US20020156245A1 - Patched-2 antibodies - Google Patents

Patched-2 antibodies Download PDF

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US20020156245A1
US20020156245A1 US09/990,046 US99004601A US2002156245A1 US 20020156245 A1 US20020156245 A1 US 20020156245A1 US 99004601 A US99004601 A US 99004601A US 2002156245 A1 US2002156245 A1 US 2002156245A1
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Frederic de Sauvage
David Carpenter
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Genentech Inc
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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
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • 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
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • the present invention relates generally to signaling molecules, specifically to signaling and mediator molecules in the hedgehog (Hh) cascade which are involved in cell proliferation and differentiation.
  • Hh hedgehog
  • TGF- ⁇ transforming growth factor-beta
  • Wnt fibroblast growth factors
  • hedgehog families have been associated with patterning activity of different cells and structures in Drosophila as well as in vertebrates.
  • TGF- ⁇ transforming growth factor-beta
  • Wnt Wnt
  • fibroblast growth factors and hedgehog families have been associated with patterning activity of different cells and structures in Drosophila as well as in vertebrates.
  • Segment polarity genes were first discovered in Drosophila, which when mutated caused a change in the pattern of structures of the body segments. These changes affected the pattern along the head to tail axis.
  • Hedgehog Hedgehog was first identified as a segment-polarity gene by a genetic screen in Drosophila melanogaster , Nusslein-Volhard et al., Roux. Arch. Dev. Biol. 193: 267-282 (1984), that plays a wide variety of developmental functions. Perrimon, supra.
  • Hh also plays a role in the development of limbs (Krauss et al., Cell 75: 1431-44 (1993); Laufer et al., Cell 79, 993-1003 (1994)), somites (Fan and Tessier-Lavigne, Cell 79, 1175-86 (1994); Johnson et al., Cell 79: 1165-73 (1994)), lungs (Bellusci et al., Develop.
  • Ihh and Dhh are involved in bone, gut and germinal cell development, Apelqvist et al., Curr. Biol. 7: 801-4 (1997); Bellusci et al., Dev. Suppl. 124: 53-63 (1997); Bitgood et al., Curr. Biol. 6: 298-304 (1996); Roberts et al., Development 121: 3163-74 (1995).
  • Ihh has been implicated in chondrocyte development [Vortkamp, A.
  • Hh function appears to be mediated by a multicomponent receptor complex involving patched (e.g., Ptch) and Smoothened (e.g., Smo), two multi-transmembrane proteins initially identified as segment polarity genes in Drosophila and later characterized in vertebrates.
  • patched e.g., Ptch
  • Smoothened e.g., Smo
  • Patched-2 was recently isolated [Motoyama, J. et al., Nature Genetics 18: 104-106 (1998)], but its function as a Hh receptor has not been established.
  • Patched-2 In order to characterize Patched-2 and compare it to Patched with respect to the biological function of the various Hh family members, Applicants have isolated the human Patched-2 gene. Biochemical analysis of Patched and Patched-2 show that both bind to all members of the Hh family with similar affinity and that both molecules can form a complex with Smo. However, the expression patterns of Patched-2 and Patched do not overlap. While Patched is expressed throughout the mouse embryo, Patched-2 is found mainly in spermatocytes which require Desert Hedgehog (Dhh) for proper development suggesting that Patched-2 mediates Dhh's activity in the testis. Chromosomal localization of Patched-2 places it on chromosome 1p33-34, a region deleted in some germ cell tumors, raising the possibility that Patched-2 may be a tumor suppressor in Dhh target cells.
  • Dhh Desert Hedgehog
  • the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a patched-2 polypeptide comprising the sequence of amino acids 1 to 1203 of FIG. 1 (SEQ ID NO:2), or (b) the complement of the DNA molecule of (a); and encoding a polypeptide having patched-2 biological activity.
  • the sequence identity preferably is >91%, more preferably about 92%, most preferably about 95%.
  • the isolated nucleic acid has at least >91%, preferably at least about 92%, and even more preferably at least about 95% sequence identity with a polypeptide having amino acid residues 1 to about 1203 of FIG. 1 (SEQ ID NO:2).
  • the isolated nucleic acid molecule comprises DNA encoding a human patched-2 polypeptide having amino acid residues 1 to about 1203 of FIG. 1.
  • the invention provides for an isolated nucleic acid comprising DNA having at least a 95% sequence identity to (a) a DNA molecule encoding the same mature polypeptide encoded by the cDNA in ATCC Deposit No. 209778 (designation: pRK7.hptc2.Flag-1405), alternatively the coding sequence of clone pRK7.hptc2.Flag-1405, deposited under accession number ATCC 209778.
  • the invention provides for a nucleic acid comprising human patched-2 encoding sequence of the cDNA in ATCC Deposit No. 209778 (designation: pRK7.hptc2.Flag-1405) or a sequence which hybridizes thereto under stringent conditions.
  • the invention provides a vector comprising DNA encoding a human patched-2 polypeptide.
  • a host cell comprising such a vector is also provided.
  • the host cells may be mammalian cells, (e.g. CHO cells), prokaryotic cells (e.g., E. coli ) or yeast cells (e.g., Saccharomyces cerevisiae ).
  • a process for producing patched-2 polypeptides is further provided and comprises culturing host cells under conditions suitable for expression of patched-2 and recovering the same from the cell culture.
  • the invention provides an isolated patched-2 polypeptide.
  • the invention provides isolated native sequence patched-2 polypeptide, which in one embodiment is a human patched-2 including an amino acid sequence comprising residues 1 to about 1203 of FIG. 1 (SEQ ID NO:2). Human patched-2 polypeptides with or without the initiating methionine are specifically included.
  • the invention provides a human patched-2 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209778.
  • the invention provides chimeric molecules comprising a patched-2 polypeptide fused to a heterologous polypeptide or amino acid sequence.
  • a chimeric molecule comprises a patched-2 polypeptide fused to an epitope tag sequence or a constant region of an immunoglobulin.
  • the invention provides expressed sequence tag (EST) comprising the nucleotide sequences identified in FIG. 2A (905531) (SEQ ID NO:3) and FIG. 2B (1326258) (SEQ ID NO:5).
  • EST expressed sequence tag
  • the invention provides for alternatively spliced variants of human patched-2 having patched-2 biological activity.
  • the invention provides for method of using patched-2 for the treatment of disorders which are mediated at least in part by Hedgehog (Hh), especially Desert hedgehog (Dhh). In particular, testicular cancer.
  • the invention provides a method of using antagonists or agonists of patched-2 for treating disorders or creating a desirable physiological condition effected by blocking Hh signaling, especially Dhh signaling. (E.g, contraception).
  • FIGS. 1 A- 1 E shows the nucleotide (SEQ ID NO:1) and derived amino acid (SEQ ID NO:2) sequence of a native sequence of human Ptch-2 polypeptide.
  • FIG. 2A shows EST 905531 (SEQ ID NO:3) and FIG. 2B shows EST 1326258 (SEQ ID NO:5) in alignment with human Ptch (SEQ ID NO: 18). These ESTs were used in the cloning of human full-length Ptch-2 (SEQ ID NO:1).
  • FIGS. 3 A- 3 D show a comparison between human Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2). Gaps introduced for optimal alignment are indicated by dashes. Identical amino acids are boxed. The 12 transmembrane domains are indicated by the gray boxes, all of which are conserved between the two sequences. Alignment results between the two sequences indicate 53% identity. The most significant difference is a shorter C-terminal intracellular domain in human Ptch-2 (SEQ ID NO:2) in comparison with human Ptch (SEQ ID NO:4).
  • FIG. 4 shows a northern blot of Ptch-2 (SEQ ID NO:2) which indicates expression is limited to the testis. Multiple human fetal and adult tissue northern blots were probe fragments corresponding to the 3′-untranslated region of murine Ptch-2.
  • FIG. 5 shows a chromosomal localization of two BAC clones which were isolated by PCR screening with human patched-2 derived probes. Both probes were mapped by FISH to human chromosome 1p33-34.
  • FIGS. 6 A-F is an in situ hybridization comparing Ptch (SEQ ID NO:4), Ptch-2 (SEQ ID NO:2) and Fused (FuRK) (SEQ ID NO:10).
  • High magnification of mouse testis showing expression of (A) Ptch (SEQ ID NO:4), Ptch-2 (SEQ ID NO:2) (B) and FuRK (SEQ ID NO:10) (C).
  • FIG. 6(F) shows low magnification of testis section hybridized with FuRK (SEQ ID NO:10).
  • Scale bar A, B, C: 0.05 mm; D, E, F: 0.33 mm.
  • FIG. 7A is logarithmic plot comparing the binding Ptch-2 (SEQ ID NO:2) to Dhh (SEQ ID NO:13) and Shh (SEQ ID NO:14).
  • FIG. 7B is a western blot illustrating co-immunoprecipitation of epitope tagged Ptch (SEQ ID NO:4) or Ptch-2 (SEQ ID NO:2) with epitope tagged Smo (SEQ ID NO:15).
  • Immunoprecipitation was performed with antibodies to the Flag tagged Ptch (SEQ ID NO:4) and analyzed on a 6% acrylamide gel with antibodies to the Myc tagged Smo (SEQ ID NO:15). Protein complexes can be detected for both Ptch (SEQ ID NO:4)and Ptch-2 (SEQ ID NO:2) with Smo (SEQ ID NO:15). Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) express at similar levels as shown by immunoprecipitation using antibodies to the Flag-tag and western blot using the same anti-Flag antibody.
  • FIGS. 8 A- 8 D is a sequence comparison between human Ptch-2 (SEQ ID NO:2) and murine Ptch-2 (SEQ ID NO:7), which indicates that there is about 91% identity between the two sequences.
  • FIG. 9 is an in situ hybridization which demonstrates the accumulation of Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) mRNA detected by in situ hybridization in basal cells of E18 transgenic mice overexpressing SMO-M2 (SEQ ID NO:16) (Xie et al., Nature 391: 90-92 (1998).
  • FIGS. 10 A- 10 D depict a partial sequence representing clone 3A (SEQ ID NO:8), a partial patched-2 fragment which was initially isolated from a fetal brain library.
  • FIGS. 11 A-B depict a partial sequence representing clone 16.1 (SEQ ID NO:9), a partial patched-2 fragment which isolated from a testis library.
  • patched-2 and “patched-2 polypeptide” when used herein encompass native sequence patched-2 and patched-2 variants (which are further defined herein) having patched-2 biological activity. Patched-2 may be isolated from a variety of sources, such as from testes tissue types or from another source, or prepared by recombinant or synthetic methods.
  • a “native sequence patched-2” comprises a polypeptide having the same amino acid sequence as a human patched-2 derived from nature. Such native sequence patched-2 can be isolated from nature or can be produced by recombinant and/or synthetic means.
  • the term “native sequence vertebrate patched-2” specifically encompasses naturally occurring truncated forms of human patched-2, naturally occurring variant forms (e.g., alternatively spliced forms) and naturally-occurring allelic variants of human patched-2.
  • the native sequence patched-2 is a mature or full-length native patched-2 comprising amino acids 1 to 1203 of FIG. 1 (SEQ ID NO:2) with or without the initiating methionine at position 1.
  • “Patched-2 variant” means an active human patched-2 as defined below having at least >91% amino acid sequence identity to (a) a DNA molecule encoding a patched-2 polypeptide, or (b) the complement of the DNA molecule of (a).
  • the patched-2 variant has at least >91% amino acid sequence homology with the human Ptch-2 (SEQ ID NO:2) having the deduced amino acid sequence shown in FIG. 1 for a full-length native sequence human patched-2.
  • Such patched-2 variants include, without limitation, patched-2 polypeptides wherein one or more amino acid residues are added, or deleted, at the N- or C-terminus of the sequence of FIG. 1 (SEQ ID NO:2).
  • the nucleic acid or amino acid sequence identity is at least about 92%, more preferably at least about 93%, and even more preferably at least about 95%.
  • Ptch or “Ptch-2” refer to the particular species of molecules isolated and characterized in the application, while the terms “patched” and patched-2” refer to the more generalized description as defined above.
  • Percent (%) amino acid sequence identity with respect to the patched-2 sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the patched-2 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST-2 software that are set to their default parameters. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • % identity can be determined by Align-2, authored by Genentech, Inc., which was filed with user documentation in the United States Copyright Office, Washington, D.C. 20559, on Dec. 10, 1991, and is registered under U.S. Copyright Registration No. TXU 510087.
  • Percent (%) nucleic acid sequence identity with respect to the patched-2 sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the patched-2 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST-2 software that are set to their default parameters. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • % identity can be determined by Align-2, authored by Genentech, Inc., which was filed with user documentation in the United States Copyright Office, Washington, D.C. 20559, on Dec. 10, 1991, and is registered under U.S. Copyright Registration No. TXU 510087.
  • epitope tagged when used herein refers to a chimeric polypeptide comprising patched-2 polypeptide, or a portion thereof, patched-2 to a “tag polypeptide”.
  • the tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the patched-2 polypeptide.
  • the tag polypeptide preferably also is fairly unique so that the antibody does not substantially cross-react with other epitopes.
  • Suitable tag polypeptides generally have at least six amino acid residues and usually between about 8 to about 50 amino acid residues (preferably, between about 10 to about 20 residues).
  • the term “immunoadhesin” designates antibody-like molecules which combine the binding specificity of a heterologous protein (an “adhesin”) with the effector functions of immunoglobulin constant domains.
  • the immunoadhesin comprise a fusion of an amino acid sequence with the desired binding specificity which is other than the antigen recognition and binding site of an antibody (i.e., is “heterologous”), and an immunoglobulin constant domain sequence.
  • the adhesin part of an immunoadhesin molecule typically is a contiguous amino acid sequence comprising at least the binding site of a receptor or a ligand.
  • the immunoglobulin constant domain sequence in the immunoadhesins may be obtained from any immunoglobulin, such as IgG-1, IgG-2, IgG-3 or IgG-4 subtypes, IgA (including IgA-1 and IgA-2, IgE, IgD or IgM.
  • Immunoadhesion reported in the literature include fusions of the T cell receptor* [Gascoigne et al., Proc. Natl. Acad. Sci.
  • CD4* Capron et al., Nature 337: 525-531 (1989); Traunecker et al., Nature 339: 68-70 (1989); Zettmeissl et al., DNA Cell Biol. USA 9: 347-353 (1990); Byrn et al., Nature 344, 667-670 (1990)]; L-selectin (homing receptor) [Watson et al., J. Cell. Biol.
  • “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends upon the ability of denatured DNA to reanneal when complementary strands are present in an environment near but below their T m (melting temperature). The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. Moreover, stringency is also inversely proportional to salt concentrations. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology (1995).
  • “Stringent conditions,” as defined herein may be identified by those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (vol/vol) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; (3) employ 50% formamide, 5 ⁇ SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 ⁇ Denhardt's solution, sonicated salmon sperm DNA (50 ⁇ g/ml), 0.1% SDS, and 10% dextran sulfate at 42°
  • Isolated when used to describe the various polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes.
  • the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the vertebrate patched-2 natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
  • An “isolated” patched-2 nucleic acid molecule is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the patched-2 nucleic acid.
  • An isolated patched-2 nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated patched-2 nucleic acid molecules therefore are distinguished from the corresponding native patched-2 nucleic acid molecule as it exists in natural cells.
  • control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism.
  • the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
  • Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
  • Nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence.
  • DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide;
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or
  • a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
  • “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading frame. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
  • antibody is used in the broadest sense and specifically covers single monoclonal antibodies (including agonist and antagonist antibodies), antibody compositions with polyepitopic specificity, as well as antibody fragments (e.g., Fab, F(ab′) 2 and Fv), so long as they exhibit the desired biological activity.
  • the term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations that typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they are synthesized by the hybridoma culture, uncontaminated by other immunoglobulins.
  • the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler & Milstein, Nature 256:495 (1975), or may be made by recombinant DNA methods [see, e.g. U.S. Pat. No. 4,816,567 (Cabilly et al)].
  • the monoclonal antibodies herein specifically include “chimeric” antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity [U.S. Pat. No. 4,816,567; Cabilly et al.; Morrison et al., Proc. Natl. Acad. Sci. USA 81, 6851-6855 (1984)].
  • chimeric antibodies immunoglobulins in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with
  • “Humanized” forms of non-human (e.g. murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′) 2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin.
  • humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity.
  • humanized antibody may comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and optimize antibody performance.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence.
  • the humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • “Active” or “activity” for the purposes herein refers to form(s) of patched-2 which retain the biologic and/or immunologic activities of native or naturally occurring patched-2.
  • a preferred activity is the ability to bind to and affect, e.g., block or otherwise modulate, hedgehog, especially Desert hedgehog signaling.
  • hedgehog especially Desert hedgehog signaling.
  • antagonist is used herein in the broadest sense to include any molecule which blocks, prevents, inhibits, neutralizes the normal functioning of patched-2 in the Hh signaling pathway.
  • One particular form of antagonist includes a molecule that interferes with the interaction between Dhh (SEQ ID NO:13) and Ptch-2 (SEQ ID NO:2).
  • an antagonist cold also be a molecule which increases the levels of patched-2.
  • the term “agonist” is used herein to include any molecule which promotes, enhances or stimulates the binding of a Hh to patched-2 in the Hh signaling pathway (e.g., blocking binding of Ptch-2 (SEQ ID NO:2) to Smo (SEQ ID NO:17)).
  • Suitable molecules that affect the protein-protein interaction of Hh and Ptch-2 and its binding proteins include fragments of the latter or small bioorganic molecules, e.g., peptidomimetics, which will prevent or enhance, as the case may be, the binding of Hh to Ptch-2.
  • Non-limiting examples include proteins, peptides, glycoproteins, glycopeptides, glycolipids, polysaccharides, oligosaccharides, nucleic acids, bioorganic molecules, peptidomimetics, pharmacological agents and their metabolites, transcriptional and translation control sequences, and the like.
  • Another preferred form of antagonist includes antisense oligonucleotides that inhibit proper transcription of wild type patched-2.
  • modulation means upregulation or downregulation of a signaling pathway.
  • Cellular processes under the control of signal transduction may include, but are not limited to, transcription of specific genes; normal cellular functions, such as metabolism, proliferation, differentiation, adhesion, apoptosis and survival, as well as abnormal processes, such as transformation, blocking of differentiation and metastasis.
  • PCR polymerase chain reaction
  • sequence information from the ends of the region of interest or beyond needs to be available, such that oligonucleotide primers can be designed; these primers will be identical or similar in sequence to opposite strands of the template to be amplified.
  • the 5′ terminal nucleotides of the two primers may coincide with the ends of the amplified material.
  • PCR sequences form total genomic DNA, and cDNA transcribed from total cellular RNA, bacteriophage, or plasmid sequences, etc. See generally Mullis et al., Cold Spring Harbor Symp. Quant. Biol. 51: 263 (1987); Erlich, Ed., PCR Technology, (Stockton Press, NY, 1989).
  • PCR is considered to be one, but not the only, example of a nucleic acid test sample comprising the use of a known nucleic acid as a primer and a nucleic acid polymerase to amplify or generate a specific piece of nucleic acid.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as patched-2.
  • patched-2 polypeptides referred to in the present application as patched-2.
  • Applicants have identified and isolated cDNA encoding a human patched-2 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST, BLAST-2 and FastA sequence alignment computer programs set to the default parameters
  • Applicants found that a full-length native sequence human Ptch-2 (SEQ ID NO:2) (shown in FIG. 3) has 53% amino acid sequence identity with human patched (SEQ ID NO:4).
  • human full-length patched-2 (SEQ ID NO:2) has about a 91% sequence identity with murine Ptch-2 (SEQ ID NO:7) (FIG. 8). Accordingly, it is presently believed that the human patched-2 (SEQ ID NO:2) disclosed in the present application is a newly identified member of the mammalian hedgehog signaling cascade, specifically Desert hedgehog.
  • the full-length native sequence of human patched-2 gene, or portions thereof, may be used as hybridization probes for a cDNA library to isolate the full-length gene or to isolate still other vertebrate homolog genes (for instance, those encoding naturally-occurring variants of patched-2 or patched-2 from other species) which have a desired sequence identity to the human patched-2 sequence disclosed in FIG. 1 (SEQ ID NO:2).
  • the length of the probes will be about 20 to about 50 bases.
  • the hybridization probes may be derived from the nucleotide sequence of FIG. 1 (SEQ ID NO:1) or from genomic sequences including promoters, enhancer elements and introns of native sequence vertebrate patched-2.
  • a screening method will comprise isolating the coding region of the vertebrate patched-2 gene using the known DNA sequence to synthesize a selected probe of about 40 bases.
  • Hybridization probes may be labeled by a variety of labels, including radionucleotides such as 32 P or 35 S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems.
  • Labeled probes having a sequence complementary to that of the vertebrate patched-2 gene of the present invention can be used to screen libraries of human cDNA, genomic DNA or mRNA to determine which members of such libraries the probe hybridizes to.
  • patched-2 variants can be prepared. Patched-2 variants can be prepared by introducing appropriate nucleotide changes into a known patched-2 DNA, or by synthesis of the desired patched-2 polypeptides. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of patched-2.
  • Variations in the native full-length sequence patched-2 or in various domains of the patched-2 described herein, can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Pat. No. 5,364,934.
  • Variations may be a substitution, deletion or insertion of one or more codons encoding the patched-2 that results in a change in the amino acid sequence of patched-2 as compared with the native sequence patched-2.
  • the variation is by substitution of at least one amino acid with any other amino acid in one or more of the domains of patched-2.
  • Guidance in determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired activity may be found by comparing the sequence of the patched-2 with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology.
  • Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements.
  • Insertions or deletions may optionally be in the range of 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity in the in vitro assay described in the Examples below.
  • the variations can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis.
  • Site-directed mutagenesis [Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10: 6487 (1987)]
  • cassette mutagenesis [Wells et al., Gene, 34:315 (1985)]
  • restriction selection mutagenesis [Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)] or other known techniques can be performed on the cloned DNA to produce the vertebrate patched-2 variant DNA.
  • Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence.
  • preferred scanning amino acids are relatively small, neutral amino acids.
  • Such amino acids include alanine, glycine, serine, and cysteine.
  • Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant.
  • Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions [Creighton, The Proteins, (W. H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)]. If alanine substitution does not yield adequate amounts of variant, an isoteric amino acid can be used.
  • Covalent modifications of patched-2 are included within the scope of this invention.
  • One type of covalent modification includes reacting targeted amino acid residues of patched-2 with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of the vertebrate patched-2.
  • Derivatization with bifunctional agents is useful, for instance, for crosslinking patched-2 to a water-insoluble support matrix or surface for use in the method for purifying anti-patched-2 antibodies, and vice-versa.
  • crosslinking agents include, e.g., 1,1-bis(diazo-acetyl)-2-phenylethane, glutaraldehyde, N-hydroxy-succinimide esters, for example, esters with 4-azido-salicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3′-dithiobis-(succinimidyl-propionate), bifunctional maleimides such as bis-N-maleimido-1,8-octane and agents such as methyl-3-[(p-azidophenyl)-dithio]proprioimidate.
  • 1,1-bis(diazo-acetyl)-2-phenylethane glutaraldehyde
  • N-hydroxy-succinimide esters for example, esters with 4-azido-salicylic acid
  • homobifunctional imidoesters including disuccinimidyl esters
  • Another type of covalent modification of patched-2 comprises linking the patched-2 polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.
  • Such modifications would be expected in increase the half-life of the molecules in circulation in a mammalian system; Extended half-life of patched-2 molecules might be useful under certain circumstances, such as where the patched-2 variant is administered as a therapeutic agent.
