screening procedure is given in Figure 4.
EXAMPLE 4: Screening strategy to identify cell clones producing highly immunogenic antigens. To test the immunogenic potential that the altered polypeptides identified from
EXAMPLE 3 have in vivo, Balb/C mice will be injected with the 6 most antigenic polypeptides and the wild type sec-hist polypeptide produced from TKEFempty/sec-hist cells in the absence of adjuvant. Briefly, mice will be immunized with 30 μgs of purified sec-hist protein in sterile phosphate buffered saline (PBS) without adjuvant by subcutaneous injection in the tail. One group of mice will receive a lOOμls of a mixture of polypeptides diluted 1/1 in complete Freund's adjuvant (CFA) (Difco) as a positive control. Two subcutaneous boosts will be performed with the same quantity of antigen, and the mouse receiving the polypeptide mixture with adjuvant will be boosted with a 1/1 mixture with incomplete Freund's adjuvant (Difco), at 2 and 4 weeks after the initial injection. Mice will be bled 5 and 15 days after the second boost (at day 33) to measure for antigen titers. Control mice will receive PBS alone. Before the start of immunization, a prebleed will be obtained from each mouse.
Immune responses will be measured by screening for whole Ig and sec-hist specific antibody titers by ELISA following the protocol described above. For antigen specific antisera titers, 96-well plates will be coated with a 50uls of a solution containing 5μg/ml each antigen used for vaccination in PBS. Plates will then be probed with serial dilutions of prebleeds, 5 day and 15 day bleeds. Detection of antibodies will be done using a sheep anti-mouse-HRP conjugated secondary antibody followed by incubation with TMB substrate as described above.
Success of the strategy proposed in this program will be demonstrated with the generation of antisera from mice immunized with altered sec-hist protein that is able to cross react with the native sec-hist protein. If no titers are found in the samples without adjuvant, mice will be administrated antigen in complete Freund's Adjuvant and titers analyzed 14 days later, followed by immunization in Incomplete Freund's at day 17 if no titers are found and analyzed at day 31.
A potential problem that may occur with the outlined strategy is that antibody titers may be generated against the sec-polyhistidine fusion domain. To determine if antisera is able to identify authentic sec-his polypeptides, the antigen lacking the polyhistidine domain will be generated by in vitro transcription-translation (TNT) in the presence of radiolabelled methionine. A template containing the sec-hist polypeptide will also be made and the encoded protein used as a control. Templates for the TNT reactions will be generated by PCR as described (Nicolaides, N.C. et al. (1998) Mol. Cell. Biol.18:1635- 1641). Briefly, the TAsec-hist plasmid will be used as template to amplify gene segments that encode for the untqagged antigen or the sec-hist tagged protein.
Translated polypeptides are first analyzed by SDS-PAGE gel electrophoresis and autoradiography to ensure that the polypeptide with the expected molecular weight are synthesized. Proteins are then immunoprecipitated using antiserum from vaccinated mice to determine if these antibodies recognize authentic antigen sequences. Briefly, immunoprecipitations are performed on in vttro-translated proteins by mixing the translation reaction mixtures with lOOμls of mouse antiserum or 1 μgof a HIS-specific monoclonal antibody (MAB) (Santa Cruz) in 400 μls of EBC buffer (50 mM Tris [pH 7.5], 0.1 M NaCl, 0.5% Nonidet P-40). After incubation for 1 h at 4°C, protein A-
Sepharose (Sigma) is added to a final concentration of 10% and the reaction mixtures are incubated at 4°C for 1 h. Proteins bound to protein A are washed five times in EBC and separated by electrophoresis on 4-20% Tris-glycine gradient gels, which are then dried and autoradiographed. If antisera are able to react with authentic sequences lacking HIS residues, the data from these studies will be continued in further preclinical animal studies. Discussion
The initial steps of MMR are dependent on two protein complexes, called MutSα and MutLα. The use of dominant negative MMR alleles are able to perturb the formation of these complexes with downstream biochemicals involved in the excision and polymerization of nucleotides comprising the "corrected" nucleotides. Examples from this application show the ability of a truncated MMR allele (PMS 134 is capable of blocking MMR resulting in a hypermutable cell line that gains genetic alterations throughout its entire genome per cell division. Once a cell line is produced that contains genetic alterations within genes encoding for an antigen, it is desirable to restore the genomic integrity of the cell host. This can be achieved by the use of inducible vectors whereby dominant negative MMR genes are cloned into such vectors, introduced into antigen- producing cells and the cells are cultured in the presence of inducer molecules and/or conditions. Inducible vectors include but are not limited to chemical regulated promoters such as the steroid inducible MMTV, tetracycline regulated promoters, temperature sensitive MMR gene alleles, and temperature sensitive promoters.