  • the patched-2 of the present invention may also be modified in a way to form a chimeric molecule comprising patched-2 bonded to another, heterologous polypeptide or amino acid sequence.
  • a chimeric molecule comprises a fusion of patched-2 with a tag polypeptide, which provides an epitope to which an anti-tag antibody can selectively bind.
  • the epitope tag is generally placed at the amino- or carboxyl-terminus of the patched-2. The presence of such epitope-tagged forms of the patched-2 can be detected using an antibody against the tag polypeptide.
  • the epitope tag enables the patched-2 to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag.
  • the chimeric molecule may comprise a fusion of the patched-2 with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule, such a fusion could be to the Fc region of an IgG molecule.
  • the C-terminus of a contiguous amino acid sequence of a patched-2 receptor is fused to the N-terminus of a contiguous amino acid sequence of an immunoglobulin constant region, in place of the variable region(s), however N-terminal fusions are also possible.
  • such fusions retain at least functionally active hinge, CH2 and CH3 domains of the constant region of an immunoglobulin heavy chain. Fusions are also made to the C-terminus of the Fc portion of a constant domain, or immediately N-terminal to the CH1 of the heavy chain or the corresponding region of the light chain. This ordinarily is accomplished by constructing the appropriate DNA sequence and expressing it in recombinant cell culture. Alternatively, immunoadhesins may be synthesized according to known methods.
  • the precise site at which the fusion is made is not critical; particular sites are well known and may be selected in order to optimize the biological activity, secretion or binding characteristics of the immunoadhesins.
  • an immunoglobulin e.g., immunoglobulin G 1 (IgG-1).
  • a sequence beginning in the hinge region just upstream of the papain cleavage site (which defines IgG Fc chemically; residue 216, taking the first residue of heavy chain constant region to be 114 [Kobat et al., supra], or analogous sites of other immunoglobulins) is used in the fusion.
  • residue 216 taking the first residue of heavy chain constant region to be 114 [Kobat et al., supra], or analogous sites of other immunoglobulins
  • the immunoglobulin heavy chain constant domain sequence used in the construction of the immunoadhesins of the present invention may be devoid of a light chain binding site. This can be achieved by removing or sufficiently altering immunoglobulin heavy chain sequence elements to which the light chain is ordinarily linked so that such binding is no longer possible.
  • the CH1 domain can be entirely removed in certain embodiments of the patched-2/immunoglobulin chimeras.
  • the amino acid sequence containing the extracellular domain(s) of patched-2 is fused to the hinge region and CH2, CH3; or CH1, hinge, CH2 and CH3 domains of an IgG-1, IgG-2, IgG-3, or IgG-4 heavy chain.
  • the patched-2/immunoglobulin molecules are assembled as monomers, dimers or multimers, and particularly as dimers or tetramers.
  • these assembled immunoadhesins will have known unit structures similar to those of the corresponding immunoglobulins.
  • a basic four chain structural unit (a dimer of two immunoglobulin heavy chain-light chain pairs) is the form in which IgG, IgA and IgE exist.
  • a four chain unit is repeated in the high molecular weight immunoglobulins; IgM generally exists as a pentamer of basic four-chain units held together by disulfide bonds.
  • IgA globulin, and occasionally IgG globulin may also exist in a multimeric form in serum. In the case of multimers, each four chain unit may be the same or different.
  • the entire immunoglobulin portion of the patched-2/immunoglobulin chimeras be from the same immunoglobulin.
  • Various portions of different immunoglobulins may be combined, and variants and derivatives of native immunoglobulins can be made as herein above described with respect to patched-2, in order to optimize the properties of the immunoadhesin molecules.
  • immunoadhesin constructs in which the hinge of IgG-1 was replaced with that of IgG-3 were found to be functional and showed pharmacokinetics comparable to those of immunoadhesins comprising the entire IgG-1 heavy chain.
  • tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags; the flu HA tag polypeptide and its antibody 12CA5 [Field et al., Mol. Cell.
  • tag polypeptides include the Flag-peptide [Hopp et al., BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin et al., Science, 255:192-194 (1992)]; an ⁇ -tubulin epitope peptide [Skinner et al., J. Biol. Chem., 266:15163-15166 (1991)]; and the T7 gene 10 protein peptide tag [Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA, 87:6393-6397 (1990)].
  • a preferred tag is the influenza HA tag.
  • patched-2 sequence or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart et al., Solid - Phase Peptide Synthesis, W. H. Freeman Co., San Francisco, Calif. (1969); Merrifield, J. Am. Chem. Soc., 85:2149-2154 (1963)].
  • In vitro protein synthesis may be performed using manual techniques or by automation.
  • Automated synthesis may be accomplished, for instance, using an Applied Biosystems Peptide Synthesizer (Foster City, Calif.) using manufacturer's instructions.
  • Various portions of the vertebrate patched-2 may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full-length patched-2.
  • DNA encoding patched-2 may be obtained from a cDNA library prepared from tissue believed to possess the patched-2 mRNA and to express it at a detectable level. Accordingly, human patched-2 DNA can be conveniently obtained from a cDNA library prepared from human tissue, such as described in the Examples.
  • the vertebrate patched-2-encoding gene may also be obtained from a genomic library or by oligonucleotide synthesis.
  • Libraries can be screened with probes (such as antibodies to the patched-2 or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989). An alternative means to isolate the gene encoding vertebrate patched-2 is to use PCR methodology [Sambrook et al., supra; Dieffenbach et al., PCR Primer. A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].
  • the oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized.
  • the oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like 32 P-labeled ATP, biotinylation or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook et al., supra.
  • Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available in public databases such as GenBank or other private sequence databases. Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined through sequence alignment using computer software programs such as BLAST, BLAST-2, ALIGN, DNAstar, and INHERIT which employ various algorithms to measure homology.
  • Nucleic acid having protein coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.
  • Host cells are transfected or transformed with expression or cloning vectors described herein for patched-2 production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the culture conditions such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology: A Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook et al., supra.
  • Methods of transfection are known to the ordinarily skilled artisan, for example, CaPO 4 and electroporation.
  • transformation is performed using standard techniques appropriate to such cells.
  • the calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes or other cells that contain substantial cell-wall barriers.
  • Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw et al., Gene, 23:315 (1983) and WO 89/05859 published Jun. 29, 1989.
  • DNA into cells such as by nuclear microinjection, electroporation, bacterial protoplast fusion with intact cells, or polycations, e.g., polybrene, polyornithine, may also be used.
  • polycations e.g., polybrene, polyornithine.
  • Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells.
  • Suitable prokaryotes include but are not limited to eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriae such as E. coli .
  • Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W3110 (ATCC 27,325) and K5 772 (ATCC 53,635).
  • eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for vertebrate patched-2-encoding vectors.
  • Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism.
  • Suitable host cells for the expression of vertebrate patched-2 are derived from multicellular organisms.
  • invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells.
  • useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., J. Gen Virol., 36:59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci.
  • mice sertoli cells TM4, Mather, Biol. Reprod. 23:243-251 (1980)
  • human lung cells W138, ATCC CCL 75
  • human liver cells Hep G2, HB 8065
  • mouse mammary tumor MMT 060562, ATCC CCL51. The selection of the appropriate host cell is deemed to be within the skill in the art.
  • the nucleic acid (e.g., cDNA or genomic DNA) encoding patched-2 may be inserted into a replicable vector for cloning (amplification of the DNA) or for expression.
  • a replicable vector for cloning (amplification of the DNA) or for expression.
  • the vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage.
  • the appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art.
  • Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques, which are known to the skilled artisan.
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses.
  • the origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2 ⁇ plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
  • a preferred replicable expression vector is the plasmid is pRK5. Holmes et al., Science, 253:1278-1280 (1991).
  • Selection genes will typically contain a selection gene, also termed a selectable marker.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g. ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
  • Suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the patched-2 nucleic acid, such as DHFR or thymidine kinase.
  • An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980).
  • a suitable selection gene for use in yeast is the trp1 gene present in the yeast plasmid YRp7 [Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)].
  • the trp1 gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].
  • Expression and cloning vectors usually contain a promoter operably linked to the patched-2 nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the ⁇ -lactamase and lactose promoter systems [Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281:544 (1979)], alkaline phosphatase, a tryptophan (trp) promoter system [Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], and hybrid promoters such as the tac promoter [deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21-25 (1983)]. Promoters for use in bacterial systems also will contain a Shine-Dalgamo (S.D.) sequence operably linked to the DNA encoding
  • Suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase [Hitzeman et al., J. Biol. Chem., 255:2073 (1980)] or other glycolytic enzymes [Hess et al., J. Adv.
  • yeast promoters which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.
  • Patched-2 transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published Jul. 5, 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published Jul. 5, 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retro
  • Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription.
  • Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, ⁇ -fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus.
  • Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the enhancer may be spliced into the vector at a position 5′ or 3′ to the patched-2 coding sequence, but is preferably located at a site 5′ from the promoter.
  • Expression vectors used in eukaryotic host cells will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding patched-2.
  • Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, Proc. Natl. Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein.
  • antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.
  • Gene expression may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product.
  • Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence patched-2 polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence patched-2 to patched-2 DNA and encoding a specific antibody epitope.
  • Forms of patched-2 may be recovered from host cell lysates. Since patched-2 is membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g. Triton-X 100) or by enzymatic cleavage. Cells employed in expression of patched-2 can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents.
  • a suitable detergent solution e.g. Triton-X 100
  • Cells employed in expression of patched-2 can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents.
  • patched-2 may be desired to purify patched-2 from recombinant cell proteins or polypeptides.
  • the following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanol precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; protein A Sepharose columns to remove contaminants such as IgG; and metal chelating columns to bind epitope-tagged forms of the patched-2.
  • Patched-2 is a specific receptor for Dhh
  • the hedgehog signaling pathway has been implicated in the formation of embryonic structures in mammals and invertebrates.
  • the multi-pass transmembrane receptor Ptch is a negative regulator of the hedgehog pathway, repressing the serpentine signaling molecule Smoothened (Smo). Data have shown that loss of Ptch leads to deregulation of the hedgehog pathway leading to formation of aberrant structures in the embryos and carcinoma in the adult.
  • patched-2 has a similar 12 transmembrane domain topology as does patched, and can bind to all the members of the Hh family and can complex with Smo (SEQ ID NO:17).
  • Smo SEQ ID NO:17
  • Ptch-2 and Ptch do not overlap.
  • Ptch-2 is expressed mainly in the developing spermatocytes, which are supported directly by the Dhh producing Sertoli cells, which suggests that Ptch-2 is a receptor for Desert hedgehog.
  • Sertoli cells which are unusually large secretory cells, traverse the seminiferous tubule from the basal lamina to the luminal aspect, sending out cytoplasmic protrusions that engulf the germ cells. These contacts are particularly close during spermiogenesis, in which the haploid round spermatids undergo differentiation to produce the highly specialized, motile sperm. Tight junctions between adjacent Sertoli cells compartmentalize the tubule into a basal region, which contains mitotic spermatogonia and early spermtocytes, and an adluminal compartment, which contains meiotic spermatocytes and maturing spermatids.
  • a Sertoli-derived cell line supports the meiotic progression of germ cells in culture, consistent with the view that factors derived from Sertoli cells contribute to germ cell maturation, Rassoulzadegan, M., et al., Cell 1993, 75: 997-1006. Loss of Dhh activity results in a recessive, sex-specific phentotype. Female mice homozygous for the mutation were fully viable and fertile, whereas male mice were viable but infertile. A gross examination indicated that, as early as 18.5 dpc, the testes of mutant males were noticeably smaller than those of heterozygous littermates. Bitgood et al., Curr. Biol., 1996 6(3): 298-304.
  • patched-2 appears to be the receptor for Dhh (SEQ ID NO:13), molecules which modulate the binding of Dhh (SEQ ID NO:13) to Ptch-2 would affect the activation of Dhh signaling, and thereby would have utility in the treatment of conditions which are modulated by Dhh (SEQ ID NO:13).
  • Dhh SEQ ID NO:13
  • antagonists or agonists of patched-2 may be used for treating disorders or creating a desirable physiological condition effected by blocking Dhh (SEQ ID NO:13) signaling. (E.g, contraception, infertility treatment).
  • Nucleotide sequences (or their complement) encoding patched-2 have various applications in the art of molecular biology, including uses as hybridization probes, in chromosome and gene mapping and in the generation of anti-sense RNA and DNA. Patched-2 nucleic acid will also be useful for the preparation of patched-2 polypeptides by the recombinant techniques described herein.
  • the full-length native sequence patched-2 gene, or portions thereof, may be used as hybridization probes for a cDNA library to isolate the full-length gene or to isolate still other genes (for instance, those encoding naturally-occurring variants of patched-2) which have a desired sequence identity to the patched-2 sequence disclosed in FIG. 1 (SEQ ID NO:1).
  • the length of the probes will be about 20 to about 50 bases.
  • the hybridization probes may be derived from the nucleotide sequence of FIG. 1 (SEQ ID NO:1) or from genomic sequences including promoters, enhancer elements and introns of native sequence patched-2.
  • a screening method will comprise isolating the coding region of the patched-2 gene using the known DNA sequence to synthesize a selected probe of about 40 bases.
  • Hybridization probes may be labeled by a variety of labels, including radionucleotides such as 32 P or 35 S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems. Labeled probes having a sequence complementary to that of the patched-2 gene of the present invention can be used to screen libraries of human cDNA, genomic DNA or mRNA to determine to which members of such libraries the probe hybridizes. Hybridization techniques are described in further detail in the Examples below.
  • the probes may also be employed in PCR techniques to generate a pool of sequences for identification of closely related patched-2 sequences.
  • Nucleotide sequences encoding patched-2 can also be used to construct hybridization probes for mapping the gene, which encodes patched-2 and for the genetic analysis of individuals with genetic disorders.
  • the nucleotide sequences provided herein may be mapped to a chromosome and specific regions of a chromosome using known techniques, such as in situ hybridization, linkage analysis against known chromosomal markers, and hybridization screening with libraries.
  • Patched-2 polypeptides can be used in assays to identify the other proteins or molecules involved in complexing with patched-2 which ultimately results in the modulation of hedgehog signaling. Alternatively, these molecules can modulate the binding of patched-2 to Dhh (SEQ ID NO:13). By such methods, inhibitors of the binding interaction can be identified. Proteins involved in such binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction. Also, the substrate of patched-2 can be used to isolate correlative complexing proteins. Screening assays can be designed to find lead compounds that mimic the biological activity of a native patched-2 or to find those that act as a substrate for patched-2.
  • screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates.
  • small molecule inhibitors could block the enzymatic action of patched-2, and thereby inhibit hedgehog signaling.
  • Small molecules contemplated include synthetic organic or inorganic compounds.
  • the assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays and cell based assays, which are well characterized in the art.
  • Nucleic acids which encode patched-2 or its modified forms can also be used to generate either transgenic animals or “knock out” animals which, in turn, are useful in the development and screening of therapeutically useful reagents.
  • a transgenic animal e.g., a mouse or rat
  • a transgene is a DNA sequence that is integrated into the genome of a cell from which a transgenic animal develops.
  • cDNA encoding patched-2 can be used to clone genomic DNA encoding patched-2 in accordance with established techniques and the genomic sequences used to generate transgenic animals that contain cells which express DNA encoding patched-2.
  • Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. Nos. 4,736,866 and 4,870,009.
  • particular cells would be targeted for patched-2 transgene incorporation with tissue-specific enhancers.
  • Transgenic animals that include a copy of a transgene encoding patched-2 introduced into the germ line of the animal at an embryonic stage can be used to examine the effect of increased expression of DNA encoding patched-2.
  • Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression.
  • Non-human homologues of vertebrate patched-2 can be used to construct a patched-2 “knock out” animal which has a defective or altered gene encoding patched-2 as a result of homologous recombination between the endogenous gene encoding patched-2 and altered genomic DNA encoding patched-2 introduced into an embryonic cell of the animal.
  • cDNA encoding patched-2 can be used to clone genomic DNA encoding patched-2 in accordance with established techniques. A portion of the genomic DNA encoding patched-2 can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration.
  • flanking DNA typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector [see e.g., Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologous recombination vectors].
  • the vector is introduced into an embryonic stem cell line (e.g. by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected [see e.g., Li et al, Cell, 69:915 (1992)].
  • the selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras [see e.g.
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a “knock out” animal.
  • Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA.
  • Knockout animals can be characterized for instance, for their ability to defend against certain pathological conditions and for their development of pathological conditions due to absence of the patched-2 polypeptide.
  • Suppression or inhibition (antagonism) of Dhh signaling is also an objective of therapeutic strategies. Since patched-2 can combine with all members of the hedgehog family (i.e., Shh, Dhh, Ihh), antagonist molecules which prevent the binding of hedgehog molecules to Ptch-2 (SEQ ID NO:2) have therapeutic utility.
  • SHh signaling is known to be activated in Basal Cell Carcinoma
  • Dhh (SEQ ID NO:13) is known to be involved in the regulation of spermatogenesis.
  • Inhibitor or antagonist of Hh signaling would be effective therapeutics in the treatment of Basal Cell Carcinoma or male contraception, respectively.
  • Dhh signaling (agonism) is also an objective of therapeutic strategies. Since Ptch-2 (SEQ ID NO:2) also binds to the other members of the Hh family, Ihh and Shh, activating Dhh signaling would be useful in disease states or disorders characterized by inactive or insufficient Hh signaling. For example, degenerative disorders of the nervous system, e.g., Parkinson's disease, memory deficits, Alzheimer's disease, Lou Gehrig's disease, Huntington's disease, schizophrenia, stroke and drug addiction. Additionally, patched-2 agonists could be used to treat gut diseases, bone diseases, skin diseases, diseases of the testis (including infertility), ulcers, lung diseases, diseases of the pancreas, diabetes, osteoporosis.
  • Ptch-2 SEQ ID NO:2
  • Ihh and Shh activating Dhh signaling would be useful in disease states or disorders characterized by inactive or insufficient Hh signaling.
  • degenerative disorders of the nervous system e.g., Parkinson's disease
  • the present invention further provides anti-vertebrate patched-2 antibodies.
  • Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies.
  • the anti-patched-2 antibodies may comprise polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections.
  • the immunizing agent may include the patched-2 polypeptide or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized.
  • immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.
  • adjuvants examples include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.
  • the anti-patched-2 antibodies may, alternatively, be monoclonal antibodies.
  • Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975).
  • a hybridoma method a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
  • the lymphocytes may be immunized in vitro.
  • the immunizing agent will typically include the patched-2 polypeptide or a fusion protein thereof.
  • PBLs peripheral blood lymphocytes
  • spleen cells or lymph node cells are used if non-human mammalian sources are desired.
  • the lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell [Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103].
  • Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin.
  • rat or mouse myeloma cell lines are employed.
  • the hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused immortalized cells.
  • a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused immortalized cells.
  • the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.
  • Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Rockville, Maryland. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies [Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al, Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63].
  • the culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against patched-2.
  • the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA).
  • RIA radioimmunoassay
  • ELISA enzyme-linked immunoabsorbent assay
  • the binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107:220 (1980).
  • the clones may be subcloned by limiting dilution procedures and grown by standard methods [Goding, supra]. Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal.
  • the monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
  • the monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567.
  • DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies).
  • the hybridoma cells of the invention serve as a preferred source of such DNA.
  • the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.
  • host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.
  • the DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences [U.S. Pat. No. 4,816,567; Morrison et al., supra] or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide.
  • non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.
  • the antibodies may be monovalent antibodies.
  • Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain.
  • the heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosslinking.
  • the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking.
  • the anti-patched-2 antibodies of the invention may further comprise humanized antibodies or human antibodies.
  • Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′) 2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin.
  • Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity.
  • CDR complementary determining region
  • Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • Humanized antibodies may also comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence.
  • the humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Bol., 2:593-596 (1992)].
  • Fc immunoglobulin constant region
  • a humanized antibody has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain.
  • Humanization can be essentially performed following the method of Winter and co-workers [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)], by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.
  • rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.
  • such “humanized” antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species.
  • humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
  • Human antibodies can also be produced using various techniques known in the art, including phage display libraries [Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991)].
  • the techniques of Cole et al. and Boerner et al. are also available for the preparation of human monoclonal antibodies (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al., J. Immunol., 147(1):86-95 (1991)].
  • Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens.
  • one of the binding specificities is for the vertebrate patched-2, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit.
  • bispecific antibodies Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities [Milstein and Cuello, Nature, 305:537-539 (1983)]. Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., EMBO J., 10:3655-3659(1991).
  • Antibody variable domains with the desired binding specificities can be fused to immunoglobulin constant domain sequences.
  • the fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions.
  • DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain are inserted into separate expression vectors, and are co-transfected into a suitable host organism.
  • Heteroconjugate antibodies are also within the scope of the present invention.
  • Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells [U.S. Pat. No. 4,676,980], and for treatment of HIV infection [WO 91/00360; WO 92/200373; EP 03089].
  • the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents.
  • immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Pat. No. 4,676,980.
  • anti-patched-2 antibodies of the invention have various utilities.
  • anti-patched-2 antibodies may be used in diagnostic assays for patched-2, e.g., detecting its expression in specific cells, tissues, or serum.
  • diagnostic assay techniques known in the art may be used, such as competitive binding assays, direct or indirect sandwich assays and immunoprecipitation assays conducted in either heterogeneous or homogeneous phases [Zola, Monoclonal Antibodies: A Manual of Techniques, CRC Press, Inc. (1987) pp. 147-158].
  • the antibodies used in the diagnostic assays can be labeled with a detectable moiety.
  • the detectable moiety should be capable of producing, either directly or indirectly, a detectable signal.
  • the detectable moiety may be a radioisotope, such as 3 H, 14 C, 32 P, 35 S, or 125 I, a fluorescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin, or an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • a radioisotope such as 3 H, 14 C, 32 P, 35 S, or 125 I
  • a fluorescent or chemiluminescent compound such as fluorescein isothiocyanate, rhodamine, or luciferin
  • an enzyme such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • Any method known in the art for conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al., Nature, 144: 945 (1962); David et
  • Anti-patched-2 antibodies also are useful for the affinity purification of patched-2 from recombinant cell culture or natural sources.
  • the antibodies against patched-2 are immobilized on a suitable support, such a Sephadex resin or filter paper, using methods well known in the art.
  • the immobilized antibody then is contacted with a sample containing the patched-2 to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except the patched-2, which is bound to the immobilized antibody. Finally, the support is washed with another suitable solvent that will release the patched-2 from the antibody.
  • Basal cell carcinoma is the most common human cancer.
  • the Hh signaling pathway was found to activated in all BCCs. Loss of Ptch function is thought to lead to unregulated Smo activity and is responsible for about half of all BCCs.
  • Ptch being a target of the Hh pathway itself, increases in Ptch mRNA levels have been detected in BCC [Galiani, et al., Nature Genet. 14: 78-81 (1996)] as well as in animal models of BCC. Oro et al., Science 276: 817-821 (1997); Xie et al., Nature 391: 90-92 (1998).
  • Anti-patched-2 antibodies also have utilities similar to those articulated for under the previous section “E. Uses of Patched-2”. Depending on whether anti-patched-2 antibodies will bind patched-2 receptors so as to either inhibit Hh signaling (antagonist) or inhibit patched-2 complexing with Smo (SEQ ID NO:17) and thereby remove the normal inhibitory effect of Smo (SEQ ID NO:17) on Hh signaling (agonist) the antibody will have utilities corresponding to those articulated previously for patched-2.
  • any approach where the antagonist molecule can be targeted to the interior of the cell, which interferes or prevents wild type patched-2 from normal operation is suitable.
  • competitive inhibitors including mutant patched-2 receptors which prevent wild type patched-2 from properly binding with other proteins necessary for Dhh and Hh signaling. Additional properties of such antagonist or agonist molecules are readily determinable by one of ordinary skill, such as size, charge and hydrophobicity suitable for transmembrane transport.
  • the cells are exposed to the test compound and compared to positive controls which are exposed only to human patched-2, and to negative controls which were not exposed to either the compound or the natural ligand.
  • the cells are exposed to the compound of the invention in the presence of the natural ligand and compared to controls which are not exposed to the test compound.
  • Detection assays may by employed as a primary screen to evaluate the Hh signaling inhibition/enhancing activity of the antagonist/agonist compounds of the invention.
  • the assays may also be used to assess the relative potency of a compound by testing a range of concentrations, in a range from 100 mM to 1 pM, for example, and computing the concentration at which the amount of phosphorylation or signal transduction is reduced or increased by 50% (IC 50 ) compared to controls.
  • Assays can be performed to identify compounds that affect Hh signaling of patched-2 substrates. Specifically, assays can be performed to identify compounds that increase the phosphorylation activity of patched-2 or assays can be performed to identify compounds that decrease the Hh signaling of patched-2 substrates. These assays can be performed either on whole cells themselves or on cell extracts. The assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays, cell based assays, etc. Such assay formats are well known in the art.
  • the screening assays of the present invention are amenable to high-throughput screening of chemical libraries, and are particularly suitable for identifying small molecule drug candidates.
  • the assay mixture is incubated under conditions whereby, but for the presence of the candidate pharmacological agent, patched-2 induces hedgehog signaling with a reference activity.
  • the mixture components can be added in any order that provides for the requisite hedgehog activity.
  • Incubation may be performed at any temperature that facilitates optimal binding, typically between about 4° and 40° C., more commonly between about 15° and 40° C.
  • Incubation periods are likewise selected for optimal binding but also minimized to facilitate rapid, high-throughput screening, and are typically between about 0.1 and 10 hours, preferably less than 5 hours, more preferably less than 2 hours.
  • the effect of the candidate pharmacological agent on the patched-2 signaling is determined in any convenient way.
  • a separation step is often used to separate bound and unbound components. Separation may, for example, be effected by precipitation (e.g. TCA precipitation, immunoprecipitation, etc.), immobilization (e.g. on a solid substrate), followed by washing.
  • the bound protein is conveniently detected by taking advantage of a detectable label attached to it, e.g. by measuring radioactive emission, optical or electron density, or by indirect detection using, e.g. antibody conjugates.
  • a method of screening for suitable patched-2 antagonists and/or agonists could involve the application of Dhh and other hedgehog ligands.
  • Such a screening assay could compare in situ hybridization in the presence and absence of the candidate antagonist and/or agonist in a patched-2 expressing tissue as well as confirmation or absence of patched-2 modulated cellular development.
  • these methods involve exposing an immobilized patched-2 to a molecule suspected of binding thereto and determining the level of ligand binding downstream activation of reporter constructs and/or evaluating whether or not the molecule activates (or blocks activation of) patched-2.
  • patched-2 can be expressed on the surface of a cell and used to screen libraries of synthetic candidate compounds or naturally-occurring compounds (e.g., from endogenous sources such as serum or cells).
  • Suitable molecules that affect the protein-protein interaction of patched-2 and its binding proteins include fragments of the latter or small molecules, e.g., peptidomimetics, which will inhibit ligand-receptor interaction.
  • small molecules which are usually less than 10 K molecular weight, are preferable as therapeutics since they are more likely to be permeable to cells, are less susceptible to degradation by various cellular mechanisms, and are not as apt to elicit an immune response as proteins.
  • Small molecules include but are not limited to synthetic organic or inorganic compounds. Many pharmaceutical companies have extensive libraries of such molecules, which can be conveniently screened by using the assays of the present invention.
  • Non-limiting examples include proteins, peptides, glycoproteins, glycopeptides, glycolipids, polysaccharides, oligosacchardies, nucleic acids, bioorganic molecules, peptidomimetics, pharmacological agents and their metabolites, transcriptional and translation control sequences, and the like.
  • a preferred technique for identifying molecules which bind to patched-2 utilizes a chimeric substrate (e.g., epitope-tagged patched-2 or patched-2 immunoadhesin) attached to a solid phase, such as the well of an assay plate.
  • a chimeric substrate e.g., epitope-tagged patched-2 or patched-2 immunoadhesin
  • the binding of the candidate molecules, which are optionally labeled (e.g., radiolabeled) to the immobilized receptor can be measured.
  • competition for various Hh pathways, especially Dhh (SEQ ID NO:13) can be measured.
  • patched-2 can be exposed to a patched-2 substrate followed by the putative antagonist and/or agonist, or the patched-2 binding protein and antagonist and/or agonist can be added simultaneously, and the ability of the antagonist and/or agonist to block patched-2 activation can be evaluated.
  • the patched-2 polypeptides are useful in assays for identifying lead compounds for therapeutically active agents that modulate patched-2 receptor/ligand hedgehog signaling. Specifically, lead compounds that either prevent the formation of patched-2 signaling complexes or prevent or attenuate patched-2 modulated hedgehog signaling (e.g., binding to patched-2) can be conveniently identified.
  • patched-2 is believed to be a receptor for Dhh (SEQ ID NO:13), but also binds Shh (SEQ ID NO:14) and Ihh (SEQ ID NO:29), techniques known for use with identifying ligand/receptor modulators may also be employed with the present invention.
  • assays involve exposing target cells in culture to the compounds and a) biochemically analyzing cell lysates to assess the level and/or identity of binding; or (b) scoring phenotypic or functional changes in treated cells as compared to control cells that were not exposed to the test substance.
  • biotechniques are described in U.S. Pat. No. 5,602,171, U.S. Pat. No. 5,710,173, WO 96/35124 and WO 96/40276.
  • Biochemical analysis can be evaluated by a variety of techniques.
  • One typical assay mixture which can be used with the present invention contains patched-2 and a ligand protein with which patched-2 is normally associated (e.g., Dhh (SEQ ID NO:13)) usually in an isolated, partially pure or pure form.
  • patched-2 e.g., Dhh (SEQ ID NO:13)
  • Dhh SEQ ID NO:13
  • One or both of these components may be patched-2 to another peptide or polypeptide, which may, for example, provide or enhance protein-protein binding, improve stability under assay conditions, etc.
  • one of the components usually comprises or is coupled to a detectable label.
  • the label may provide for direct detection by measuring radioactivity, luminescence, optical or electron density, etc., or indirect detection such as an epitope tag, an enzyme, etc.
  • the assay mixture can additionally comprise a candidate pharmacological agent, and optionally a variety of other components, such as salts, buffers, carrier proteins, e.g. albumin, detergents, protease inhibitors, nuclease inhibitors, antimicrobial agents, etc., which facilitate binding, increase stability, reduce non-specific or background interactions, or otherwise improve the efficiency or sensitivity of the assay.
  • a candidate pharmacological agent e.g. albumin, detergents, protease inhibitors, nuclease inhibitors, antimicrobial agents, etc.
  • the following detection methods may also be used in a cell-free system wherein cell lysate containing the signal transducing substrate molecule and patched-2 is mixed with a compound of the invention.
  • the reaction mixture may be analyzed by the SDS-PAGE technique or it may be added to substrate-specific anchoring antibody bound to a solid support, and a detection procedure as described above is performed on the separated or captured substrate to assess the presence or absence of a patched-2 binding ligand. The results are compared to those obtained with reaction mixtures to which the compound is not added.
  • the cell-free system does not require the natural ligand or knowledge of its identity. For example, Posner et al. (U.S. Pat. No.
  • a common technique involves incubating cells with patched-2 and radiolabeled ligand, lysing the cells, separating cellular protein components of the lysate using an SDS-polyacrylamide gel (SDS-PAGE) technique, in either one or two dimensions, and detecting the presence of labeled proteins by exposing X-ray film. Detection can also be effected without using radioactive labeling.
  • SDS-PAGE SDS-polyacrylamide gel
  • the anti-patched-2 ligand antibody can be conjugated with an enzyme, such as horseradish peroxidase, and detected by subsequent addition of a colorimetric substrate for the enzyme.
  • an enzyme such as horseradish peroxidase
  • a further alternative involves detecting the anti-patched-2 ligand by reacting with a second antibody that recognizes anti-patched-2 ligand, this second antibody being labeled with either a radioactive moiety or an enzyme as previously described. Examples of these and similar techniques are described in Hansen et al., Electrophoresis 14: 112-126 (1993); Campbell et al., J. Biol. Chem. 268: 7427-7434 (1993); Donato et al., Cell Growth Diff.
  • the anti-patched-2 ligand can be detected by labeling it with a radioactive substance, followed by scanning the labeled nitrocellulose to detect radioactivity or exposure of X-ray film.
  • Tumor cell lines propagated in in vitro cell cultures can be introduced in experimental rodents, e.g. mice by injection, for example by the subcutaneous route. Techniques for chemical inducement of tumors in experimental animals are well known in the art.
  • patched-2 is a negative regulator of Hh signaling, which when activated by Hh releases the normal inhibitory effect on Smo, the inhibition of patched-2 binding to Smo can be measured by activation of various kinase substrate associated with Hh signaling.
  • the target kinase e.g. fused
  • the target kinase can be a substantially purified polypeptide.
  • the kinase substrate (e.g., MBP, Gli) is a substantially purified substrate, which in the assay is phosphorylated in a reaction with a substantially purified phosphate source that is catalyzed by the kinase.
  • the extent of phosphorylation is determined by measuring the amount of substrate phosphorylated in the reaction.
  • a variety of possible substrates may be used, including the kinase itself in which instance the phosphorylation reaction measured in the assay is autophosphorylation. Exogenous substrates may also be used, including standard protein substrates such as myelin basic protein (MBP); yeast protein substrates; synthetic peptide substrates, and polymer substrates. Of these, MBP and other standard protein substrates may be regarded as preferred.
  • substrates may be identified, however, which are superior by way of affinity for the kinase, minimal perturbation of reaction kinetics, possession of single or homogenous reaction sites, ease of handling and post-reaction recover, potential for strong signal generation, and resistance or inertness to test compounds.
  • Measurement of the amount of substrate phosphorylated in the ex vivo assay of the invention may be carried out by means of immunoassay, radioassay or other well-known methods.
  • an antibody such as a goat or mouse anti-phosphoserine/threonine antibody
  • the phosphoserine/threonine antibody complex would itself be detected by a further antibody linked to a label capable of developing a measurable signal (as for example a fluorescent or radioactive label).
  • ELISA-type assays in microtitre plates may be used to test purified substrates.
  • detection schemes can measure substrate depletion during the kinase reaction.
  • the phosphate source may be radiolabeled with an isotope such as 32 P or 33 P, and the amount of substrate phosphorylation may be measured by determining the amount of radiolabel incorporated into the substrate during the reaction.
  • Detection may be accomplished by: (a) commercially available scintillant-containing plates and beads using a beta-counter, after adsorption to a filter or a microtitre well surface, or (b) photometric means after binding to a scintillation proximity assay bead or scintillant plate. Weemink and Kijken, J. Biochem. Biophs.
  • the substrate is attached to a solid support surface by means of non-specific or, preferably, specific binding.
  • Such attachment permits separation of the phosphorylated substrate from unincorporated, labeled phosphate source (such as adenosine triphosphate prior to signal detection.
  • the substrate may be physically immobilized prior to reaction, as through the use of NuncTM high protein binding plate (Hanke et al., J. Biol. Chem. 271: 695 (1996)) or Wallac ScintiStripTM plates (Braunwalder et al., Anal. Biochem. 234: 23 (1996).
  • Substrate may also be immobilized after reaction by capture on, for example, P81 phophocellulose (for basic peptides), PEI/acidic molybdate resin or DEAE, or TCA precipitation onto WhatmanTM 3MM paper, Tiganis et al., Arch. Biochem. Biophys. 325: 289 (1996); Morawetz et al., Mol. Gen. Genet. 250; 17 (1996); Budde et al., Int J. Pharmacognosy 33: 27 (1995) and Casnellie, Meth. Enz. 200: 115 (1991).
  • P81 phophocellulose for basic peptides
  • PEI/acidic molybdate resin or DEAE or TCA precipitation onto WhatmanTM 3MM paper, Tiganis et al., Arch. Biochem. Biophys. 325: 289 (1996); Morawetz et al., Mol. Gen. Genet. 250; 17 (1996); Budde et al., Int J. Pharma
  • Yet another possibility is the attachment of the substrate to the support surface, as by conjugation with binding partners such as glutathione and streptavidin (in the case of GST and biotin), respectively) which have been attached to the support, or via antibodies specific for the tags which are likewise attached to the support.
  • binding partners such as glutathione and streptavidin (in the case of GST and biotin), respectively) which have been attached to the support, or via antibodies specific for the tags which are likewise attached to the support.
  • Tumor cell lines propagated in in vitro cell cultures can be introduced in experimental rodents, e.g. mice by injection, for example by the subcutaneous route. Techniques for chemical inducement of tumors in experimental animals are well known in the art.
  • the ability of the antagonist/agonist compounds of the invention to modulate the activity of patched-2, which itself modulates hedgehog signaling may also be measured by scoring for morphological or functional changes associated with ligand binding. Any qualitative or quantitative technique known in the art may be applied for observing and measuring cellular processes which comes under the control of patched-2.
  • the activity of the compounds of the invention can also be assessed in animals using experimental models of disorders caused by or related to dysfunctional hedgehog signaling. For example, ineffective Dhh hedgehog signaling in mice leads to viable but sterile mice. Additionally, proper Shh signaling is critical to murine embryonic development at the notochord and floor plate, neural tube, distal limb structures, spinal column and ribs.
  • Improper Shh signaling is also correlative with cyclopia. Any of these phenotypic properties could be evaluated and quantified in a screening assay for patched-2 antagonists and/or agonist. Disease states associated with overexpression of hedgehog is associated with basal cell carcinoma while inactive Shh signaling leads to improper neural development.
  • the data obtained from these cell culture assays and animal studies can be used in formulating a range of dosages for use in humans.
  • the dosage of the compounds of the invention should lie within a range of circulating concentrations with little or no toxicity.
  • the dosage may vary within this range depending on the dosage form employed and the route of administration.
  • Another preferred class of antagonists involves the use of gene therapy techniques, include the administration of antisense oligonucleotides.
  • Applicable gene therapy techniques include single or multiple administrations of therapeutically effective DNA or mRNA.
  • Antisense RNAs and DNAs can be used as therapeutic agents for blocking the expression of certain genes in vivo.
  • Reference short antisense oligonucleotides can be imported into cells where they act as inhibitors, despite their low intracellular concentrations caused by restricted uptake by the cell membrane, Zamecnik et al., Proc. Natl. Acad. Sci. USA 83: 4143-4146 (1986).
  • the anti-sense oligonucleotides can be modified to enhance their uptake, e.g., by substituting their negatively charged phophodiester groups by uncharged groups.
  • nucleic acids there are a variety of techniques known for introducing nucleic acids into viable cells.
  • the techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, ex vivo, or in vivo in the cells of the intended host.
  • Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microinjection, cell fusion, DEAE-dextran, the calcium phosphate precipitation method, etc.
  • the currently preferred in vivo gene transfer techniques include transfection with viral (typically retroviral) vectors and viral coat protein-liposome mediated transfection, Dzau et al., Trends Biotech. 11: 205-210 (1993).
  • an agent that targets the cells such as an antibody specific for a cell surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g., capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, and proteins that target intracellular localization and enhance intracellular half-life.
  • an agent that targets the cells such as an antibody specific for a cell surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g., capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, and proteins that target intracellular localization and enhance intracellular half-life.
  • the technique of receptor-mediated endocytosis is described, for example, by Wu et al., J. Biol. Chem. 262: 4429-4432 (1987); Wagner et al., Proc. Natl. Acad. Sci. USA 87: 3410-3414 (1990).
  • patched-2 expression may be reduced by providing patched-2-expressing cells with an amount of patched-2 antisense RNA or DNA effective to reduce expression of the patched-2 protein.
  • Another use of the compounds of the invention is to help diagnose whether a disorder is driven, to some extent, by patched-2 or hedgehog signaling.
  • patched-2 or hedgehog signaling For example, basal cell carcinoma cells are associated with active hedgehog signaling, spermatocyte formation is associated with Dhh signaling, and defective Ptch and Ptch-2 suppression may be associated with testicular carcinomas.
  • a diagnostic assay to determine whether a particular disorder is driven by Ptch-2 modulated hedgehog signaling can be carried out using the following steps: (1) culturing test cells or tissues; (2) administering a compound which can prevent Ptch-2 (SEQ ID NO:2) binding with Smo (SEQ ID NO:17), thereby activating the Hh signaling pathway; and (3) measuring the amount of Hh signaling.
  • the steps can be carried out using standard techniques in light of the present disclosure. For example, standard techniques can be used to isolate cells or tissues and culturing or in vivo.
  • Compounds of varying degree of selectivity are useful for diagnosing the role of patched-2.
  • compounds which inhibit patched-2 in addition to another form of kinase can be used as an initial test compound to determine if one of several signaling ligands drive the disorder.
  • the selective compounds can then be used to further eliminate the possible role of the other ligands in driving the disorder.
  • Test compounds should be more potent in inhibiting ligand-patched-2 binding activity than in exerting a cytotoxic effect (e.g., an IC 50 /LD 50 of greater than one).
  • the IC 50 and LD 50 can be measured by standard techniques, such as an MTT assay, or by measuring the amount of LDH released.
  • the degree of IC 50 /LD 50 of a compound should be taken into account in evaluating the diagnostic assay. For example, the larger the IC 50 /LD 50 ratio the more relative the information.
  • Appropriate controls take into account the possible cytotoxic effect of a compound of a compound, such as treating cells not associated with a cell proliferative disorder (e.g., control cells) with a test compound, can also be used as part of the diagnostic assay.
  • the diagnostic methods of the invention involve the screening for agents that modulate the effects of patched-2 upon hedgehog signaling. Exemplary detection techniques include radioactive labeling and immunoprecipitating (U.S. Pat. No. 5,385,915).
  • compositions of the invention are prepared for storage as lyophilized formulations or aqueous solutions by mixing the patched-2 molecule, agonist and/or antagonist having the desired degree of purity with optional “pharmaceutically-acceptable” or “physiologically-acceptable” carriers, excipients or stabilizers typically employed in the art (all of which are termed “excipients”).
  • excipients typically employed in the art
  • buffering agents, stabilizing agents, preservatives, isotonifiers, non-ionic detergents, antioxidants and other miscellaneous additives See Remington's Pharmaceutical Sciences, 16 th Ed., A. Osol, Ed. (1980)).
  • Such additives must be nontoxic to the recipients at the dosages and concentrations employed.
  • Buffering agents help to maintain the pH in the range which approximates physiological conditions. They are preferably present at concentration ranging from about 2 mM to about 50 mM.
  • Suitable buffering agents for use with the present invention include both organic and inorganic acids and salts thereof such as citrate buffers (e.g., monosodium citrate-disodium citrate mixture, citric acid-trisodium citrate mixture, citric acid-monosodium citrate mixture, etc.), succinate buffers (e.g., succinic acid-monosodium succinate mixture, succinic acid-sodium hydroxide mixture, succinic acid-disodium succinate mixture, etc.), tartrate buffers (e.g., tartaric acid-sodium tartrate mixture, tartaric acid-potassium tartrate mixture, tartaric acid-sodium hydroxide mixture, etc.), fumarate buffers (e.g., fumaric acid-monosodium fumarate mixture, etc.), fuma
  • Preservatives are added to retard microbial growth, and are added in amounts ranging from 0.2%-1% (w/v).
  • Suitable preservatives for use with the present invention include phenol, benzyl alcohol, meta-cresol, methyl paraben, propyl paraben, octadecyldimethylbenzyl ammonium chloride, benzalconium halides (e.g., chloride, bromide, iodide), hexamethonium chloride, alkyl parabens such as methyl or propyl paraben, catechol, resorcinol, cyclohexanol, and 3-pentanol.
  • Isotonifiers sometimes known as “stabilizers” are present to ensure isotonicity of liquid compositions of the present invention and include polyhydric sugar alcohols, preferably trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol and mannitol.
  • Polyhydric alcohols can be present in an amount between 0.1% to 25% by weight, preferably 1% to 5% taking into account the relative amounts of the other ingredients.
  • Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the therapeutic agent or helps to prevent denaturation or adherence to the container wall.
  • Typical stabilizers can be polyhydric sugar alcohols (enumerated above); amino acids such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, threonine, etc., organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol and the like, including cyclitols such as inositol; polyethylene glycol; amino acid polymers; sulfur containing reducing agents, such as
  • proteins such as human serum albumin, bovine serum albumin, gelatin or immunoglobulins
  • hydrophilic polymers such as polyvinylpyrrolidone monosaccharides, such as xylose, mannose, fructose, glucose; disaccharides such as lactose, maltose, sucrose and trisaccacharides such as raffinose; polysaccharides such as dextran.
  • Stabilizers can be present in the range from 0.1 to 10,000 weights per part of weight active protein.
  • Non-ionic surfactants or detergents are present to help solubilize the therapeutic agent as well as to protect the therapeutic protein against agitation-induced aggregation, which also permits the formulation to be exposed to shear surface stressed without causing denaturation of the protein.
  • Suitable non-ionic surfactants include polysorbates (20, 80, etc.), polyoxamers (184, 188 etc.), Pluronic® polyols, polyoxyethylene sorbitan monoethers (Tween®-20, Tween®-80, etc.).
  • Non-ionic surfactants are present in a range of about 0.05 mg/ml to about 1.0 mg/ml, preferably about 0.07 mg/ml to about 0.2 mg/ml.
  • Additional miscellaneous excipients include bulking agents, (e.g. starch), chelating agents (e.g. EDTA), antioxidants (e.g., ascorbic acid, methionine, vitamin E), and cosolvents.
  • bulking agents e.g. starch
  • chelating agents e.g. EDTA
  • antioxidants e.g., ascorbic acid, methionine, vitamin E
  • cosolvents e.g., ascorbic acid, methionine, vitamin E
  • the formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • active compound preferably those with complementary activities that do not adversely affect each other.
  • Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
  • the active ingredients may also be entrapped in microcapsule prepared, for example, by coascervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • formulations to be used for in vivo administration must be sterile. This is readily accomplished, for example, by filtration through sterile filtration membranes.
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semi-permeable matrices of solid hydrophobic polymers containing the compounds of the invention, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat.
  • copolymers of L-glutamic acid and ethyl-L-glutamate non-degradable ethylene-vinyl acetate
  • degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOTTM (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate)
  • poly-D-( ⁇ )-3-hydroxybutyric acid While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogens release proteins for shorter time periods.
  • encapsulated compounds of the invention When encapsulated compounds of the invention remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37° C., resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S—S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.
  • a pharmaceutical composition effective in modulating Dhh and Hh signaling may provide a local patched-2 protein concentration of between about 10 and 1000 ng/ml, preferably between 100 and 800 ng/ml and most preferably between about 200 ng/ml and 600 ng/ml of Ptch-2 (SEQ ID NO:2).
  • an aqueous solution of therapeutic polypeptide, antibody or fragment thereof is administered by subcutaneous injection.
  • Each dose may range from about 0.5 ⁇ g to about 50 ⁇ g per kilogram of body weight, or more preferably, from about 3 ⁇ g to about 30 ⁇ g per kilogram body weight.