The results described above lead to several conclusions. First, expression of PMS 134 results in an increase in microsattelite instability in TK cells. That this elevated microsattelite instability is due to MMR deficiency was proven by evaluation of extracts from stably transduced cells and stability of a tract contained within the pCAR-OF vector. The expression of PMS 134 results in a polar defect in MMR, which was only observed using heteroduplexes designed to test repair from the 5' direction (no significant defect in repair from the 3' direction was observed in the same extracts). Interestingly, cells deficient in hMLHl also have a polar defect in MMR, but in this case preferentially affecting repair from the 3' direction. It is known from previous studies in both prokaryotes and eukaryotes that the separate enzymatic components mediate repair from the two different directions. These results strongly suggest a model in which 5' repair is primarily dependent on hPMS2 while 3' repair is primarily dependent on hMLHl. It is easy to envision how the dimeric complex between PMS2 and MLHl might set up this directionality. The combined results also demonstrate that a defect in directional MMR is sufficient to produce a MMR defective phenotype and suggests that any MMR gene allele is useful to produce genetically altered TK cells, or a cell line that is producing antigenic gene products. Moreover, the use of such MMR alleles will be useful for generating genetically altered polypeptides with altered structures as effective vaccine agents.
This application also teaches us that ANY method used to block MMR can be performed to generate hypermutablility in an antigen-producing cell that can lead to genetically altered proteins with enhanced biochemical features such as but not limited to increased antigenicity, increased immunogenicity, and enhanced pharmacokinetic profiles.
The blockade of MMR in such cells can be through the use of dominant negative MMR gene alleles from any species including bacteria, yeast, protozoa, insects, rodents, primates, mammalian cells, and man. Blockade of MMR can also be generated through the use of antisense RNA or deoxynucleotides directed to any of the genes involved in the MMR biochemical pathway. Blockade of MMR can be through the use of polypeptides that interfere with subunits of the MMR complex including but not limited to antibodies. Finally, the blockade of MMR may be through the use chemicals such as but not limited to nonhydrolyzable ATP analogs, which have been shown to block MMR (Galio, L. et al. (1999) Nucl. Acids Res. 27:2325-2331 ; Spampinato, C and P. Modrich (2000) J Biol Chem. 275:9863-9869).

Claims

We claim:
1. A method for making a hypermutated antigen, comprising introducing into a mammalian cell that expresses a preselected antigen a polynucleotide comprising a dominant negative allele of a mismatch repair gene.
2. The method of claim 1 wherein the polynucleotide is introduced by transfection of a suspension of cells in vitro.
3. The method of claim 1 wherein the mismatch repair gene is PMS2.
4. The method of claim 1 wherein the mismatch repair gene is human PMS2.
5. The method of claim 1 wherein the mismatch repair gene is MLHL
6. The method of claim 1 wherein the mismatch repair gene is PMSl.
I. The method of claim 1 wherein the mismatch repair gene is MSH2.
8. The method of claim 1 wherein the mismatch repair gene is MSH2.
9. The method of claim 4 wherein the allele comprises a truncation mutation.
10. The method of claim 4 wherein the allele comprises a tπmcation mutation at codon 134.
I I . The method of claim 10 wherein the truncation mutation is a thymidine at nucleotide 424 of wild-type PMS2.
12. The method of claim 1 wherein the polynucleotide is introduced into a fertilized egg of an animal.
13. The method of claim 12 wherein the fertilized egg is subsequently implanted into a pseudo-pregnant female whereby the fertilized egg develops into a mature transgenic animal.
14. The method of claim 12 wherein the mismatch repair gene is PMS2.
15. The method of claim 12 wherein the mismatch repair gene is human PMS2.
16. The method of claim 12 wherein the mismatch repair gene is human MLHl.
11. The method of claim 12 wherein the mismatch repair gene is human PMSl .
18. The method of claim 11 wherein the mismatch repair gene is human a human mutL homolog.
19. The method of claim 15 wherein the allele comprises a truncation mutation.
20. The method of claim 15 wherein the allele comprises a truncation mutation at codon 134.
21. The method of claim 19 wherein the truncation mutation is a thymidine at nucleotide 424 of wild-type PMS2.
22. A homogeneous composition of cultured, hypermutable, mammalian cells which comprise a preselected antigen and a dominant negative allele of a mismatch repah gene.
23. The isolated hypermutable cell of claim 22 wherein the mismatch repair gene is PMS2.
24. The isolated hypermutable cell of claim 23 wherein the mismatch repair gene is human PMS2.
25. The isolated hypermutable cell of claim 22 wherein the mismatch repair gene is MLHl.
26. The isolated hypermutable cell of claim 22 wherein the mismatch repair gene is PMSl.
27. The isolated hypermutable cell of claim 22 wherein the mismatch repair gene is a human mutL homolog.
28. The isolated hypermutable cell of claim 22 wherein the cells express a protein consisting of the first 133 amino acids of hPMS2.
29. A method for generating a mutation in a gene encoding an antigen of interest comprising growing a mammalian cell comprising said gene encoding an antigen of interest and a dominant negative allele of a mismatch repair gene, and determining whether said gene encoding an antigen of interest harbors a mutation.