  • the dosing schedule for subcutaneous administration may vary from once a week to daily depending on a number of clinical factors, including the type of disease, severity of disease, and the subject's sensitivity to the therapeutic agent.
  • Patched-2 polypeptide may comprise an amino acid sequence or subsequence thereof as indicated in FIG. 1 (SEQ ID NO:2), active amino acid sequence derived therefrom, or functionally equivalent sequence as this subsequence is believed to comprise the functional portion of the patched-2 polypeptide.
  • the subject manifests undesired side effects such as temperature elevation, cold or flu-like symptoms, fatigue, etc.
  • One or more additional drugs may be administered in combination with patched-2 to alleviate such undesired side effects, for example, an anti-pyretic, anti-inflammatory or analgesic agent.
  • Hh function appears to be mediated by a multicomponent receptor complex involving Ptch (SEQ ID NO:4) and Smo (SEQ ID NO:17), two multi-transmembrane proteins initially identified as segment polarity genes in Drosophila and later characterized in vertebrates.
  • Ptch SEQ ID NO:4
  • Smo SEQ ID NO:17
  • a full length cDNA encoding human Ptch-2 (SEQ ID NO:2) was cloned from a testis library.
  • the initiation ATG defines a 3612 nucleotide open reading frame encoding a 1204 amino acid long protein with a predicted molecular weight of approximately 131 kDa.
  • the overall identity between human Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) is 54% (FIG. 1), while the identity between human Ptch-2 (SEQ ID NO:2) and the recently described mouse Ptch-2 (SEQ ID NO:7) is 90%. (FIG. 8).
  • Ptch-2 The most obvious structural difference between the two human Ptch proteins is a truncated C-terminal cytoplasmic domain in Ptch-2 (SEQ ID NO:2). In addition, only one of the two glycosylation sites present in Ptch (SEQ ID NO:4) is conserved in Ptch-2 (SEQ ID NO:2).
  • Ptch-2 (SEQ ID NO:2) is a Hh receptor and if the two patched molecules are capable of discriminating between the various Hh ligands through specific binding
  • Ptch SEQ ID NO:4
  • Ptch-2 SEQ ID NO:2 expression constructs and analyzed the cells for binding of Shh, Dhh and Ihh (SEQ ID NOS:14, 13, and 29, respectively).
  • FIG. 7A binding of 125 I-Shh can be competed with an excess of Shh, Dhh or Ihh (SEQ ID NOS: 14, 13, and 29, respectively).
  • Ptch SEQ ID NO:4
  • Smo SEQ ID NO:17
  • Ptch SEQ ID NO:4
  • Ptch-2 SEQ ID NO:2
  • Ptch-2 SEQ ID NO:2
  • Dhh (SEQ ID NO:13) is required for proper differentiation of germ cells since male Dhh-deficient mice are sterile due to lack of mature sperm (Bitgood et al., supra).
  • Dhh acts directly on germ cells through Ptch-2 (SEQ ID NO:2) while the function of Ptch (SEQ ID NO:4) expressed at low levels on testosterone producing Leydig cells is unclear.
  • patched-2 mediates the function of Dhh
  • loss of Ptch-2 (SEQ ID NO:2) may lead to tumor formation in tissues where Smo (SEQ ID NO:17) activity is controlled by patched-2.
  • the gene encoding patched-2 was mapped by fluorescence in situ hybridization and by PCR using a radiation hybrid panel to human chromosome 1p33-34 (data not shown).
  • recent analysis of recurrent chromosomal abnormalities in testicular tumors, including seminomas revealed a deletion of the region 1p32-36 [Summersgill et al., B. J. Cancer 77: 305-313 (1998)].
  • patched-2 may be a tumor suppressor in Dhh (SEQ ID NO:13) target cells such as spermatocytes, further implicating Hh signaling in cancer.
  • patched-2 plays a role when expressed in Shh expressing cells present in the developing tooth and skin Motoyama et al., Nature Genet. 18: 104-106 (1998). Finally, the existence of patched-2 raises the question of whether additional patched receptors exist, in particular one that mediates the function of Ihh (SEQ ID NO:29).
  • EST DNA database (LIFESEQ®, Incyte Pharmaceuticals, Palo Alto, Calif.) was searched for a human homologue of the Drosophila segment polarity gene patched-2.
  • Two ESTs (Incyte #905531 and 1326258) (FIG. 2) (SEQ ID NOS: 3 and 5, respectively) were identified as a potential candidates.
  • human cDNA libraries in pRK5 were first screened by PCR using the following primers: 5′-905531(A): 5′-AGGCGGGGGATCACAGCA-3′ (SEQ ID NO:19) 3′-905531(A): 5′-ATACCAAAGAGTTCCACT-3′ (SEQ ID NO:20)
  • a fetal lung library was selected and enriched for patched-2 cDNA clones by extension of single stranded DNA from plasmid libraries grown in dut ⁇ /ung ⁇ host using the 3′-905531(A) primer in a reaction containing 10 ⁇ l of 10 ⁇ PCR Buffer (Klentaq®), 1 ⁇ l dNTP (200 ⁇ M), 1 ⁇ l library DNA (200 ng), 0.5 ⁇ l primer, 86.5 ⁇ l H 2 O and 1 ⁇ l of Klentaq® (Clontech) added after a hot start. The reaction was denatured for 1 min. at 95° C., annealed for 1 min. at 60° C. then extended for 20 min.
  • DNA was extracted with phenol/CHCl 3 , ethanol precipitated, then transformed by electroporation into DH10B (Gibco/BRL) host bacteria. Colonies from each transformation were replica plated on nylon membranes and screened with an overlapping oligo probe derived from the EST sequence (#905531) of the following sequence: 5′-Ptch2 probe: 5′-CTGCGGCGCTGCTTCCTGCTGGCCGTCTGCATCCTGCTGGTGTGC-3′ (SEQ ID NO:21) 3′-Ptch2 probe: 5′-AGAGCACAGACGAGGAAAGTGCACACCAGCAGGATGCAGACGGCC-3′ (SEQ ID NO:22)
  • the oligo probe was labeled with [ ⁇ - 32 P]-ATP and T4 polynucleotide kinase. Filters were hybridized overnight at 42° C. in 50% formamide, 5 ⁇ SSC, 10 ⁇ Denhardt's, 0.05M sodium phosphate (pH 6.5), 0.1% sodium pyrophosphate, 50 ⁇ g/ml of sonicated salmon sperm DNA. The filters were then rinsed in 2 ⁇ SSC and washed in 0.1 ⁇ SSC, 0.1% SDS then exposed to Kodak® X Ray films.
  • a partial clone was isolated from the fetal brain library (clone 3A—FIG. 10) (SEQ ID NO:8).
  • a testis library (see northern blot analysis, infra) was screened.
  • the primer set used to amplify a 204 bp probe from clone 3A to probe the testis library was: RACE 5: 5′-ACTCCTGACTTGTAGCAGATT-3′ (SEQ ID NO: 23) and RACE 6: 5′-AGGCTGCATACACCTCTCAGA-3′. (SEQ ID NO: 24)
  • the amplified probe was purified by excision from an agarose gel and labeled with a random primer labeling kit (Boehringer Mannheim). Several clones were isolated, including one (clone 16.1—FIG. 11 (SEQ ID NO:9)) containing a potential initiation methionine. A full length cDNA encoding patched-2 was reconstructed by assembling several of these clones.
  • the full length cDNA encoding human Ptch-2 (FIG. 1) (SEQ ID NO:1) has a 3612 nucleotide long open reading frame encoding a 1204 amino acid protein with a 144 kDa predicted molecular weight.
  • the resulting fragment was gel purified and labeled by random priming.
  • the blots were hybridized in ExpressHyb® hybridization solution (Clontech) in the presence of 1 ⁇ 10 6 cpm/ml 32 P-labeled probe at 42° C. overnight.
  • the blots were washed in 2 ⁇ SSC at room temperature for 10 minutes and washed in 0.1 ⁇ SSC/0.1% SDS at 42° C. for 30 minutes then exposed to x-ray film overnight.
  • FIG. 4 shows that Ptch-2 message is expressed at high levels in only the testis.
  • patched-2 (SEQ ID NO:2) localizes to chromosome 1p33-34 it is possible that patched-2 regulates Smo (SEQ ID NO:17) signaling in Dhh target cells and that loss of patched-2 function leads to abnormal Smo (SEQ ID NO:17) signaling in these cells and subsequent tumor formation.
  • FuRK sense and antisense were synthesized from a mouse fused DNA fragment using T3 and T7, respectively, corresponding to the region encoding amino acid residues 317-486 of the human sequence (Zhang et al., submitted, 1998; copending U.S. Ser. No. 09/031,563, filed Feb. 26, 1998).
  • FIG. 6 illustrates that, although both Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) are expressed in testis, their expression pattern does not overlap.
  • Ptch (SEQ ID NO:4) is expressed in the Leydig cells of the interstitium while Ptch-2 (SEQ ID NO:2) is expressed in the primary and secondary spermatocytes.
  • FuRK SEQ ID NO:10
  • Ptch-2 SEQ ID NO:2
  • Ptch SEQ ID NO:4
  • Ptch-2 mRNA levels in Smo-M2 (SEQ ID NO:16) transgenic mice [A Smo mutation which results in autonomous phenotypes similar to BCC, Xie et al., Nature 391: 90-92 (1998)] can be increased upon abnormal activation of the Hh signaling pathway. As indicated in FIG. 9, patch-2 levers were high in tumor cells (although lower than Ptch levels). This suggests that antibodies directed toward Ptch-2 may be useful in the treatments of BCC.
  • the DNA sequence encoding human patched-2 is initially amplified using selected PCR primers.
  • the primers should contain restriction enzyme sites that correspond to the restriction enzyme sites on the selected expression vector.
  • a variety of expression vectors may be employed.
  • An example of a suitable vector is pBR322 (derived from E. coli ; see Bolivar et al., Gene, 2:95 (1977)) which contains genes for ampicillin and tetracycline resistance.
  • the vector is digested with restriction enzyme and dephosphorylated.
  • the PCR amplified sequences are then ligated into the vector.
  • the vector will preferably include sequences that encode for an antibiotic resistance gene, a trp promoter, a polyhis leader (including the first six STII codons, polyhis sequence, and enterokinase cleavage site), the vertebrate patched-2 coding region, lambda transcriptional terminator, and an argU gene.
  • the ligation mixture is then used to transform a selected E. coli strain using the methods described in Sambrook et al., supra. Transformants are identified by their ability to grow on LB plates and antibiotic resistant colonies are then selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing.
  • Selected clones can be grown overnight in liquid culture medium such as LB broth supplemented with antibiotics.
  • the overnight culture may subsequently be used to inoculate a larger scale culture.
  • the cells are then grown to a desired optical density, during which the expression promoter is turned on.
  • the cells After culturing the cells for several more hours, the cells can be harvested by centrifugation.
  • the cell pellet obtained by the centrifugation can be solubilized using various agents known in the art, and the solubilized vertebrate patched-2 protein can then be purified using a metal chelating column under conditions that allow tight binding of the protein.
  • the vector, pRK5 (see EP 307,247, published Mar. 15, 1989), is employed as the expression vector.
  • the vertebrate patched-2 DNA is ligated into pRK5 with selected restriction enzymes to allow insertion of the vertebrate patched-2 DNA using ligation methods such as described in Sambrook et al., supra.
  • the resulting vector is called pRK5-patched-2.
  • the selected host cells may be 293 cells.
  • Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue culture plates in medium such as DMEM supplemented with fetal calf serum and optionally, nutrient components and/or antibiotics.
  • About 10 ⁇ g pRK5-patched-2 DNA is mixed with about 1 ⁇ g DNA encoding the VA RNA gene [Thimmappaya et al., Cell, 31:543 (1982)] and dissolved in 500 ⁇ l of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCl 2 .
  • the culture medium is removed and replaced with culture medium (alone) or culture medium containing 200 ⁇ Ci/ml 35 S-cysteine and 200 ⁇ Ci/ml 35 S-methionine.
  • culture medium alone
  • culture medium containing 200 ⁇ Ci/ml 35 S-cysteine and 200 ⁇ Ci/ml 35 S-methionine After a 12 hour incubation, the conditioned medium is collected, concentrated on a spin filter, and loaded onto a 15% SDS gel. The processed gel may be dried and exposed to film for a selected period of time to reveal the presence of vertebrate patched-2 polypeptide.
  • the cultures containing transfected cells may undergo further incubation (in serum free medium) and the medium is tested in selected bioassays.
  • vertebrate patched-2 may be introduced into 293 cells transiently using the dextran sulfate method described by Somparyrac et al., Proc. Natl. Acad. Sci, 12:7575 (1981). 293 cells are grown to maximal density in a spinner flask and 700 ⁇ g pRK5-patched-2 DNA is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA-dextran precipitate is incubated on the cell pellet for four hours.
  • the cells are treated with 20% glycerol for 90 seconds, washed with tissue culture medium, and re-introduced into the spinner flask containing tissue culture medium, 5 ⁇ g/ml bovine insulin and 0.1 ⁇ g/ml bovine transferrin. After about four days, the conditioned media is centrifuged and filtered to remove cells and debris. The sample containing expressed vertebrate patched-2 can then be concentrated and purified by any selected method, such as dialysis and/or column chromatography.
  • vertebrate patched-2 can be expressed in CHO cells.
  • the pSVi-patched-2 can be transfected into CHO cells using known reagents such as CaPO 4 or DEAE-dextran.
  • the cell cultures can be incubated, and the medium replaced with culture medium (alone) or medium containing a radiolabel such as 35 S-methionine.
  • the culture medium may be replaced with serum free medium.
  • the cultures are incubated for about 6 days, and then the conditioned medium is harvested.
  • the medium containing the expressed vertebrate patched-2 can then be concentrated and purified by any selected method.
  • Epitope-tagged vertebrate patched-2 may also be expressed in host CHO cells.
  • the vertebrate patched-2 may be subcloned out of the pRK5 vector.
  • the subclone insert can undergo PCR to fuse in frame with a selected epitope tag such as a poly-his tag into an expression vector.
  • the poly-his tagged vertebrate patched-2 insert can then be subcloned into a SV40 driven vector containing a selection marker such as DHFR for selection of stable clones.
  • the CHO cells can be transfected (as described above) with the SV40 driven vector. Labeling may be performed, as described above, to verify expression.
  • the culture medium containing the expressed poly-His tagged vertebrate patched-2 can then be concentrated and purified by any selected method, such as by Ni 2+ -chelate affinity chromatography.
  • yeast expression vectors are constructed for intracellular production or secretion of vertebrate patched-2 from the ADH2/GAPDH promoter.
  • DNA encoding vertebrate patched-2, a selected signal peptide and the promoter is inserted into suitable restriction enzyme sites in the selected plasmid to direct intracellular expression of vertebrate patched-2.
  • DNA encoding vertebrate patched-2 can be cloned into the selected plasmid, together with DNA encoding the ADH2/GAPDH promoter, the yeast alpha-factor secretory signal/leader sequence, and linker sequences (if needed) for expression of vertebrate patched-2.
  • yeast cells such as yeast strain AB110
  • yeast cells can then be transformed with the expression plasmids described above and cultured in selected fermentation media.
  • the transformed yeast supernatants can be analyzed by precipitation with 10% trichloroacetic acid and separation by SDS-PAGE, followed by staining of the gels with Coomassie Blue stain.
  • Recombinant vertebrate patched-2 can subsequently be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using selected cartridge filters.
  • the concentrate containing vertebrate patched-2 may further be purified using selected column chromatography resins.
  • the vertebrate patched-2 is patched-2 upstream of an epitope tag contained within a baculovirus expression vector.
  • epitope tags include poly-his tags and immunoglobulin tags (like Fc regions of IgG).
  • a variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen).
  • the vertebrate patched-2 or the desired portion of the vertebrate patched-2 (such as the sequence encoding the extracellular domain of a transmembrane protein) is amplified by PCR with primers complementary to the 5′ and 3′ regions.
  • the 5′ primer may incorporate flanking (selected) restriction enzyme sites.
  • the product is then digested with those selected restriction enzymes and subcloned into the expression vector.
  • Recombinant baculovirus is generated by co-transfecting the above plasmid and BaculoGoldTM virus DNA (Pharmingen) into Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL). After 4-5 days of incubation at 28° C., the released viruses are harvested and used for further amplifications. Viral infection and protein expression is performed as described by O'Reilley et al., Baculovirus expression vectors: A laboratory Manual, Oxford: Oxford University Press (1994).
  • Expressed poly-his tagged vertebrate patched-2 can then be purified, for example, by Ni 2+ -chelate affinity chromatography as follows. Extracts are prepared from recombinant virus-infected Sf9 cells as described by Rupert et al., Nature, 362:175-179 (1993). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 mL Hepes, pH 7.9; 12.5 mM MgCl 2 ; 0.1 mM EDTA; 10% Glycerol; 0.1% NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice.
  • sonication buffer 25 mL Hepes, pH 7.9; 12.5 mM MgCl 2 ; 0.1 mM EDTA; 10% Glycerol; 0.1% NP-40; 0.4 M KCl
  • the sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl, 10% Glycerol, pH 7.8) and filtered through a 0.45 ⁇ m filter.
  • loading buffer 50 mM phosphate, 300 mM NaCl, 10% Glycerol, pH 7.8
  • a Ni 2+ -NTA agarose column (commercially available from Qiagen) is prepared with a bed volume of 5 mL, washed with 25 mL of water and equilibrated with 25 mL of loading buffer.
  • the filtered cell extract is loaded onto the column at 0.5 mL per minute.
  • the column is washed to baseline A 280 with loading buffer, at which point fraction collection is started.
  • the column is washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% Glycerol, pH 6.0), which elutes nonspecifically bound protein.
  • a secondary wash buffer 50 mM phosphate; 300 mM NaCl, 10% Glycerol, pH 6.0
  • the column is developed with a 0 to 500 mM Imidazole gradient in the secondary wash buffer.
  • One mL fractions are collected and analyzed by SDS-PAGE and silver staining or western blot with Ni 2+ -NTA-conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted His 10 -tagged vertebrate patched-2 are pooled and dialyzed against loading buffer.
  • purification of the IgG tagged (or Fc tagged) vertebrate patched-2 can be performed using known chromatography techniques, including for instance, Protein A or protein G column chromatography.
  • This example illustrates preparation of monoclonal antibodies, which can specifically bind vertebrate patched-2.
  • Immunogens that may be employed include purified vertebrate patched-2, fusion proteins containing vertebrate patched-2, and cells expressing recombinant vertebrate patched-2 on the cell surface. Selection of the immunogen can be made by the skilled artisan without undue experimentation.
  • mice such as Balb/c are immunized with the vertebrate patched-2 immunogen (E.g., extracellular portions or cells expressed Ptch-2) emulsified in complete Freund's adjuvant and injected subcutaneously or intraperitoneally in an amount from 1-100 micrograms.
  • the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, Mont.) and injected into the animal's hind foot pads.
  • the immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice may also be boosted with additional immunization injections. Serum samples may be periodically obtained from the mice by retro-orbital bleeding for testing in ELISA assays to detect vertebrate patched-2 antibodies.
  • the animals “positive” for antibodies can be injected with a final intravenous injection of vertebrate patched-2. Three to four days later, the mice are sacrificed and the spleen cells are harvested. The spleen cells are then patched-2 (using 35% polyethylene glycol) to a selected murine myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL 1597.
  • a selected murine myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL 1597.
  • the fusions generate hybridoma cells which can then be plated in 96 well tissue culture plates containing HAT (hypoxanthine, aminopterin, and thymidine) medium to inhibit proliferation of non-patched-2 cells, myeloma hybrids, and spleen cell hybrids.
  • HAT hyperxanthine, aminopterin, and thymidine
  • hybridoma cells will be screened in an ELISA for reactivity against vertebrate patched-2. Determination of “positive” hybridoma cells secreting the desired monoclonal antibodies against vertebrate patched-2 is within the skill in the art.
  • the positive hybridoma cells can be injected intraperitoneally into syngeneic Balb/c mice to produce ascites containing the anti-vertebrate patched-2 monoclonal antibodies.
  • the hybridoma cells can be grown in tissue culture flasks or roller bottles. Purification of the monoclonal antibodies produced in the ascites can be accomplished using ammonium sulfate precipitation, followed by gel exclusion chromatography. Alternatively, affinity chromatography based upon binding of antibody to protein A or protein G can be employed.
  • the following assay may be used to measure the activation of the transcription factor GLI, the mammalian homologue of the Drosophila cubitus interruptus (Ci). It has been shown that GLI is a transcription factor activated upon SHh stimulation of cells.
  • constructs are cotransfected with the full length Ptch-2 and Smo in C3H10T1/2 cells grown in F12, DMEM (50:50), 10% FCS heat inactivated.
  • the day before transfection 1 ⁇ 10 5 cells per well was inoculated in 6 well plates, in 2 ml of media.
  • the following day, 1 ⁇ g of each construct is cotransfected in duplicate with 0.025 mg ptkRenilla luciferase plasmid using lipofectamine (Gibco-BRL) in 100 ⁇ l OptiMem (with GlutaMAX) as per manufacturer's instructions for 3 hours at 37° C.
  • Serum (20%, 1 ml) is then added to each well and the cells were incubated for 3 more hours at 37° C. Cells are then washed twice with PBS, then incubated for 48 hours at 37° C. in 2 ml of media. Each well is then washed with PBS, and the cells lysed in 0.5 ml Passive Lysis Buffer (Promega) for 15 min. at room temperature on a shaker. The lysate is transferred in eppendorf tubes on ice, spun in a refrigerated centrifuge for 30 seconds and the supernatant saved on ice.
  • Passive Lysis Buffer Promega
  • LARII luciferase assay reagent, Promega

Abstract

The present invention relates to nucleotide sequences, including expressed sequence tags (ESTs), oligonucleotide probes, polypeptides, antibodies, vectors and host cells expressing, immunoadhesins, agonists and antagonists to patched-2.

Description

    RELATED APPLICATIONS
  • This application is a continuation of U.S. Ser. No. 09/293,505 filed Apr. 15, 1999, now allowed, which claims priority under 35 U.S.C. § 119(e) to provisional application No. 60/081,884, filed Apr. 15, 1998, all of which the entire disclosure is hereby incorporated by reference.[0001]
    • FIELD OF THE INVENTION
  • The present invention relates generally to signaling molecules, specifically to signaling and mediator molecules in the hedgehog (Hh) cascade which are involved in cell proliferation and differentiation. [0002]
    • BACKGROUND OF THE INVENTION
  • Development of multicellular organisms depends, at least in part, on mechanisms which specify, direct or maintain positional information to pattern cells, tissues, or organs. Various secreted signaling molecules, such as members of the transforming growth factor-beta (TGF-β), Wnt, fibroblast growth factors and hedgehog families have been associated with patterning activity of different cells and structures in Drosophila as well as in vertebrates. Perrimon, [0003] Cell: 80: 517-520 (1995).
  • Segment polarity genes were first discovered in Drosophila, which when mutated caused a change in the pattern of structures of the body segments. These changes affected the pattern along the head to tail axis. Hedgehog (Hh) was first identified as a segment-polarity gene by a genetic screen in [0004] Drosophila melanogaster, Nusslein-Volhard et al., Roux. Arch. Dev. Biol. 193: 267-282 (1984), that plays a wide variety of developmental functions. Perrimon, supra. Although only one Drosophila Hh gene has been identified, three mammalian Hh homologues have been isolated: Sonic Hh (Shh), Desert Hh (Dhh) and Indian Hh (Ihh), Echelard et al., Cell 75: 1417-30 (1993); Riddle et al., Cell 75: 1401-16 (1993). Shh is expressed at high level in the notochord and floor plate of developing vertebrate embryos, and acts to establish cell fate in the developing limb, somites and neural tube. In vitro explant assays as well as ectopic expression of Shh in transgenic animals show that SHh plays a key role in neural tube patterning, Echelard et al. (1993), supra.; Ericson et al., Cell 81: 747-56 (1995); Marti et al., Nature 375: 322-5 (1995); Roelink et al. (1995), supra; Hynes et al., Neuron 19: 15-26 (1997). Hh also plays a role in the development of limbs (Krauss et al., Cell 75: 1431-44 (1993); Laufer et al., Cell 79, 993-1003 (1994)), somites (Fan and Tessier-Lavigne, Cell 79, 1175-86 (1994); Johnson et al., Cell 79: 1165-73 (1994)), lungs (Bellusci et al., Develop. 124: 53-63 (1997) and skin (Oro et al., Science 276: 817-21 (1997). Likewise, Ihh and Dhh are involved in bone, gut and germinal cell development, Apelqvist et al., Curr. Biol. 7: 801-4 (1997); Bellusci et al., Dev. Suppl. 124: 53-63 (1997); Bitgood et al., Curr. Biol. 6: 298-304 (1996); Roberts et al., Development 121: 3163-74 (1995). Specifically, Ihh has been implicated in chondrocyte development [Vortkamp, A. et al., Science 273: 613-22 (1996)] while Dhh plays a key role in testis development. Bitgood et al., supra. With the exception of the gut, in which both Ihh and Shh are expressed, the expression patterns of the hedgehog family members do not overlap. Bitgood et al., supra.
  • At the cell surface, Hh function appears to be mediated by a multicomponent receptor complex involving patched (e.g., Ptch) and Smoothened (e.g., Smo), two multi-transmembrane proteins initially identified as segment polarity genes in Drosophila and later characterized in vertebrates. Nakano et al., [0005] Nature 341: 508-513 (1989); Goodrich et al., Genes Dev. 10: 301-312 (1996); Marigo et al., Develop. 122: 1225-1233 (1996); van den Heuvel, M. & Ingham, P. W., Nature 382: 547-551 (1996); Alcedo, J. et al., Cell 86: 221-232 (1996); Stone, D. M. et al., Nature 384: 129-34 (1996). Upon binding of Hh to Patched, the normal inhibitory effect of Patched on Smo is relieved, allowing Smo to transduce the Hh signal across the plasma membrane. It remains to be established if the Patched/Smo receptor complex mediates the action of all 3 mammalian hedgehogs or if specific components exist. Interestingly, a second murine Patched gene, Patched-2 was recently isolated [Motoyama, J. et al., Nature Genetics 18: 104-106 (1998)], but its function as a Hh receptor has not been established. In order to characterize Patched-2 and compare it to Patched with respect to the biological function of the various Hh family members, Applicants have isolated the human Patched-2 gene. Biochemical analysis of Patched and Patched-2 show that both bind to all members of the Hh family with similar affinity and that both molecules can form a complex with Smo. However, the expression patterns of Patched-2 and Patched do not overlap. While Patched is expressed throughout the mouse embryo, Patched-2 is found mainly in spermatocytes which require Desert Hedgehog (Dhh) for proper development suggesting that Patched-2 mediates Dhh's activity in the testis. Chromosomal localization of Patched-2 places it on chromosome 1p33-34, a region deleted in some germ cell tumors, raising the possibility that Patched-2 may be a tumor suppressor in Dhh target cells.
    • SUMMARY OF THE INVENTION
  • In one embodiment, the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a patched-2 polypeptide comprising the sequence of [0006] amino acids 1 to 1203 of FIG. 1 (SEQ ID NO:2), or (b) the complement of the DNA molecule of (a); and encoding a polypeptide having patched-2 biological activity. The sequence identity preferably is >91%, more preferably about 92%, most preferably about 95%. In one aspect, the isolated nucleic acid has at least >91%, preferably at least about 92%, and even more preferably at least about 95% sequence identity with a polypeptide having amino acid residues 1 to about 1203 of FIG. 1 (SEQ ID NO:2). In a further aspect, the isolated nucleic acid molecule comprises DNA encoding a human patched-2 polypeptide having amino acid residues 1 to about 1203 of FIG. 1. In yet another aspect, the invention provides for an isolated nucleic acid comprising DNA having at least a 95% sequence identity to (a) a DNA molecule encoding the same mature polypeptide encoded by the cDNA in ATCC Deposit No. 209778 (designation: pRK7.hptc2.Flag-1405), alternatively the coding sequence of clone pRK7.hptc2.Flag-1405, deposited under accession number ATCC 209778. In a still further aspect, the invention provides for a nucleic acid comprising human patched-2 encoding sequence of the cDNA in ATCC Deposit No. 209778 (designation: pRK7.hptc2.Flag-1405) or a sequence which hybridizes thereto under stringent conditions.
  • In another embodiment, the invention provides a vector comprising DNA encoding a human patched-2 polypeptide. A host cell comprising such a vector is also provided. By way of example, the host cells may be mammalian cells, (e.g. CHO cells), prokaryotic cells (e.g., [0007] E. coli) or yeast cells (e.g., Saccharomyces cerevisiae). A process for producing patched-2 polypeptides is further provided and comprises culturing host cells under conditions suitable for expression of patched-2 and recovering the same from the cell culture.
  • In yet another embodiment, the invention provides an isolated patched-2 polypeptide. In particular, the invention provides isolated native sequence patched-2 polypeptide, which in one embodiment is a human patched-2 including an amino acid [0008] sequence comprising residues 1 to about 1203 of FIG. 1 (SEQ ID NO:2). Human patched-2 polypeptides with or without the initiating methionine are specifically included. Alternatively, the invention provides a human patched-2 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209778.
  • In yet another embodiment, the invention provides chimeric molecules comprising a patched-2 polypeptide fused to a heterologous polypeptide or amino acid sequence. An example of such a chimeric molecule comprises a patched-2 polypeptide fused to an epitope tag sequence or a constant region of an immunoglobulin. [0009]
  • In yet another embodiment, the invention provides expressed sequence tag (EST) comprising the nucleotide sequences identified in FIG. 2A (905531) (SEQ ID NO:3) and FIG. 2B (1326258) (SEQ ID NO:5). [0010]
  • In yet another embodiment, the invention provides for alternatively spliced variants of human patched-2 having patched-2 biological activity. [0011]
  • In yet another embodiment, the invention provides for method of using patched-2 for the treatment of disorders which are mediated at least in part by Hedgehog (Hh), especially Desert hedgehog (Dhh). In particular, testicular cancer. In yet another embodiment, the invention provides a method of using antagonists or agonists of patched-2 for treating disorders or creating a desirable physiological condition effected by blocking Hh signaling, especially Dhh signaling. (E.g, contraception).[0012]
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIGS. [0013] 1A-1E shows the nucleotide (SEQ ID NO:1) and derived amino acid (SEQ ID NO:2) sequence of a native sequence of human Ptch-2 polypeptide.
  • FIG. 2A shows EST 905531 (SEQ ID NO:3) and FIG. 2B shows EST 1326258 (SEQ ID NO:5) in alignment with human Ptch (SEQ ID NO: 18). These ESTs were used in the cloning of human full-length Ptch-2 (SEQ ID NO:1). [0014]
  • FIGS. [0015] 3A-3D show a comparison between human Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2). Gaps introduced for optimal alignment are indicated by dashes. Identical amino acids are boxed. The 12 transmembrane domains are indicated by the gray boxes, all of which are conserved between the two sequences. Alignment results between the two sequences indicate 53% identity. The most significant difference is a shorter C-terminal intracellular domain in human Ptch-2 (SEQ ID NO:2) in comparison with human Ptch (SEQ ID NO:4).
  • FIG. 4 shows a northern blot of Ptch-2 (SEQ ID NO:2) which indicates expression is limited to the testis. Multiple human fetal and adult tissue northern blots were probe fragments corresponding to the 3′-untranslated region of murine Ptch-2. [0016]
  • FIG. 5 shows a chromosomal localization of two BAC clones which were isolated by PCR screening with human patched-2 derived probes. Both probes were mapped by FISH to human chromosome 1p33-34. [0017]
  • FIGS. [0018] 6A-F is an in situ hybridization comparing Ptch (SEQ ID NO:4), Ptch-2 (SEQ ID NO:2) and Fused (FuRK) (SEQ ID NO:10). High magnification of mouse testis showing expression of (A) Ptch (SEQ ID NO:4), Ptch-2 (SEQ ID NO:2) (B) and FuRK (SEQ ID NO:10) (C). Low magnification of testis section hybridized with Ptch-2 sense (SEQ ID NO:11) (D) and anti-sense probe (SEQ ID NO:12) (E) respectively. FIG. 6(F) shows low magnification of testis section hybridized with FuRK (SEQ ID NO:10). Scale bar: A, B, C: 0.05 mm; D, E, F: 0.33 mm.
  • FIG. 7A is logarithmic plot comparing the binding Ptch-2 (SEQ ID NO:2) to Dhh (SEQ ID NO:13) and Shh (SEQ ID NO:14). Competitive binding of recombinant murine [0019] 125I-Shh to 293 cells overexpressing hPtch (SEQ ID NO:4) or hPtch-2 (SEQ ID NO:2). There was no detectable binding to mock transfected cells (data not shown). FIG. 7B is a western blot illustrating co-immunoprecipitation of epitope tagged Ptch (SEQ ID NO:4) or Ptch-2 (SEQ ID NO:2) with epitope tagged Smo (SEQ ID NO:15). Immunoprecipitation was performed with antibodies to the Flag tagged Ptch (SEQ ID NO:4) and analyzed on a 6% acrylamide gel with antibodies to the Myc tagged Smo (SEQ ID NO:15). Protein complexes can be detected for both Ptch (SEQ ID NO:4)and Ptch-2 (SEQ ID NO:2) with Smo (SEQ ID NO:15). Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) express at similar levels as shown by immunoprecipitation using antibodies to the Flag-tag and western blot using the same anti-Flag antibody.
  • FIGS. [0020] 8A-8D is a sequence comparison between human Ptch-2 (SEQ ID NO:2) and murine Ptch-2 (SEQ ID NO:7), which indicates that there is about 91% identity between the two sequences.
  • FIG. 9 is an in situ hybridization which demonstrates the accumulation of Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) mRNA detected by in situ hybridization in basal cells of E18 transgenic mice overexpressing SMO-M2 (SEQ ID NO:16) (Xie et al., [0021] Nature 391: 90-92 (1998).
  • FIGS. [0022] 10A-10D depict a partial sequence representing clone 3A (SEQ ID NO:8), a partial patched-2 fragment which was initially isolated from a fetal brain library.
  • FIGS. [0023] 11A-B depict a partial sequence representing clone 16.1 (SEQ ID NO:9), a partial patched-2 fragment which isolated from a testis library.
    • DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS I. Definitions
  • The terms “patched-2” and “patched-2 polypeptide” when used herein encompass native sequence patched-2 and patched-2 variants (which are further defined herein) having patched-2 biological activity. Patched-2 may be isolated from a variety of sources, such as from testes tissue types or from another source, or prepared by recombinant or synthetic methods. [0024]
  • A “native sequence patched-2” comprises a polypeptide having the same amino acid sequence as a human patched-2 derived from nature. Such native sequence patched-2 can be isolated from nature or can be produced by recombinant and/or synthetic means. The term “native sequence vertebrate patched-2” specifically encompasses naturally occurring truncated forms of human patched-2, naturally occurring variant forms (e.g., alternatively spliced forms) and naturally-occurring allelic variants of human patched-2. Thus, one embodiment of the invention, the native sequence patched-2 is a mature or full-length native patched-2 comprising [0025] amino acids 1 to 1203 of FIG. 1 (SEQ ID NO:2) with or without the initiating methionine at position 1.
  • “Patched-2 variant” means an active human patched-2 as defined below having at least >91% amino acid sequence identity to (a) a DNA molecule encoding a patched-2 polypeptide, or (b) the complement of the DNA molecule of (a). In a particular embodiment, the patched-2 variant has at least >91% amino acid sequence homology with the human Ptch-2 (SEQ ID NO:2) having the deduced amino acid sequence shown in FIG. 1 for a full-length native sequence human patched-2. Such patched-2 variants include, without limitation, patched-2 polypeptides wherein one or more amino acid residues are added, or deleted, at the N- or C-terminus of the sequence of FIG. 1 (SEQ ID NO:2). Preferably, the nucleic acid or amino acid sequence identity is at least about 92%, more preferably at least about 93%, and even more preferably at least about 95%. [0026]
  • The term “Ptch” or “Ptch-2” refer to the particular species of molecules isolated and characterized in the application, while the terms “patched” and patched-2” refer to the more generalized description as defined above. [0027]
  • “Percent (%) amino acid sequence identity” with respect to the patched-2 sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the patched-2 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST-2 software that are set to their default parameters. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. Alternatively, % identity can be determined by Align-2, authored by Genentech, Inc., which was filed with user documentation in the United States Copyright Office, Washington, D.C. 20559, on Dec. 10, 1991, and is registered under U.S. Copyright Registration No. TXU 510087. [0028]
  • “Percent (%) nucleic acid sequence identity” with respect to the patched-2 sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the patched-2 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST-2 software that are set to their default parameters. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. Alternatively, % identity can be determined by Align-2, authored by Genentech, Inc., which was filed with user documentation in the United States Copyright Office, Washington, D.C. 20559, on Dec. 10, 1991, and is registered under U.S. Copyright Registration No. TXU 510087. [0029]
  • The term “epitope tagged” when used herein refers to a chimeric polypeptide comprising patched-2 polypeptide, or a portion thereof, patched-2 to a “tag polypeptide”. The tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the patched-2 polypeptide. The tag polypeptide preferably also is fairly unique so that the antibody does not substantially cross-react with other epitopes. Suitable tag polypeptides generally have at least six amino acid residues and usually between about 8 to about 50 amino acid residues (preferably, between about 10 to about 20 residues). [0030]
  • As used herein, the term “immunoadhesin” designates antibody-like molecules which combine the binding specificity of a heterologous protein (an “adhesin”) with the effector functions of immunoglobulin constant domains. Structurally, the immunoadhesin comprise a fusion of an amino acid sequence with the desired binding specificity which is other than the antigen recognition and binding site of an antibody (i.e., is “heterologous”), and an immunoglobulin constant domain sequence. The adhesin part of an immunoadhesin molecule typically is a contiguous amino acid sequence comprising at least the binding site of a receptor or a ligand. The immunoglobulin constant domain sequence in the immunoadhesins may be obtained from any immunoglobulin, such as IgG-1, IgG-2, IgG-3 or IgG-4 subtypes, IgA (including IgA-1 and IgA-2, IgE, IgD or IgM. Immunoadhesion reported in the literature include fusions of the T cell receptor* [Gascoigne et al., [0031] Proc. Natl. Acad. Sci. USA 84: 2936-2940 (1987)]; CD4* [Capron et al., Nature 337: 525-531 (1989); Traunecker et al., Nature 339: 68-70 (1989); Zettmeissl et al., DNA Cell Biol. USA 9: 347-353 (1990); Byrn et al., Nature 344, 667-670 (1990)]; L-selectin (homing receptor) [Watson et al., J. Cell. Biol. 110, 2221-2229 (1990); Watson et al., Nature 349, 164-167 (1991)]; CD44* [Aruffo et al., Cell 61, 1303-1313 (1990)]; CD28* and B7* [Linsley et al., J. Exp. Med 173, 721-730 (1991)]; CTLA-4* [Lisley et al., J. Exp. Med. 174, 561-569 (1991)]; CD22* [Stamenkovic et al., Cell 66. 1133-1144 (1991)]; TNF receptor [Ashkenazi et al., Proc. Natl. Acad. Sci. USA 88, 10535-10539 (1991); Lesslauer et al., Eur. J. Immunol. 27, 2883-2886 (1991); Peppel et al., J. Exp. Med. 174, 1483-1489 (1991)]; NP receptors [Bennett et al., J. Biol. Chem. 266, 23060-23067 (1991)]; IgE receptor α-chain [Ridgway and Gorman, J. Cell. Biol. 115, abstr. 1448 (1991)]; HGF receptor [Mark, M. R. et al., J. Biol. Chem., 267(36): 26166-26171 (1992) ], where the asterisk (*) indicates that the receptor is a member of the immunoglobulin superfamily.
  • “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends upon the ability of denatured DNA to reanneal when complementary strands are present in an environment near but below their T[0032] m (melting temperature). The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. Moreover, stringency is also inversely proportional to salt concentrations. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology (1995).
  • “Stringent conditions,” as defined herein may be identified by those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (vol/vol) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C. [0033]
  • “Isolated,” when used to describe the various polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In preferred embodiments, the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain. Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the vertebrate patched-2 natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step. [0034]
  • An “isolated” patched-2 nucleic acid molecule is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the patched-2 nucleic acid. An isolated patched-2 nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated patched-2 nucleic acid molecules therefore are distinguished from the corresponding native patched-2 nucleic acid molecule as it exists in natural cells. [0035]
  • The term “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers. [0036]
  • Nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading frame. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. [0037]
  • The term “antibody” is used in the broadest sense and specifically covers single monoclonal antibodies (including agonist and antagonist antibodies), antibody compositions with polyepitopic specificity, as well as antibody fragments (e.g., Fab, F(ab′)[0038] 2 and Fv), so long as they exhibit the desired biological activity.
  • The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations that typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they are synthesized by the hybridoma culture, uncontaminated by other immunoglobulins. The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler & Milstein, [0039] Nature 256:495 (1975), or may be made by recombinant DNA methods [see, e.g. U.S. Pat. No. 4,816,567 (Cabilly et al)].
  • The monoclonal antibodies herein specifically include “chimeric” antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity [U.S. Pat. No. 4,816,567; Cabilly et al.; Morrison et al., [0040] Proc. Natl. Acad. Sci. USA 81, 6851-6855 (1984)].
  • “Humanized” forms of non-human (e.g. murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′)[0041] 2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In some instances, corresponding non-human residues replace Fv framework residues of the human immunoglobulin. Furthermore, humanized antibody may comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and optimize antibody performance. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details see: Jones et al., Nature 321, 522-525 (1986); Reichmann et al., Nature 332, 323-329 (1988); Presta, Curr. Op. Struct. Biol. 2 593-596 (1992) and U.S. Pat. No. 5,225,539 (Winter) issued Jul. 6, 1993.
  • “Active” or “activity” for the purposes herein refers to form(s) of patched-2 which retain the biologic and/or immunologic activities of native or naturally occurring patched-2. A preferred activity is the ability to bind to and affect, e.g., block or otherwise modulate, hedgehog, especially Desert hedgehog signaling. For example, the regulation of the pathogenesis of testicular cancer, male spermatocyte formation and basal cell carcinoma. [0042]
  • The term “antagonist” is used herein in the broadest sense to include any molecule which blocks, prevents, inhibits, neutralizes the normal functioning of patched-2 in the Hh signaling pathway. One particular form of antagonist includes a molecule that interferes with the interaction between Dhh (SEQ ID NO:13) and Ptch-2 (SEQ ID NO:2). Alternatively, an antagonist cold also be a molecule which increases the levels of patched-2. In a similar manner, the term “agonist” is used herein to include any molecule which promotes, enhances or stimulates the binding of a Hh to patched-2 in the Hh signaling pathway (e.g., blocking binding of Ptch-2 (SEQ ID NO:2) to Smo (SEQ ID NO:17)). Suitable molecules that affect the protein-protein interaction of Hh and Ptch-2 and its binding proteins include fragments of the latter or small bioorganic molecules, e.g., peptidomimetics, which will prevent or enhance, as the case may be, the binding of Hh to Ptch-2. Non-limiting examples include proteins, peptides, glycoproteins, glycopeptides, glycolipids, polysaccharides, oligosaccharides, nucleic acids, bioorganic molecules, peptidomimetics, pharmacological agents and their metabolites, transcriptional and translation control sequences, and the like. Another preferred form of antagonist includes antisense oligonucleotides that inhibit proper transcription of wild type patched-2. [0043]
  • The term “modulation” or “modulating” means upregulation or downregulation of a signaling pathway. Cellular processes under the control of signal transduction may include, but are not limited to, transcription of specific genes; normal cellular functions, such as metabolism, proliferation, differentiation, adhesion, apoptosis and survival, as well as abnormal processes, such as transformation, blocking of differentiation and metastasis. [0044]
  • The techniques of “polymerase chain reaction,” or “PCR”, as used herein generally refers to a procedure wherein minute amounts of a specific piece of nucleic acid, RNA and/or DNA are amplified as described in U.S. Pat. No. 4,683,195 issued Jul. 28, 1987. Generally, sequence information from the ends of the region of interest or beyond needs to be available, such that oligonucleotide primers can be designed; these primers will be identical or similar in sequence to opposite strands of the template to be amplified. The 5′ terminal nucleotides of the two primers may coincide with the ends of the amplified material. PCR sequences form total genomic DNA, and cDNA transcribed from total cellular RNA, bacteriophage, or plasmid sequences, etc. See generally Mullis et al., [0045] Cold Spring Harbor Symp. Quant. Biol. 51: 263 (1987); Erlich, Ed., PCR Technology, (Stockton Press, NY, 1989). As used herein, PCR is considered to be one, but not the only, example of a nucleic acid test sample comprising the use of a known nucleic acid as a primer and a nucleic acid polymerase to amplify or generate a specific piece of nucleic acid.
    • II. Compositions and Methods of the Invention A. Full-length patched-2
  • The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as patched-2. In particular, Applicants have identified and isolated cDNA encoding a human patched-2 polypeptide, as disclosed in further detail in the Examples below. Using BLAST, BLAST-2 and FastA sequence alignment computer programs (set to the default parameters), Applicants found that a full-length native sequence human Ptch-2 (SEQ ID NO:2) (shown in FIG. 3) has 53% amino acid sequence identity with human patched (SEQ ID NO:4). Moreover human full-length patched-2 (SEQ ID NO:2) has about a 91% sequence identity with murine Ptch-2 (SEQ ID NO:7) (FIG. 8). Accordingly, it is presently believed that the human patched-2 (SEQ ID NO:2) disclosed in the present application is a newly identified member of the mammalian hedgehog signaling cascade, specifically Desert hedgehog. [0046]
  • The full-length native sequence of human patched-2 gene, or portions thereof, may be used as hybridization probes for a cDNA library to isolate the full-length gene or to isolate still other vertebrate homolog genes (for instance, those encoding naturally-occurring variants of patched-2 or patched-2 from other species) which have a desired sequence identity to the human patched-2 sequence disclosed in FIG. 1 (SEQ ID NO:2). Optionally, the length of the probes will be about 20 to about 50 bases. The hybridization probes may be derived from the nucleotide sequence of FIG. 1 (SEQ ID NO:1) or from genomic sequences including promoters, enhancer elements and introns of native sequence vertebrate patched-2. By way of example, a screening method will comprise isolating the coding region of the vertebrate patched-2 gene using the known DNA sequence to synthesize a selected probe of about 40 bases. Hybridization probes may be labeled by a variety of labels, including radionucleotides such as [0047] 32P or 35S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems. Labeled probes having a sequence complementary to that of the vertebrate patched-2 gene of the present invention can be used to screen libraries of human cDNA, genomic DNA or mRNA to determine which members of such libraries the probe hybridizes to.