30. The method of claim 29 wherein determining whether said gene encoding an antigen of interest harbors a mutation is accomplished by analyzing the nucleotide sequence of said gene.
31. The method of claim 30 wherein said nucleotide sequence is an mRNA transcribed from said gene.
32. The method of claim 29 wherein determining whether said gene encoding an antigen of interest harbors a mutation is accomplished by analyzing a protein encoded by said gene.
33. The method of claim 30 wherein determining whether said gene encoding an antigen of interest harbors a mutation is accomplished by analyzing the phenotype of said gene.
34. The method of claim 32 wherein analyzing of said protein comprises analyzing the antigenicity and immunogenicity of said protein.
35. A method for generating a mutation in a gene encoding an antigen of interest comprising growing a cell comprising said gene and a polynucleotide encoding a dominant negative allele of a mismatch repair gene; and testing the cell to determine whether the cell harbors a mutation in said gene yielding at least one new biochemical feature of said antigen.
36. The method of claim 35 wherein said new biochemical feature is selected from the group consisting of increased antigenicity and increased immunogenicity.
37. The method of claim 35 wherein said testing comprises analyzing primary structure of said gene.
38. The method of claim 35 wherein said testing comprises analyzing the secondary structure of said gene.
39. The method of claim 35 wherein said testing comprises analyzing the antigenicity and immunogenicity of the polypeptide encoded by said gene.
40. The method of claim 1 wherein said introduction of said polynucleotideis in the presence of at least one DNA mutagen.
41. The method of claim 35 wherein said testing comprises analyzing a nucleotide sequence said gene.
42. The method of claim 35 wherein said testing comprises analyzing mRNA transcribed from said gene.
43. The method of claim 35 wherein said testing comprises analyzing the antigen protein encoded by the gene of interest.
44. The method of claim 35 wherein said testing comprises analyzing the biochemical activity of the protein encoded by said gene.
45. A hypermutable transgenic mammalian cell made by the method of claim 35.
46. The transgenic mammalian cell of claim 45 wherein the cell is from primate.
47. The transgenic mammalian cell of claim 45 wherein the cell is from rodent.
48. The transgenic mammalian cell of claim 45 wherein the cell is from human.
49. The transgenic mammalian cell of claim 45 wherein the cell is eucaryotic.
50. The transgenic mammalian cell of claim 45 wherein the cell is prokaryotic
51. A method for making randomly altered forms of a secreted antigen comprising introducing a polynucleotide encoding a tagged antigen into an MMR defective cell.
52. The method of claim 51 wherein said tagged antigen is screened for increased antigenicity.
53. The method of claim 51 wherein said tagged antigen is screened for increased immunogenicity.
54. The method of claim 51 wherein the cells are made MMR defective by introducing at least one dominant negative allele of an MMR gene.
55. The method of claim 51 wherein the cells are naturally MMR defective.
56. A method of producing a mutated antigen in a reversibly unstable cell comprising introducing into a cell containing a preselected antigen of interest, an inducible expression vector comprising a polynucleotide encoding a dominant negative allele of a mismatch repair gene; inducing said cell to express said dominant negative mismatch repair gene; and detecting at least one new biochemical feature of said antigen.
57. The method of claim 56 wherein said new biochemical feature is selected from the group consisting of a nucleotide mutation, increased antigenicity and increased immunogenicity.
58. The method of claim 56 wherein said preselected antigen of interest is encoded on a polynucleotide previously transfected into said cell.
59. The method of claim 56 further comprising ceasing induction of said dominant negative allele of a mismatch repair gene, thereby stabilizing said cell.
60. The method of claim 58 further comprising isolating the polynucleotide previously transfected into said cell after detection of said new biochemical feature.
61. An polynucleotide molecule for expressing an antigen in a hypermutable cell comprising an expression cassette wherein said cassette comprises a 3' sequence encoding a plurality of histidine residues, a 5' leader sequence of an expressed gene, and a polylinker to allow cloning of a nucleotide sequence encoding a preselected antigen.
62. The polynucleotide molecule of claim 61 wherein said cell is a mammalian cell.
63. The polynucleotide molecule of claim 61 wherein said cell is a human cell.
64. The method of claim 63 wherein said 5' leader sequence is a 5 'leader sequence of IL-2.
65. A method of producing a mutated antigen comprising introducing a polynucleotide encoding a preselected antigen in the expression cassette said polynucleotide molecule of claim 61, and introducing said polynucleotide molecule into a cell comprising a dominant negative allele of a mismatch repair gene.
66. A hypermutated antigen produced by the method of claim 65.
67. A method of eliciting an immune response in an animal comprising administering to said animal an immunogenic amount of at least one hypermutated antigen of claim 66.
68. The method of claim 67 wherein said antigen is a mutated form of an antigen derived from a pathogenic organism selected from the group consisting of, bacteria, fungi, protozoa, helminths, and viruses.
69. An immunogenic composition comprising at least one hypermutated antigen of claim 66 and a pharmaceutically acceptable carrier.
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CA2429134C (en) 2011-03-15

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