    • B. Patched-2 Variants
  • In addition to the full-length native sequence patched-2 described herein, it is contemplated that patched-2 variants can be prepared. Patched-2 variants can be prepared by introducing appropriate nucleotide changes into a known patched-2 DNA, or by synthesis of the desired patched-2 polypeptides. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of patched-2. [0048]
  • Variations in the native full-length sequence patched-2 or in various domains of the patched-2 described herein, can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Pat. No. 5,364,934. Variations may be a substitution, deletion or insertion of one or more codons encoding the patched-2 that results in a change in the amino acid sequence of patched-2 as compared with the native sequence patched-2. Optionally, the variation is by substitution of at least one amino acid with any other amino acid in one or more of the domains of patched-2. Guidance in determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired activity may be found by comparing the sequence of the patched-2 with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology. Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements. Insertions or deletions may optionally be in the range of 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity in the in vitro assay described in the Examples below. [0049]
  • The variations can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis [Carter et al., [0050] Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10: 6487 (1987)], cassette mutagenesis [Wells et al., Gene, 34:315 (1985)], restriction selection mutagenesis [Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)] or other known techniques can be performed on the cloned DNA to produce the vertebrate patched-2 variant DNA.
  • Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions [Creighton, [0051] The Proteins, (W. H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)]. If alanine substitution does not yield adequate amounts of variant, an isoteric amino acid can be used.
  • In the comparison between human Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) sequences depicted in FIG. 3, the 12 transmembrane domains are identified in gray, while identical residues are boxed. Gaps are indicated by dashes (-) and are inserted to maximize the total identity score between the two sequences. [0052]
    • C. Modifications of patched-2
  • Covalent modifications of patched-2 are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of patched-2 with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of the vertebrate patched-2. Derivatization with bifunctional agents is useful, for instance, for crosslinking patched-2 to a water-insoluble support matrix or surface for use in the method for purifying anti-patched-2 antibodies, and vice-versa. Commonly used crosslinking agents include, e.g., 1,1-bis(diazo-acetyl)-2-phenylethane, glutaraldehyde, N-hydroxy-succinimide esters, for example, esters with 4-azido-salicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3′-dithiobis-(succinimidyl-propionate), bifunctional maleimides such as bis-N-maleimido-1,8-octane and agents such as methyl-3-[(p-azidophenyl)-dithio]proprioimidate. [0053]
  • Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, respectively, hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the α-amino groups of lysine, arginine, and histidine side chains [T. E. Creighton, [0054] Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco, pp. 79-86 (1983)], acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group.
  • Another type of covalent modification of patched-2 comprises linking the patched-2 polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337. Such modifications would be expected in increase the half-life of the molecules in circulation in a mammalian system; Extended half-life of patched-2 molecules might be useful under certain circumstances, such as where the patched-2 variant is administered as a therapeutic agent. [0055]
  • The patched-2 of the present invention may also be modified in a way to form a chimeric molecule comprising patched-2 bonded to another, heterologous polypeptide or amino acid sequence. In one embodiment, such a chimeric molecule comprises a fusion of patched-2 with a tag polypeptide, which provides an epitope to which an anti-tag antibody can selectively bind. The epitope tag is generally placed at the amino- or carboxyl-terminus of the patched-2. The presence of such epitope-tagged forms of the patched-2 can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the patched-2 to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag. In an alternative embodiment, the chimeric molecule may comprise a fusion of the patched-2 with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule, such a fusion could be to the Fc region of an IgG molecule. Ordinarily, the C-terminus of a contiguous amino acid sequence of a patched-2 receptor is fused to the N-terminus of a contiguous amino acid sequence of an immunoglobulin constant region, in place of the variable region(s), however N-terminal fusions are also possible. [0056]
  • Typically, such fusions retain at least functionally active hinge, CH2 and CH3 domains of the constant region of an immunoglobulin heavy chain. Fusions are also made to the C-terminus of the Fc portion of a constant domain, or immediately N-terminal to the CH1 of the heavy chain or the corresponding region of the light chain. This ordinarily is accomplished by constructing the appropriate DNA sequence and expressing it in recombinant cell culture. Alternatively, immunoadhesins may be synthesized according to known methods. [0057]
  • The precise site at which the fusion is made is not critical; particular sites are well known and may be selected in order to optimize the biological activity, secretion or binding characteristics of the immunoadhesins. [0058]
  • In a preferred embodiment, the C-terminus of a contiguous amino acid sequence which comprises the binding site(s) of patched-2, at the N-terminal end, to the C-terminal portion of an antibody (in particular the Fc domain), containing the effector functions of an immunoglobulin, e.g., immunoglobulin G[0059] 1 (IgG-1). As herein above mentioned, it is possible to fuse the entire heavy chain constant region to the sequence containing the binding site(s). However, more preferably, a sequence beginning in the hinge region just upstream of the papain cleavage site (which defines IgG Fc chemically; residue 216, taking the first residue of heavy chain constant region to be 114 [Kobat et al., supra], or analogous sites of other immunoglobulins) is used in the fusion. Although it was earlier thought that in immunoadhesins the immunoglobulin light chain would be required for efficient secretion of the heterologous protein-heavy chain fusion proteins, it has been found that even the immunoadhesins containing the whole IgG1 heavy chain are efficiently secreted in the absence of light chain. Since the light chain is unnecessary, the immunoglobulin heavy chain constant domain sequence used in the construction of the immunoadhesins of the present invention may be devoid of a light chain binding site. This can be achieved by removing or sufficiently altering immunoglobulin heavy chain sequence elements to which the light chain is ordinarily linked so that such binding is no longer possible. Thus, the CH1 domain can be entirely removed in certain embodiments of the patched-2/immunoglobulin chimeras.
  • In a particularly preferred embodiment, the amino acid sequence containing the extracellular domain(s) of patched-2 is fused to the hinge region and CH2, CH3; or CH1, hinge, CH2 and CH3 domains of an IgG-1, IgG-2, IgG-3, or IgG-4 heavy chain. [0060]
  • In some embodiments, the patched-2/immunoglobulin molecules (immunoadhesins) are assembled as monomers, dimers or multimers, and particularly as dimers or tetramers. Generally, these assembled immunoadhesins will have known unit structures similar to those of the corresponding immunoglobulins. A basic four chain structural unit (a dimer of two immunoglobulin heavy chain-light chain pairs) is the form in which IgG, IgA and IgE exist. A four chain unit is repeated in the high molecular weight immunoglobulins; IgM generally exists as a pentamer of basic four-chain units held together by disulfide bonds. IgA globulin, and occasionally IgG globulin, may also exist in a multimeric form in serum. In the case of multimers, each four chain unit may be the same or different. [0061]
  • It is not necessary that the entire immunoglobulin portion of the patched-2/immunoglobulin chimeras be from the same immunoglobulin. Various portions of different immunoglobulins may be combined, and variants and derivatives of native immunoglobulins can be made as herein above described with respect to patched-2, in order to optimize the properties of the immunoadhesin molecules. For example, immunoadhesin constructs in which the hinge of IgG-1 was replaced with that of IgG-3 were found to be functional and showed pharmacokinetics comparable to those of immunoadhesins comprising the entire IgG-1 heavy chain. [0062]
  • Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags; the flu HA tag polypeptide and its antibody 12CA5 [Field et al., [0063] Mol. Cell. Biol., 8: 2159-2165 (1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto [Evan et al., Molecular and Cellular Biology, 5:3610-3616 (1985)]; and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody [Paborsky et al., Protein Engineering, 3(6):547-553 (1990)]. Other tag polypeptides include the Flag-peptide [Hopp et al., BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin et al., Science, 255:192-194 (1992)]; an α-tubulin epitope peptide [Skinner et al., J. Biol. Chem., 266:15163-15166 (1991)]; and the T7 gene 10 protein peptide tag [Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA, 87:6393-6397 (1990)]. A preferred tag is the influenza HA tag.
    • D. Preparation of patched-2
  • The description below relates primarily to production of a particular patched-2 by culturing cells transformed or transfected with a vector containing patched-2 nucleic acid. It is, of course, contemplated that alternative methods, which are well known in the art, may be employed to prepare patched-2. For instance, the patched-2 sequence, or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart et al., [0064] Solid-Phase Peptide Synthesis, W. H. Freeman Co., San Francisco, Calif. (1969); Merrifield, J. Am. Chem. Soc., 85:2149-2154 (1963)]. In vitro protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be accomplished, for instance, using an Applied Biosystems Peptide Synthesizer (Foster City, Calif.) using manufacturer's instructions. Various portions of the vertebrate patched-2 may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full-length patched-2.
    • 1. Isolation of DNA Encoding Vertebrate patched-2
  • DNA encoding patched-2 may be obtained from a cDNA library prepared from tissue believed to possess the patched-2 mRNA and to express it at a detectable level. Accordingly, human patched-2 DNA can be conveniently obtained from a cDNA library prepared from human tissue, such as described in the Examples. The vertebrate patched-2-encoding gene may also be obtained from a genomic library or by oligonucleotide synthesis. [0065]
  • Libraries can be screened with probes (such as antibodies to the patched-2 or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al., [0066] Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989). An alternative means to isolate the gene encoding vertebrate patched-2 is to use PCR methodology [Sambrook et al., supra; Dieffenbach et al., PCR Primer. A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].
  • The Examples below describe techniques for screening a cDNA library. The oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized. The oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like [0067] 32P-labeled ATP, biotinylation or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook et al., supra.
  • Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available in public databases such as GenBank or other private sequence databases. Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined through sequence alignment using computer software programs such as BLAST, BLAST-2, ALIGN, DNAstar, and INHERIT which employ various algorithms to measure homology. [0068]
  • Nucleic acid having protein coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA. [0069]
    • 2. Selection and Transformation of Host Cells
  • Host cells are transfected or transformed with expression or cloning vectors described herein for patched-2 production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. The culture conditions, such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in [0070] Mammalian Cell Biotechnology: A Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook et al., supra.
  • Methods of transfection are known to the ordinarily skilled artisan, for example, CaPO[0071] 4 and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes or other cells that contain substantial cell-wall barriers. Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw et al., Gene, 23:315 (1983) and WO 89/05859 published Jun. 29, 1989. For mammalian cells without such cell walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology 52:456-457 (1978) can be employed. General aspects of mammalian cell host system transformations have been described in U.S. Pat. No. 4,399,216. Transformations into yeast are typically carried out according to the method of Van Solingen et al., J. Bact., 130:946 (1977) and Hsiao et al., Proc. Natl. Acad. Sci. (USA), 76:3829 (1979). However, other methods for introducing DNA into cells, such as by nuclear microinjection, electroporation, bacterial protoplast fusion with intact cells, or polycations, e.g., polybrene, polyornithine, may also be used. For various techniques for transforming mammalian cells, see Keown et al., Methods in Enzymology, 185:527-537 (1990) and Mansour et al., Nature, 336:348-352 (1988).
  • Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells. Suitable prokaryotes include but are not limited to eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriae such as [0072] E. coli. Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W3110 (ATCC 27,325) and K5 772 (ATCC 53,635).
  • In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for vertebrate patched-2-encoding vectors. [0073] Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism.
  • Suitable host cells for the expression of vertebrate patched-2 are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells. Examples of useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., [0074] J. Gen Virol., 36:59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA, 77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251 (1980)); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); and mouse mammary tumor (MMT 060562, ATCC CCL51). The selection of the appropriate host cell is deemed to be within the skill in the art.
    • 3. Selection and Use of a Replicable Vector
  • The nucleic acid (e.g., cDNA or genomic DNA) encoding patched-2 may be inserted into a replicable vector for cloning (amplification of the DNA) or for expression. Various vectors are publicly available. The vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage. The appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art. Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques, which are known to the skilled artisan. [0075]
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2μ plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells. A preferred replicable expression vector is the plasmid is pRK5. Holmes et al., [0076] Science, 253:1278-1280 (1991).
  • Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g. ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli. [0077]
  • An example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the patched-2 nucleic acid, such as DHFR or thymidine kinase. An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., [0078] Proc. Natl. Acad. Sci. USA, 77:4216 (1980). A suitable selection gene for use in yeast is the trp1 gene present in the yeast plasmid YRp7 [Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)]. The trp1 gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].
  • Expression and cloning vectors usually contain a promoter operably linked to the patched-2 nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the β-lactamase and lactose promoter systems [Chang et al., [0079] Nature, 275:615 (1978); Goeddel et al., Nature, 281:544 (1979)], alkaline phosphatase, a tryptophan (trp) promoter system [Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], and hybrid promoters such as the tac promoter [deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21-25 (1983)]. Promoters for use in bacterial systems also will contain a Shine-Dalgamo (S.D.) sequence operably linked to the DNA encoding patched-2.
  • Examples of suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase [Hitzeman et al., [0080] J. Biol. Chem., 255:2073 (1980)] or other glycolytic enzymes [Hess et al., J. Adv. Enzyme Reg., 7:149 (1968); Holland, Biochemistry, 17:4900 (1978)], such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phospho-fructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase.
  • Other yeast promoters, which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for [0081] alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.
  • Patched-2 transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published Jul. 5, 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems. [0082]
  • Inserting an enhancer sequence into the vector may increase transcription of a DNA encoding the vertebrate patched-2 by higher eukaryotes. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. The enhancer may be spliced into the vector at a [0083] position 5′ or 3′ to the patched-2 coding sequence, but is preferably located at a site 5′ from the promoter.
  • Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding patched-2. [0084]
  • Still other methods, vectors, and host cells suitable for adaptation to the synthesis of patched-2 in recombinant vertebrate cell culture are described in Gething et al., [0085] Nature, 293:620-625 (1981); Mantei et al. Nature, 281:40-46 (1979); EP 117,060; and EP 117,058.
    • 4. Detecting Gene Amplification/Expression
  • Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, [0086] Proc. Natl. Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.
  • Gene expression, alternatively, may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence patched-2 polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence patched-2 to patched-2 DNA and encoding a specific antibody epitope. [0087]
    • 5. Purification of Polypeptide
  • Forms of patched-2 may be recovered from host cell lysates. Since patched-2 is membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g. Triton-X 100) or by enzymatic cleavage. Cells employed in expression of patched-2 can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents. [0088]
  • It may be desired to purify patched-2 from recombinant cell proteins or polypeptides. The following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanol precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; protein A Sepharose columns to remove contaminants such as IgG; and metal chelating columns to bind epitope-tagged forms of the patched-2. Various methods of protein purification may be employed and such methods are known in the art and described for example in Deutscher, [0089] Methods in Enzymology, 182 (1990); Scopes, Protein Purification: Principles and Practice, Springer-Verlag, New York (1982). The purification step(s) selected will depend, for example, on the nature of the production process used and the particular patched-2 produced.
    • E. Uses for patched-2
  • (1) Patched-2 is a specific receptor for Dhh [0090]
  • The hedgehog signaling pathway has been implicated in the formation of embryonic structures in mammals and invertebrates. The multi-pass transmembrane receptor Ptch, is a negative regulator of the hedgehog pathway, repressing the serpentine signaling molecule Smoothened (Smo). Data have shown that loss of Ptch leads to deregulation of the hedgehog pathway leading to formation of aberrant structures in the embryos and carcinoma in the adult. [0091]
  • Applicants' newly identified second human patched gene, termed patched-2, has a similar 12 transmembrane domain topology as does patched, and can bind to all the members of the Hh family and can complex with Smo (SEQ ID NO:17). However, the expression patterns of Ptch-2 and Ptch do not overlap. Ptch-2 is expressed mainly in the developing spermatocytes, which are supported directly by the Dhh producing Sertoli cells, which suggests that Ptch-2 is a receptor for Desert hedgehog. [0092]
  • In the adult tubule, Sertoli cells, which are unusually large secretory cells, traverse the seminiferous tubule from the basal lamina to the luminal aspect, sending out cytoplasmic protrusions that engulf the germ cells. These contacts are particularly close during spermiogenesis, in which the haploid round spermatids undergo differentiation to produce the highly specialized, motile sperm. Tight junctions between adjacent Sertoli cells compartmentalize the tubule into a basal region, which contains mitotic spermatogonia and early spermtocytes, and an adluminal compartment, which contains meiotic spermatocytes and maturing spermatids. In fact, a Sertoli-derived cell line supports the meiotic progression of germ cells in culture, consistent with the view that factors derived from Sertoli cells contribute to germ cell maturation, Rassoulzadegan, M., et al., [0093] Cell 1993, 75: 997-1006. Loss of Dhh activity results in a recessive, sex-specific phentotype. Female mice homozygous for the mutation were fully viable and fertile, whereas male mice were viable but infertile. A gross examination indicated that, as early as 18.5 dpc, the testes of mutant males were noticeably smaller than those of heterozygous littermates. Bitgood et al., Curr. Biol., 1996 6(3): 298-304. Thus, Sertoli cells likely independently regulate mitotic and meiotic stages of germ cell development during postnatal development. Therefore, since patched-2 appears to be the receptor for Dhh (SEQ ID NO:13), molecules which modulate the binding of Dhh (SEQ ID NO:13) to Ptch-2 would affect the activation of Dhh signaling, and thereby would have utility in the treatment of conditions which are modulated by Dhh (SEQ ID NO:13). (For example, testicular cancer). Alternatively, it is also provided that antagonists or agonists of patched-2 may be used for treating disorders or creating a desirable physiological condition effected by blocking Dhh (SEQ ID NO:13) signaling. (E.g, contraception, infertility treatment).
  • (2) General uses for patched-2 [0094]
  • Nucleotide sequences (or their complement) encoding patched-2 have various applications in the art of molecular biology, including uses as hybridization probes, in chromosome and gene mapping and in the generation of anti-sense RNA and DNA. Patched-2 nucleic acid will also be useful for the preparation of patched-2 polypeptides by the recombinant techniques described herein. [0095]
  • The full-length native sequence patched-2 gene, or portions thereof, may be used as hybridization probes for a cDNA library to isolate the full-length gene or to isolate still other genes (for instance, those encoding naturally-occurring variants of patched-2) which have a desired sequence identity to the patched-2 sequence disclosed in FIG. 1 (SEQ ID NO:1). Optionally, the length of the probes will be about 20 to about 50 bases. The hybridization probes may be derived from the nucleotide sequence of FIG. 1 (SEQ ID NO:1) or from genomic sequences including promoters, enhancer elements and introns of native sequence patched-2. By way of example, a screening method will comprise isolating the coding region of the patched-2 gene using the known DNA sequence to synthesize a selected probe of about 40 bases. Hybridization probes may be labeled by a variety of labels, including radionucleotides such as [0096] 32P or 35S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems. Labeled probes having a sequence complementary to that of the patched-2 gene of the present invention can be used to screen libraries of human cDNA, genomic DNA or mRNA to determine to which members of such libraries the probe hybridizes. Hybridization techniques are described in further detail in the Examples below.
  • The probes may also be employed in PCR techniques to generate a pool of sequences for identification of closely related patched-2 sequences. [0097]
  • Nucleotide sequences encoding patched-2 can also be used to construct hybridization probes for mapping the gene, which encodes patched-2 and for the genetic analysis of individuals with genetic disorders. The nucleotide sequences provided herein may be mapped to a chromosome and specific regions of a chromosome using known techniques, such as in situ hybridization, linkage analysis against known chromosomal markers, and hybridization screening with libraries. [0098]
  • Patched-2 polypeptides can be used in assays to identify the other proteins or molecules involved in complexing with patched-2 which ultimately results in the modulation of hedgehog signaling. Alternatively, these molecules can modulate the binding of patched-2 to Dhh (SEQ ID NO:13). By such methods, inhibitors of the binding interaction can be identified. Proteins involved in such binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction. Also, the substrate of patched-2 can be used to isolate correlative complexing proteins. Screening assays can be designed to find lead compounds that mimic the biological activity of a native patched-2 or to find those that act as a substrate for patched-2. Such screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates. Such small molecule inhibitors could block the enzymatic action of patched-2, and thereby inhibit hedgehog signaling. Small molecules contemplated include synthetic organic or inorganic compounds. The assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays and cell based assays, which are well characterized in the art. [0099]
  • Nucleic acids which encode patched-2 or its modified forms can also be used to generate either transgenic animals or “knock out” animals which, in turn, are useful in the development and screening of therapeutically useful reagents. A transgenic animal (e.g., a mouse or rat) is an animal having cells that contain a transgene, was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A transgene is a DNA sequence that is integrated into the genome of a cell from which a transgenic animal develops. In one embodiment, cDNA encoding patched-2 can be used to clone genomic DNA encoding patched-2 in accordance with established techniques and the genomic sequences used to generate transgenic animals that contain cells which express DNA encoding patched-2. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. Nos. 4,736,866 and 4,870,009. Typically, particular cells would be targeted for patched-2 transgene incorporation with tissue-specific enhancers. Transgenic animals that include a copy of a transgene encoding patched-2 introduced into the germ line of the animal at an embryonic stage can be used to examine the effect of increased expression of DNA encoding patched-2. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. [0100]
  • Non-human homologues of vertebrate patched-2 can be used to construct a patched-2 “knock out” animal which has a defective or altered gene encoding patched-2 as a result of homologous recombination between the endogenous gene encoding patched-2 and altered genomic DNA encoding patched-2 introduced into an embryonic cell of the animal. For example, cDNA encoding patched-2 can be used to clone genomic DNA encoding patched-2 in accordance with established techniques. A portion of the genomic DNA encoding patched-2 can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector [see e.g., Thomas and Capecchi, [0101] Cell, 51:503 (1987) for a description of homologous recombination vectors]. The vector is introduced into an embryonic stem cell line (e.g. by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected [see e.g., Li et al, Cell, 69:915 (1992)]. The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras [see e.g. Bradley, in Teratocarcinomas and Embryonic Stem Cells. A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152]. A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a “knock out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knockout animals can be characterized for instance, for their ability to defend against certain pathological conditions and for their development of pathological conditions due to absence of the patched-2 polypeptide.
  • Suppression or inhibition (antagonism) of Dhh signaling is also an objective of therapeutic strategies. Since patched-2 can combine with all members of the hedgehog family (i.e., Shh, Dhh, Ihh), antagonist molecules which prevent the binding of hedgehog molecules to Ptch-2 (SEQ ID NO:2) have therapeutic utility. For example, SHh signaling is known to be activated in Basal Cell Carcinoma; Dhh (SEQ ID NO:13) is known to be involved in the regulation of spermatogenesis. Inhibitor or antagonist of Hh signaling would be effective therapeutics in the treatment of Basal Cell Carcinoma or male contraception, respectively. [0102]
  • The stimulation of Dhh signaling (agonism) is also an objective of therapeutic strategies. Since Ptch-2 (SEQ ID NO:2) also binds to the other members of the Hh family, Ihh and Shh, activating Dhh signaling would be useful in disease states or disorders characterized by inactive or insufficient Hh signaling. For example, degenerative disorders of the nervous system, e.g., Parkinson's disease, memory deficits, Alzheimer's disease, Lou Gehrig's disease, Huntington's disease, schizophrenia, stroke and drug addiction. Additionally, patched-2 agonists could be used to treat gut diseases, bone diseases, skin diseases, diseases of the testis (including infertility), ulcers, lung diseases, diseases of the pancreas, diabetes, osteoporosis. [0103]
    • F. Anti-patched-2 Antibodies
  • The present invention further provides anti-vertebrate patched-2 antibodies. Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies. [0104]
    • 1. Polyclonal Antibodies
  • The anti-patched-2 antibodies may comprise polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent may include the patched-2 polypeptide or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants that may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation. [0105]
    • 2. Monoclonal Antibodies
  • The anti-patched-2 antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, [0106] Nature, 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro.
  • The immunizing agent will typically include the patched-2 polypeptide or a fusion protein thereof. Generally, either peripheral blood lymphocytes (“PBLs”) are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell [Goding, [0107] Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103]. Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.
  • Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Rockville, Maryland. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies [Kozbor, [0108] J. Immunol., 133:3001 (1984); Brodeur et al, Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63].
  • The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against patched-2. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, [0109] Anal. Biochem., 107:220 (1980).
  • After the desired hybridoma cells are identified, the clones may be subcloned by limiting dilution procedures and grown by standard methods [Goding, supra]. Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal. [0110]
  • The monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography. [0111]
  • The monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences [U.S. Pat. No. 4,816,567; Morrison et al., supra] or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody. [0112]
  • The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking. [0113]
  • In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art. [0114]
    • 3. Humanized Antibodies
  • The anti-patched-2 antibodies of the invention may further comprise humanized antibodies or human antibodies. Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′)[0115] 2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Bol., 2:593-596 (1992)].
  • Methods for humanizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain. Humanization can be essentially performed following the method of Winter and co-workers [Jones et al., [0116] Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)], by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such “humanized” antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
  • Human antibodies can also be produced using various techniques known in the art, including phage display libraries [Hoogenboom and Winter, [0117] J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991)]. The techniques of Cole et al. and Boerner et al. are also available for the preparation of human monoclonal antibodies (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al., J. Immunol., 147(1):86-95 (1991)].
    • 4. Bispecific Antibodies
  • Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for the vertebrate patched-2, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit. [0118]
  • Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities [Milstein and Cuello, [0119] Nature, 305:537-539 (1983)]. Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., EMBO J., 10:3655-3659(1991).
  • Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al., [0120] Methods in Enzymology, 121:210 (1986).
    • 5. Heteroconjugate Antibodies
  • Heteroconjugate antibodies are also within the scope of the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells [U.S. Pat. No. 4,676,980], and for treatment of HIV infection [WO 91/00360; WO 92/200373; EP 03089]. It is contemplated that the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Pat. No. 4,676,980. [0121]
    • G. Uses for anti-patched-2 Antibodies
  • The anti-patched-2 antibodies of the invention have various utilities. For example, anti-patched-2 antibodies may be used in diagnostic assays for patched-2, e.g., detecting its expression in specific cells, tissues, or serum. Various diagnostic assay techniques known in the art may be used, such as competitive binding assays, direct or indirect sandwich assays and immunoprecipitation assays conducted in either heterogeneous or homogeneous phases [Zola, [0122] Monoclonal Antibodies: A Manual of Techniques, CRC Press, Inc. (1987) pp. 147-158]. The antibodies used in the diagnostic assays can be labeled with a detectable moiety. The detectable moiety should be capable of producing, either directly or indirectly, a detectable signal. For example, the detectable moiety may be a radioisotope, such as 3H, 14C, 32P, 35S, or 125I, a fluorescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin, or an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase. Any method known in the art for conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al., Nature, 144: 945 (1962); David et al., Biochemistry, 13:1014 (1974); Pain et al., J. Immunol. Meth., 40:219 (1981); and Nygren, J. Histochem. and Cytochem., 30:407 (1982).
  • Anti-patched-2 antibodies also are useful for the affinity purification of patched-2 from recombinant cell culture or natural sources. In this process, the antibodies against patched-2 are immobilized on a suitable support, such a Sephadex resin or filter paper, using methods well known in the art. The immobilized antibody then is contacted with a sample containing the patched-2 to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except the patched-2, which is bound to the immobilized antibody. Finally, the support is washed with another suitable solvent that will release the patched-2 from the antibody. [0123]
  • Basal cell carcinoma (BCC) is the most common human cancer. The Hh signaling pathway was found to activated in all BCCs. Loss of Ptch function is thought to lead to unregulated Smo activity and is responsible for about half of all BCCs. Ptch being a target of the Hh pathway itself, increases in Ptch mRNA levels have been detected in BCC [Galiani, et al., [0124] Nature Genet. 14: 78-81 (1996)] as well as in animal models of BCC. Oro et al., Science 276: 817-821 (1997); Xie et al., Nature 391: 90-92 (1998). Abnormal activation of Sh signaling, such as that which occurs in BCC, was examined to confirm whether Ptch-2 (SEQ ID NO:2) expression was increased. As shown in FIG. 9, an in situ hybridization for Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) in Smo-M2 (SEQ ID NO:16) transgenic mice (Xie et al., supra), while lower than Ptch, was still high in tumor cells. This suggests that therapeutic antibodies directed toward Ptch-2 (SEQ ID NO:2) may be useful for the treatment of BCC.
  • Anti-patched-2 antibodies also have utilities similar to those articulated for under the previous section “E. Uses of Patched-2”. Depending on whether anti-patched-2 antibodies will bind patched-2 receptors so as to either inhibit Hh signaling (antagonist) or inhibit patched-2 complexing with Smo (SEQ ID NO:17) and thereby remove the normal inhibitory effect of Smo (SEQ ID NO:17) on Hh signaling (agonist) the antibody will have utilities corresponding to those articulated previously for patched-2. [0125]
    • H. Patched-2 Antagonists
  • Several approaches may be suitably employed to create the patched-2 antagonist and agonist compounds of the present invention. Any approach where the antagonist molecule can be targeted to the interior of the cell, which interferes or prevents wild type patched-2 from normal operation is suitable. For example, competitive inhibitors, including mutant patched-2 receptors which prevent wild type patched-2 from properly binding with other proteins necessary for Dhh and Hh signaling. Additional properties of such antagonist or agonist molecules are readily determinable by one of ordinary skill, such as size, charge and hydrophobicity suitable for transmembrane transport. [0126]
  • Where mimics or other mammalian homologues of patched-2 are to be identified or evaluated, the cells are exposed to the test compound and compared to positive controls which are exposed only to human patched-2, and to negative controls which were not exposed to either the compound or the natural ligand. Where antagonists or agonists of patched-2 signal modulation are to be identified or evaluated, the cells are exposed to the compound of the invention in the presence of the natural ligand and compared to controls which are not exposed to the test compound. [0127]
  • Detection assays may by employed as a primary screen to evaluate the Hh signaling inhibition/enhancing activity of the antagonist/agonist compounds of the invention. The assays may also be used to assess the relative potency of a compound by testing a range of concentrations, in a range from 100 mM to 1 pM, for example, and computing the concentration at which the amount of phosphorylation or signal transduction is reduced or increased by 50% (IC[0128] 50) compared to controls.
  • Assays can be performed to identify compounds that affect Hh signaling of patched-2 substrates. Specifically, assays can be performed to identify compounds that increase the phosphorylation activity of patched-2 or assays can be performed to identify compounds that decrease the Hh signaling of patched-2 substrates. These assays can be performed either on whole cells themselves or on cell extracts. The assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays, cell based assays, etc. Such assay formats are well known in the art. [0129]
  • The screening assays of the present invention are amenable to high-throughput screening of chemical libraries, and are particularly suitable for identifying small molecule drug candidates. [0130]
    • (1) Antagonist and Agonist Molecules
  • To screen for antagonists and/or agonists of patched-2 signaling, the assay mixture is incubated under conditions whereby, but for the presence of the candidate pharmacological agent, patched-2 induces hedgehog signaling with a reference activity. The mixture components can be added in any order that provides for the requisite hedgehog activity. Incubation may be performed at any temperature that facilitates optimal binding, typically between about 4° and 40° C., more commonly between about 15° and 40° C. Incubation periods are likewise selected for optimal binding but also minimized to facilitate rapid, high-throughput screening, and are typically between about 0.1 and 10 hours, preferably less than 5 hours, more preferably less than 2 hours. After incubation, the effect of the candidate pharmacological agent on the patched-2 signaling is determined in any convenient way. For cell-free binding-type assays, a separation step is often used to separate bound and unbound components. Separation may, for example, be effected by precipitation (e.g. TCA precipitation, immunoprecipitation, etc.), immobilization (e.g. on a solid substrate), followed by washing. The bound protein is conveniently detected by taking advantage of a detectable label attached to it, e.g. by measuring radioactive emission, optical or electron density, or by indirect detection using, e.g. antibody conjugates. [0131]
  • For example, a method of screening for suitable patched-2 antagonists and/or agonists could involve the application of Dhh and other hedgehog ligands. Such a screening assay could compare in situ hybridization in the presence and absence of the candidate antagonist and/or agonist in a patched-2 expressing tissue as well as confirmation or absence of patched-2 modulated cellular development. Typically these methods involve exposing an immobilized patched-2 to a molecule suspected of binding thereto and determining the level of ligand binding downstream activation of reporter constructs and/or evaluating whether or not the molecule activates (or blocks activation of) patched-2. In order to identify such patched-2 binding ligands, patched-2 can be expressed on the surface of a cell and used to screen libraries of synthetic candidate compounds or naturally-occurring compounds (e.g., from endogenous sources such as serum or cells). [0132]
  • Suitable molecules that affect the protein-protein interaction of patched-2 and its binding proteins include fragments of the latter or small molecules, e.g., peptidomimetics, which will inhibit ligand-receptor interaction. Such small molecules, which are usually less than 10 K molecular weight, are preferable as therapeutics since they are more likely to be permeable to cells, are less susceptible to degradation by various cellular mechanisms, and are not as apt to elicit an immune response as proteins. Small molecules include but are not limited to synthetic organic or inorganic compounds. Many pharmaceutical companies have extensive libraries of such molecules, which can be conveniently screened by using the assays of the present invention. Non-limiting examples include proteins, peptides, glycoproteins, glycopeptides, glycolipids, polysaccharides, oligosacchardies, nucleic acids, bioorganic molecules, peptidomimetics, pharmacological agents and their metabolites, transcriptional and translation control sequences, and the like. [0133]
  • A preferred technique for identifying molecules which bind to patched-2 utilizes a chimeric substrate (e.g., epitope-tagged patched-2 or patched-2 immunoadhesin) attached to a solid phase, such as the well of an assay plate. The binding of the candidate molecules, which are optionally labeled (e.g., radiolabeled), to the immobilized receptor can be measured. Alternatively, competition for various Hh pathways, especially Dhh (SEQ ID NO:13) can be measured. In screening for antagonists and/or agonists, patched-2 can be exposed to a patched-2 substrate followed by the putative antagonist and/or agonist, or the patched-2 binding protein and antagonist and/or agonist can be added simultaneously, and the ability of the antagonist and/or agonist to block patched-2 activation can be evaluated. [0134]
    • (2) Detection Assays
  • The patched-2 polypeptides are useful in assays for identifying lead compounds for therapeutically active agents that modulate patched-2 receptor/ligand hedgehog signaling. Specifically, lead compounds that either prevent the formation of patched-2 signaling complexes or prevent or attenuate patched-2 modulated hedgehog signaling (e.g., binding to patched-2) can be conveniently identified. [0135]
  • Various procedures known in the art may be used for identifying, evaluating or assaying the inhibition of activity of the patched-2 proteins of the invention. As patched-2 is believed to be a receptor for Dhh (SEQ ID NO:13), but also binds Shh (SEQ ID NO:14) and Ihh (SEQ ID NO:29), techniques known for use with identifying ligand/receptor modulators may also be employed with the present invention. In general, such assays involve exposing target cells in culture to the compounds and a) biochemically analyzing cell lysates to assess the level and/or identity of binding; or (b) scoring phenotypic or functional changes in treated cells as compared to control cells that were not exposed to the test substance. Such screening assays are described in U.S. Pat. No. 5,602,171, U.S. Pat. No. 5,710,173, WO 96/35124 and WO 96/40276. [0136]
    • (a) Biochemical Detection Techniques
  • Biochemical analysis can be evaluated by a variety of techniques. One typical assay mixture which can be used with the present invention contains patched-2 and a ligand protein with which patched-2 is normally associated (e.g., Dhh (SEQ ID NO:13)) usually in an isolated, partially pure or pure form. One or both of these components may be patched-2 to another peptide or polypeptide, which may, for example, provide or enhance protein-protein binding, improve stability under assay conditions, etc. In addition, one of the components usually comprises or is coupled to a detectable label. The label may provide for direct detection by measuring radioactivity, luminescence, optical or electron density, etc., or indirect detection such as an epitope tag, an enzyme, etc. The assay mixture can additionally comprise a candidate pharmacological agent, and optionally a variety of other components, such as salts, buffers, carrier proteins, e.g. albumin, detergents, protease inhibitors, nuclease inhibitors, antimicrobial agents, etc., which facilitate binding, increase stability, reduce non-specific or background interactions, or otherwise improve the efficiency or sensitivity of the assay. [0137]
  • The following detection methods may also be used in a cell-free system wherein cell lysate containing the signal transducing substrate molecule and patched-2 is mixed with a compound of the invention. To assess the activity of the compound, the reaction mixture may be analyzed by the SDS-PAGE technique or it may be added to substrate-specific anchoring antibody bound to a solid support, and a detection procedure as described above is performed on the separated or captured substrate to assess the presence or absence of a patched-2 binding ligand. The results are compared to those obtained with reaction mixtures to which the compound is not added. The cell-free system does not require the natural ligand or knowledge of its identity. For example, Posner et al. (U.S. Pat. No. 5,155,031 describes the use of insulin receptor as a substrate and rat adipocytes as target cells to demonstrate the ability of pervanadate to inhibit PTP activity. Another example, Burke et al., [0138] Biochem. Biophys. Res. Comm. 204: 129-134 (1994) describes the use of autophosphorylated insulin receptor and recombinant PTP1B in assessing the inhibitory activity of a phosphotyrosyl mimetic.
    • (i) Whole Cell Detection
  • A common technique involves incubating cells with patched-2 and radiolabeled ligand, lysing the cells, separating cellular protein components of the lysate using an SDS-polyacrylamide gel (SDS-PAGE) technique, in either one or two dimensions, and detecting the presence of labeled proteins by exposing X-ray film. Detection can also be effected without using radioactive labeling. In such a technique, the protein components (e.g., separated by SDS-PAGE) are transferred to a nitrocellulose membrane where the presence of patched-ligand complexes is detected using an anti-ligand antibody. [0139]
  • Alternatively, the anti-patched-2 ligand antibody can be conjugated with an enzyme, such as horseradish peroxidase, and detected by subsequent addition of a colorimetric substrate for the enzyme. A further alternative involves detecting the anti-patched-2 ligand by reacting with a second antibody that recognizes anti-patched-2 ligand, this second antibody being labeled with either a radioactive moiety or an enzyme as previously described. Examples of these and similar techniques are described in Hansen et al., [0140] Electrophoresis 14: 112-126 (1993); Campbell et al., J. Biol. Chem. 268: 7427-7434 (1993); Donato et al., Cell Growth Diff. 3: 258-268 (1992); Katagiri et al., J. Immunol. 150: 585-593 (1993). Additionally, the anti-patched-2 ligand can be detected by labeling it with a radioactive substance, followed by scanning the labeled nitrocellulose to detect radioactivity or exposure of X-ray film.
  • Further detection methods may be developed which are preferred to those described above. Especially for use in connection with high-throughput screening, it is expected that such methods would exhibit good sensitivity and specificity, extended linear range, low background signal, minimal fluctuation, compatibility with other reagents, and compatibility with automated handling systems. [0141]
  • The in vivo efficacy of the treatment of the present invention can be studied against chemically induced tumors in various rodent models. Tumor cell lines propagated in in vitro cell cultures can be introduced in experimental rodents, e.g. mice by injection, for example by the subcutaneous route. Techniques for chemical inducement of tumors in experimental animals are well known in the art. [0142]
    • (ii) Kinase Assays
  • Because patched-2 is a negative regulator of Hh signaling, which when activated by Hh releases the normal inhibitory effect on Smo, the inhibition of patched-2 binding to Smo can be measured by activation of various kinase substrate associated with Hh signaling. When the screening methods of the present invention for patched-2 antagonists/agonists are carried out as an ex vivo assay, the target kinase (e.g. fused) can be a substantially purified polypeptide. The kinase substrate (e.g., MBP, Gli) is a substantially purified substrate, which in the assay is phosphorylated in a reaction with a substantially purified phosphate source that is catalyzed by the kinase. The extent of phosphorylation is determined by measuring the amount of substrate phosphorylated in the reaction. A variety of possible substrates may be used, including the kinase itself in which instance the phosphorylation reaction measured in the assay is autophosphorylation. Exogenous substrates may also be used, including standard protein substrates such as myelin basic protein (MBP); yeast protein substrates; synthetic peptide substrates, and polymer substrates. Of these, MBP and other standard protein substrates may be regarded as preferred. Other substrates may be identified, however, which are superior by way of affinity for the kinase, minimal perturbation of reaction kinetics, possession of single or homogenous reaction sites, ease of handling and post-reaction recover, potential for strong signal generation, and resistance or inertness to test compounds. [0143]
  • Measurement of the amount of substrate phosphorylated in the ex vivo assay of the invention may be carried out by means of immunoassay, radioassay or other well-known methods. In an immunoassay measurement, an antibody (such as a goat or mouse anti-phosphoserine/threonine antibody) may be used which is specific for phosphorylated moieties formed during the reaction. Using well-known ELISA techniques, the phosphoserine/threonine antibody complex would itself be detected by a further antibody linked to a label capable of developing a measurable signal (as for example a fluorescent or radioactive label). Additionally, ELISA-type assays in microtitre plates may be used to test purified substrates. Peraldi et al., [0144] J. Biochem. 285: 71-78 (1992); Schraag et al., Anal. Biochem. 211: 233-239 (1993); Cleavland, Anal. Biochem. 190: 249-253 (1990); Farley, Anal. Biochem. 203: 151-157 (1992) and Lozaro, Anal. Biochem. 192: 257-261 (1991).
  • For example, detection schemes can measure substrate depletion during the kinase reaction. Initially, the phosphate source may be radiolabeled with an isotope such as [0145] 32P or 33P, and the amount of substrate phosphorylation may be measured by determining the amount of radiolabel incorporated into the substrate during the reaction. Detection may be accomplished by: (a) commercially available scintillant-containing plates and beads using a beta-counter, after adsorption to a filter or a microtitre well surface, or (b) photometric means after binding to a scintillation proximity assay bead or scintillant plate. Weemink and Kijken, J. Biochem. Biophs. Methods 31: 49, 1996; Braunwalder et al., Anal. Biochem. 234: 23 (1996); Kentrup et al., J. Biol. Chem. 271: 3488 (1996) and Rusken et al., Meth. Enzymol. 200: 98 (1991).
  • Preferably, the substrate is attached to a solid support surface by means of non-specific or, preferably, specific binding. Such attachment permits separation of the phosphorylated substrate from unincorporated, labeled phosphate source (such as adenosine triphosphate prior to signal detection. In one embodiment, the substrate may be physically immobilized prior to reaction, as through the use of Nunc™ high protein binding plate (Hanke et al., [0146] J. Biol. Chem. 271: 695 (1996)) or Wallac ScintiStrip™ plates (Braunwalder et al., Anal. Biochem. 234: 23 (1996). Substrate may also be immobilized after reaction by capture on, for example, P81 phophocellulose (for basic peptides), PEI/acidic molybdate resin or DEAE, or TCA precipitation onto Whatman™ 3MM paper, Tiganis et al., Arch. Biochem. Biophys. 325: 289 (1996); Morawetz et al., Mol. Gen. Genet. 250; 17 (1996); Budde et al., Int J. Pharmacognosy 33: 27 (1995) and Casnellie, Meth. Enz. 200: 115 (1991). Yet another possibility is the attachment of the substrate to the support surface, as by conjugation with binding partners such as glutathione and streptavidin (in the case of GST and biotin), respectively) which have been attached to the support, or via antibodies specific for the tags which are likewise attached to the support.
  • Further detection methods may be developed which are preferred to those described above. Especially for use in connection with high-throughput screening, it is expected that such methods would exhibit good sensitivity and specificity, extended linear range, low background signal, minimal fluctuation, compatibility with other reagents, and compatibility with automated handling systems. [0147]
  • The in vivo efficacy of the treatment of the present invention can be studied against chemically induced tumors in various rodent models. Tumor cell lines propagated in in vitro cell cultures can be introduced in experimental rodents, e.g. mice by injection, for example by the subcutaneous route. Techniques for chemical inducement of tumors in experimental animals are well known in the art. [0148]
    • (b) Biological Detection Techniques
  • The ability of the antagonist/agonist compounds of the invention to modulate the activity of patched-2, which itself modulates hedgehog signaling, may also be measured by scoring for morphological or functional changes associated with ligand binding. Any qualitative or quantitative technique known in the art may be applied for observing and measuring cellular processes which comes under the control of patched-2. The activity of the compounds of the invention can also be assessed in animals using experimental models of disorders caused by or related to dysfunctional hedgehog signaling. For example, ineffective Dhh hedgehog signaling in mice leads to viable but sterile mice. Additionally, proper Shh signaling is critical to murine embryonic development at the notochord and floor plate, neural tube, distal limb structures, spinal column and ribs. Improper Shh signaling, is also correlative with cyclopia. Any of these phenotypic properties could be evaluated and quantified in a screening assay for patched-2 antagonists and/or agonist. Disease states associated with overexpression of hedgehog is associated with basal cell carcinoma while inactive Shh signaling leads to improper neural development. [0149]
  • The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosages for use in humans. The dosage of the compounds of the invention should lie within a range of circulating concentrations with little or no toxicity. The dosage may vary within this range depending on the dosage form employed and the route of administration. [0150]
    • (2) Antisense Oligonucleotides
  • Another preferred class of antagonists involves the use of gene therapy techniques, include the administration of antisense oligonucleotides. Applicable gene therapy techniques include single or multiple administrations of therapeutically effective DNA or mRNA. Antisense RNAs and DNAs can be used as therapeutic agents for blocking the expression of certain genes in vivo. Reference short antisense oligonucleotides can be imported into cells where they act as inhibitors, despite their low intracellular concentrations caused by restricted uptake by the cell membrane, Zamecnik et al., [0151] Proc. Natl. Acad. Sci. USA 83: 4143-4146 (1986). The anti-sense oligonucleotides can be modified to enhance their uptake, e.g., by substituting their negatively charged phophodiester groups by uncharged groups.
  • There are a variety of techniques known for introducing nucleic acids into viable cells. The techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, ex vivo, or in vivo in the cells of the intended host. Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microinjection, cell fusion, DEAE-dextran, the calcium phosphate precipitation method, etc. The currently preferred in vivo gene transfer techniques include transfection with viral (typically retroviral) vectors and viral coat protein-liposome mediated transfection, Dzau et al., [0152] Trends Biotech. 11: 205-210 (1993). In some situations it is desirable to provide the nucleic acid source with an agent that targets the cells, such as an antibody specific for a cell surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g., capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, and proteins that target intracellular localization and enhance intracellular half-life. The technique of receptor-mediated endocytosis is described, for example, by Wu et al., J. Biol. Chem. 262: 4429-4432 (1987); Wagner et al., Proc. Natl. Acad. Sci. USA 87: 3410-3414 (1990). For a review of known gene targeting and gene therapy protocols, see Anderson et al., Science 256: 808-813 (1992).
  • In one embodiment of the invention, patched-2 expression may be reduced by providing patched-2-expressing cells with an amount of patched-2 antisense RNA or DNA effective to reduce expression of the patched-2 protein. [0153]
    • 1. Diagnostic Uses
  • Another use of the compounds of the invention (e.g., patched-2, patched-2 variant and anti-patched-2 antibodies) described herein is to help diagnose whether a disorder is driven, to some extent, by patched-2 or hedgehog signaling. For example, basal cell carcinoma cells are associated with active hedgehog signaling, spermatocyte formation is associated with Dhh signaling, and defective Ptch and Ptch-2 suppression may be associated with testicular carcinomas. [0154]
  • A diagnostic assay to determine whether a particular disorder is driven by Ptch-2 modulated hedgehog signaling, can be carried out using the following steps: (1) culturing test cells or tissues; (2) administering a compound which can prevent Ptch-2 (SEQ ID NO:2) binding with Smo (SEQ ID NO:17), thereby activating the Hh signaling pathway; and (3) measuring the amount of Hh signaling. The steps can be carried out using standard techniques in light of the present disclosure. For example, standard techniques can be used to isolate cells or tissues and culturing or in vivo. [0155]
  • Compounds of varying degree of selectivity are useful for diagnosing the role of patched-2. For example, compounds which inhibit patched-2 in addition to another form of kinase can be used as an initial test compound to determine if one of several signaling ligands drive the disorder. The selective compounds can then be used to further eliminate the possible role of the other ligands in driving the disorder. Test compounds should be more potent in inhibiting ligand-patched-2 binding activity than in exerting a cytotoxic effect (e.g., an IC[0156] 50/LD50 of greater than one). The IC50 and LD50 can be measured by standard techniques, such as an MTT assay, or by measuring the amount of LDH released. The degree of IC50/LD50 of a compound should be taken into account in evaluating the diagnostic assay. For example, the larger the IC50/LD50 ratio the more relative the information. Appropriate controls take into account the possible cytotoxic effect of a compound of a compound, such as treating cells not associated with a cell proliferative disorder (e.g., control cells) with a test compound, can also be used as part of the diagnostic assay. The diagnostic methods of the invention involve the screening for agents that modulate the effects of patched-2 upon hedgehog signaling. Exemplary detection techniques include radioactive labeling and immunoprecipitating (U.S. Pat. No. 5,385,915).
    • J. Pharmaceutical Compositions and Dosages
  • Therapeutic formulations of the compositions of the invention are prepared for storage as lyophilized formulations or aqueous solutions by mixing the patched-2 molecule, agonist and/or antagonist having the desired degree of purity with optional “pharmaceutically-acceptable” or “physiologically-acceptable” carriers, excipients or stabilizers typically employed in the art (all of which are termed “excipients”). For example, buffering agents, stabilizing agents, preservatives, isotonifiers, non-ionic detergents, antioxidants and other miscellaneous additives. (See Remington's Pharmaceutical Sciences, 16[0157] th Ed., A. Osol, Ed. (1980)). Such additives must be nontoxic to the recipients at the dosages and concentrations employed.
  • Buffering agents help to maintain the pH in the range which approximates physiological conditions. They are preferably present at concentration ranging from about 2 mM to about 50 mM. Suitable buffering agents for use with the present invention include both organic and inorganic acids and salts thereof such as citrate buffers (e.g., monosodium citrate-disodium citrate mixture, citric acid-trisodium citrate mixture, citric acid-monosodium citrate mixture, etc.), succinate buffers (e.g., succinic acid-monosodium succinate mixture, succinic acid-sodium hydroxide mixture, succinic acid-disodium succinate mixture, etc.), tartrate buffers (e.g., tartaric acid-sodium tartrate mixture, tartaric acid-potassium tartrate mixture, tartaric acid-sodium hydroxide mixture, etc.), fumarate buffers (e.g., fumaric acid-monosodium fumarate mixture, etc.), fumarate buffers (e.g., fumaric acid-monosodium fumarate mixture, fumaric acid-disodium fumarate mixture, monosodium fumarate-disodium fumarate mixture, etc.), gluconate buffers (e.g., gluconic acid-sodium glyconate mixture, gluconic acid-sodium hydroxide mixture, gluconic acid-potassium glyconate mixture, etc.), oxalate buffer (e.g., oxalic acid-sodium oxalate mixture, oxalic acid-sodium hydroxide mixture, oxalic acid-potassium oxalate mixture, etc.), lactate buffers (e.g., lactic acid-sodium lactate mixture, lactic acid-sodium hydroxide mixture, lactic acid-potassium lactate mixture, etc.) and acetate buffers (e.g., acetic acid-sodium acetate mixture, acetic acid-sodium hydroxide mixture, etc.). Additionally, there may be mentioned phosphate buffers, histidine buffers and trimethylamine salts such as Tris. [0158]
  • Preservatives are added to retard microbial growth, and are added in amounts ranging from 0.2%-1% (w/v). Suitable preservatives for use with the present invention include phenol, benzyl alcohol, meta-cresol, methyl paraben, propyl paraben, octadecyldimethylbenzyl ammonium chloride, benzalconium halides (e.g., chloride, bromide, iodide), hexamethonium chloride, alkyl parabens such as methyl or propyl paraben, catechol, resorcinol, cyclohexanol, and 3-pentanol. [0159]
  • Isotonifiers sometimes known as “stabilizers” are present to ensure isotonicity of liquid compositions of the present invention and include polyhydric sugar alcohols, preferably trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol and mannitol. Polyhydric alcohols can be present in an amount between 0.1% to 25% by weight, preferably 1% to 5% taking into account the relative amounts of the other ingredients. [0160]
  • Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the therapeutic agent or helps to prevent denaturation or adherence to the container wall. Typical stabilizers can be polyhydric sugar alcohols (enumerated above); amino acids such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, threonine, etc., organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol and the like, including cyclitols such as inositol; polyethylene glycol; amino acid polymers; sulfur containing reducing agents, such as urea, glutathione, thiocitic acid, sodium thioglycolate, thioglycerol, α-monothioglycerol and sodium thio sulfate; low molecular weight polypeptides (i.e. <10 residues); proteins such as human serum albumin, bovine serum albumin, gelatin or immunoglobulins; hydrophilic polymers, such as polyvinylpyrrolidone monosaccharides, such as xylose, mannose, fructose, glucose; disaccharides such as lactose, maltose, sucrose and trisaccacharides such as raffinose; polysaccharides such as dextran. Stabilizers can be present in the range from 0.1 to 10,000 weights per part of weight active protein. [0161]
  • Non-ionic surfactants or detergents (also known as “wetting agents”) are present to help solubilize the therapeutic agent as well as to protect the therapeutic protein against agitation-induced aggregation, which also permits the formulation to be exposed to shear surface stressed without causing denaturation of the protein. Suitable non-ionic surfactants include polysorbates (20, 80, etc.), polyoxamers (184, 188 etc.), Pluronic® polyols, polyoxyethylene sorbitan monoethers (Tween®-20, Tween®-80, etc.). Non-ionic surfactants are present in a range of about 0.05 mg/ml to about 1.0 mg/ml, preferably about 0.07 mg/ml to about 0.2 mg/ml. [0162]
  • Additional miscellaneous excipients include bulking agents, (e.g. starch), chelating agents (e.g. EDTA), antioxidants (e.g., ascorbic acid, methionine, vitamin E), and cosolvents. [0163]
  • The formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. For example, it may be desirable to further provide an immunosuppressive agent. Such molecules are suitably present in combination in amounts that are effective for the purpose intended. [0164]
  • The active ingredients may also be entrapped in microcapsule prepared, for example, by coascervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in [0165] Remington's Pharmaceutical Sciences, 16th edition, A. Osal, Ed. (1980).
  • The formulations to be used for in vivo administration must be sterile. This is readily accomplished, for example, by filtration through sterile filtration membranes. [0166]
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semi-permeable matrices of solid hydrophobic polymers containing the compounds of the invention, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No.3,773,919), copolymers of L-glutamic acid and ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogens release proteins for shorter time periods. When encapsulated compounds of the invention remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37° C., resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S—S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions. [0167]
  • The amount of therapeutic polypeptide, antibody or fragment thereof which will be effective in the treatment of a particular disorder or condition will depend on the nature of the disorder or condition, and can be determined by standard clinical techniques. Where possible, it is desirable to determine the dose-response curve and the pharmaceutical compositions of the invention first in vitro, and then in useful animal model systems prior to testing in humans. However, based on common knowledge of the art, a pharmaceutical composition effective in modulating Dhh and Hh signaling may provide a local patched-2 protein concentration of between about 10 and 1000 ng/ml, preferably between 100 and 800 ng/ml and most preferably between about 200 ng/ml and 600 ng/ml of Ptch-2 (SEQ ID NO:2). [0168]
  • In a preferred embodiment, an aqueous solution of therapeutic polypeptide, antibody or fragment thereof is administered by subcutaneous injection. Each dose may range from about 0.5 μg to about 50 μg per kilogram of body weight, or more preferably, from about 3 μg to about 30 μg per kilogram body weight. [0169]
  • The dosing schedule for subcutaneous administration may vary from once a week to daily depending on a number of clinical factors, including the type of disease, severity of disease, and the subject's sensitivity to the therapeutic agent. [0170]
  • Patched-2 polypeptide may comprise an amino acid sequence or subsequence thereof as indicated in FIG. 1 (SEQ ID NO:2), active amino acid sequence derived therefrom, or functionally equivalent sequence as this subsequence is believed to comprise the functional portion of the patched-2 polypeptide. [0171]
  • If the subject manifests undesired side effects such as temperature elevation, cold or flu-like symptoms, fatigue, etc., it may be desirable to administer a lower dose at more frequent intervals. One or more additional drugs may be administered in combination with patched-2 to alleviate such undesired side effects, for example, an anti-pyretic, anti-inflammatory or analgesic agent. [0172]
  • The following examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. [0173]
  • All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety. [0174]
    • EXAMPLES
  • Commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated. The source of those cells identified in the following examples, and throughout the specification, by ATCC accession numbers is the American Type Culture Collection, Rockville, Md. [0175]
    • Example 1
  • Introduction: [0176]
  • At the cell surface, Hh function appears to be mediated by a multicomponent receptor complex involving Ptch (SEQ ID NO:4) and Smo (SEQ ID NO:17), two multi-transmembrane proteins initially identified as segment polarity genes in Drosophila and later characterized in vertebrates. Nakano, Y. et al., [0177] Nature 341: 508-513 (1989); Goodrich et al., Gene Dev. 10: 301-312 (1996); Marigo et al., Develop. 122: 1225-1233 (1996); van den Heuvel et al., Nature 382: 547-551 (1996); Alcedo et al., Cell 86: 221-232 (1996); Stone et al. Nature 384: 129-34 (1996). Both genetic and biochemical evidence support the existence of a receptor complex where Ptch (SEQ ID NO:4) is the ligand binding subunit, and where Smo (SEQ ID NO:17), a G-protein coupled receptor like molecule, is the signaling component. Stone et al., Nature 384: 129-134 (1996), Marigo et al., Nature 384: 176-79 (1996), Chen et al., Cell 87: 553-63 (1996). Upon binding of Hh to Ptch (SEQ ID NO:4), the normal inhibitory effect of Ptch (SEQ ID NO:4) on Smo (SEQ ID NO:17) is relieved, allowing Smo (SEQ ID NO:17) to transduce the Hh signal across the plasma membrane.
  • Results: [0178]
  • It remains to be established if the patched-Smoothened receptor complex mediates the action of all 3 mammalian Hhs or if specific components exist. Recently, a second murine patched gene, Ptch-2 (SEQ ID NO:7) was recently isolated [Motoyama et al., [0179] Nature Genet. 18: 104-106 (1998)] but its function as a Hh receptor has not been established. In order to characterize Ptch-2 (SEQ ID NO:2) and compare it to Ptch (SEQ ID NO:4) with respect to the biological function of the various Hh family members, we have screened EST databases with the Ptch (SEQ ID NO:4) protein and identified 2 EST candidates for a novel human patched gene. A full length cDNA encoding human Ptch-2 (SEQ ID NO:2) was cloned from a testis library. The initiation ATG defines a 3612 nucleotide open reading frame encoding a 1204 amino acid long protein with a predicted molecular weight of approximately 131 kDa. The overall identity between human Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) is 54% (FIG. 1), while the identity between human Ptch-2 (SEQ ID NO:2) and the recently described mouse Ptch-2 (SEQ ID NO:7) is 90%. (FIG. 8). The most obvious structural difference between the two human Ptch proteins is a truncated C-terminal cytoplasmic domain in Ptch-2 (SEQ ID NO:2). In addition, only one of the two glycosylation sites present in Ptch (SEQ ID NO:4) is conserved in Ptch-2 (SEQ ID NO:2).
  • To determine if Ptch-2 (SEQ ID NO:2) is a Hh receptor and if the two patched molecules are capable of discriminating between the various Hh ligands through specific binding, Applicants transfected human 293 embryonic kidney cells with Ptch (SEQ ID NO:4) or Ptch-2 (SEQ ID NO:2) expression constructs and analyzed the cells for binding of Shh, Dhh and Ihh (SEQ ID NOS:14, 13, and 29, respectively). As shown on FIG. 7A, binding of [0180] 125I-Shh can be competed with an excess of Shh, Dhh or Ihh (SEQ ID NOS: 14, 13, and 29, respectively). Scatchard analysis of the displacement curves indicates that all Hhs have similar affinity for Ptch (SEQ ID NO:4) (Shh (SEQ ID NO:14), 1.0 nM; Dhh (SEQ ID NO:13), 2.6 nM; Ihh (SEQ ID NO:29), 1.0 nM) and Ptch-2 (SEQ ID NO:2) (Shh (SEQ ID NO:14), 1.8 nM; Dhh (SEQ ID NO:13), 0.6 nM; Ihh (SEQ ID NO:29), 0.4 nM) indicating that both Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) can serve as physiological receptors for the 3 mammalian Hh proteins.
  • Applicants next determined whether, like Ptch (SEQ ID NO:4), Ptch-2 (SEQ ID NO:2) forms a physical complex with Smo (SEQ ID NO:17). Expression constructs for Flag-tagged Ptch (SEQ ID NO:4) or Ptch-2 (SEQ ID NO:2) were transiently co-transfected in 293 cells with Myc-tagged Smo (SEQ ID NO:17). As described previously [Stone et al., [0181] Nature 384: 129-34 (1996)], in cells expressing Ptch (SEQ ID NO:4) and Smo (SEQ ID NO:17), Ptch (SEQ ID NO:4)can be immunoprecipitated with antibodies against the epitope-tagged Smo (SEQ ID NO:15) (FIG. 7B). Similarly, Ptch-2 (SEQ ID NO:2) can be immunoprecipitated with antibodies against the epitope-tagged Smo (SEQ ID NO:15) when the two proteins are co-expressed in 293 cells. Together, these results suggest a model where Ptch-2 (SEQ ID NO:2) forms a multicomponent Hh receptor complex with Smo (SEQ ID NO:17) similar to the one described for patched (Stone et al., supra). Interestingly, these results also demonstrate that the long C-terminal tail which is missing in Ptch-2 (SEQ ID NO:2) is not required for the interaction with Smo (SEQ ID NO:17) as was already suggested by the analysis of truncated patched (Stone et al., supra). However, it remains possible that the absence of a C-terminal domain affects the capacity of Ptch-2 (SEQ ID NO:2) to block signaling by Smo or leads to difference in signaling by patched compared to patched-2.
  • To further investigate whether patched-2 could mediate the action of a specific Hh molecule based on its expression profile, Applicants have compared the expression pattern of Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2). First, Northern blot analysis using a probe specific for Ptch-2 (SEQ ID NO:1) revealed high levels of patched-2 mRNA in the testis (FIG. 4). By this method, Ptch-2 (SEQ ID NO:1) expression was not detected in any other tissue analyzed including embryonic tissues (data not shown). This profile is very different from the one observed for Ptch (SEQ ID NO:18) which was not found in testis by Northern blot but in a large number of adult and embryonic tissues [Goodrich et al., [0182] Genes Dev. 10: 301-312 (1996)]. More detailed analysis of the expression pattern of Ptch (SEQ ID NO:18) and Ptch-2 (SEQ ID NO:1) was performed by in situ hybridization with particular attention to testis. As previously described (Motoyama et al., supra), low levels of Ptch-2 (SEQ ID NO:1) expression were detected in epithelial cells of the developing tooth and skin (data not shown). High levels of Ptch-2 (SEQ ID NO:2) are expressed inside the seminiferous tubule, on the primary and secondary spermatocytes (FIGS. 6B,6E) while only low levels of Ptch (SEQ ID NO:4) can be detected on the Leydig cells located in the interstitium of the seminiferous tubules (FIG. 6A). The primary and secondary spermatocytes are in close contact with the supporting Sertoli cells, the source of Dhh (SEQ ID NO:13) in the testis [Bitgood et al., Curr. Biol 6: 298-304 (1996)]. To determine which one of the 2 receptors is the most relevant mediator of Dhh (SEQ ID NO:13) activity in the testis, we have analyzed the expression profile of FuRK (SEQ ID NO:10), a Fused Related Kinase that was shown to be a component of the Hh signaling pathway (Zhang et al., submitted; copending U.S. Ser. No. 09/031,563, filed Feb. 26, 1998). Consistent with the idea that Ptch-2 (SEQ ID NO:2) is the target of Dhh in the testis, we found that FuRK (SEQ ID NO:10) is expressed only in germ cells where it colocalizes with Ptch-2 (SEQ ID NO:2) (FIGS. 4c,f). Dhh (SEQ ID NO:13) is required for proper differentiation of germ cells since male Dhh-deficient mice are sterile due to lack of mature sperm (Bitgood et al., supra). Our data suggest that Dhh (SEQ ID NO:13) acts directly on germ cells through Ptch-2 (SEQ ID NO:2) while the function of Ptch (SEQ ID NO:4) expressed at low levels on testosterone producing Leydig cells is unclear.
  • Discussion: [0183]
  • Loss of heterozygosity (LOH) for patched was reported to occur with high frequency in familial as well as sporadic basal cell carcinoma [Johnson et al., [0184] Science 272: 1668-71 (1996); Hahn et al., Cell 85: 841-51 (1996); Gailani et al., Nature Genetics 14: 78-81; Xie et al., Cancer Res. 57: 2369-72 (1997)], suggesting that it functions as a tumor suppressor. According to the receptor model described above, loss of patched function may result in aberrant signaling by Smo(SEQ ID NO:17), leading to hyperproliferation of the skin basal cell layer. If, as suggested above, patched-2 mediates the function of Dhh, loss of Ptch-2 (SEQ ID NO:2) may lead to tumor formation in tissues where Smo (SEQ ID NO:17) activity is controlled by patched-2. The gene encoding patched-2 was mapped by fluorescence in situ hybridization and by PCR using a radiation hybrid panel to human chromosome 1p33-34 (data not shown). Interestingly, recent analysis of recurrent chromosomal abnormalities in testicular tumors, including seminomas, revealed a deletion of the region 1p32-36 [Summersgill et al., B. J. Cancer 77: 305-313 (1998)]. Loss of this region encompassing the patched-2 locus was consistent in 36% of the germ cell tumor cases. These data raise the possibility that, like patched in basal cell carcinoma and medulloblastoma, patched-2 may be a tumor suppressor in Dhh (SEQ ID NO:13) target cells such as spermatocytes, further implicating Hh signaling in cancer.
  • In summary, our data demonstrate that both patched and patched-2 are genuine Hh receptors and that they are both capable of forming a complex with Smo (SEQ ID NO:17). Although binding data indicate that patched and patched-2 do not discriminate between the various Hh ligands through affinity differences, the distinct tissue distribution of these 2 receptors suggests that in vivo, patched may be the primary receptor for Shh whereas Ptch-2 will mediate mainly Dhh signaling. The function of patched expression in Leydig cells in the absence of some of the Hh signaling components remain to be explained. Similarly, it will be of interest to determine if patched-2 plays a role when expressed in Shh expressing cells present in the developing tooth and skin Motoyama et al., [0185] Nature Genet. 18: 104-106 (1998). Finally, the existence of patched-2 raises the question of whether additional patched receptors exist, in particular one that mediates the function of Ihh (SEQ ID NO:29).
    • Material and Methods
  • 1. Isolation of human patched-2 cDNA clones [0186]
  • An expressed sequence tag (EST) DNA database (LIFESEQ®, Incyte Pharmaceuticals, Palo Alto, Calif.) was searched for a human homologue of the Drosophila segment polarity gene patched-2. Two ESTs ([0187] Incyte #905531 and 1326258) (FIG. 2) (SEQ ID NOS: 3 and 5, respectively) were identified as a potential candidates. In order to identify human cDNA libraries containing human patched-2 clones, human cDNA libraries in pRK5 were first screened by PCR using the following primers:
    5′-905531(A):
    5′-AGGCGGGGGATCACAGCA-3′ (SEQ ID NO:19)
    3′-905531(A):
    5′-ATACCAAAGAGTTCCACT-3′ (SEQ ID NO:20)
  • A fetal lung library was selected and enriched for patched-2 cDNA clones by extension of single stranded DNA from plasmid libraries grown in dut[0188] −/ung− host using the 3′-905531(A) primer in a reaction containing 10 μl of 10× PCR Buffer (Klentaq®), 1 μl dNTP (200 μM), 1 μl library DNA (200 ng), 0.5 μl primer, 86.5 μl H2O and 1 μl of Klentaq® (Clontech) added after a hot start. The reaction was denatured for 1 min. at 95° C., annealed for 1 min. at 60° C. then extended for 20 min. at 72° C. DNA was extracted with phenol/CHCl3, ethanol precipitated, then transformed by electroporation into DH10B (Gibco/BRL) host bacteria. Colonies from each transformation were replica plated on nylon membranes and screened with an overlapping oligo probe derived from the EST sequence (#905531) of the following sequence:
    5′-Ptch2 probe: 5′-CTGCGGCGCTGCTTCCTGCTGGCCGTCTGCATCCTGCTGGTGTGC-3′ (SEQ ID NO:21)
    3′-Ptch2 probe: 5′-AGAGCACAGACGAGGAAAGTGCACACCAGCAGGATGCAGACGGCC-3′ (SEQ ID NO:22)
  • The oligo probe was labeled with [γ-[0189] 32P]-ATP and T4 polynucleotide kinase. Filters were hybridized overnight at 42° C. in 50% formamide, 5×SSC, 10×Denhardt's, 0.05M sodium phosphate (pH 6.5), 0.1% sodium pyrophosphate, 50 μg/ml of sonicated salmon sperm DNA. The filters were then rinsed in 2×SSC and washed in 0.1×SSC, 0.1% SDS then exposed to Kodak® X Ray films.
  • Using this procedure, a partial clone was isolated from the fetal brain library (clone 3A—FIG. 10) (SEQ ID NO:8). In order to isolate the missing 5′-sequence, a testis library (see northern blot analysis, infra) was screened. The primer set used to amplify a 204 bp probe from clone 3A to probe the testis library was: [0190]
    RACE 5: 5′-ACTCCTGACTTGTAGCAGATT-3′ (SEQ ID NO:
    23) and
    RACE 6: 5′-AGGCTGCATACACCTCTCAGA-3′. (SEQ ID NO:
    24)
  • The amplified probe was purified by excision from an agarose gel and labeled with a random primer labeling kit (Boehringer Mannheim). Several clones were isolated, including one (clone 16.1—FIG. 11 (SEQ ID NO:9)) containing a potential initiation methionine. A full length cDNA encoding patched-2 was reconstructed by assembling several of these clones. The full length cDNA encoding human Ptch-2 (FIG. 1) (SEQ ID NO:1) has a 3612 nucleotide long open reading frame encoding a 1204 amino acid protein with a 144 kDa predicted molecular weight. Alignment with human Ptch (SEQ ID NO:4) reveals a 53% identity between the 2 molecules at the amino acid level (FIG. 3). All 12 transmembrane domains are conserved. The most significant difference is a shorter C-terminal intracellular domain in Ptch-2 (SEQ ID NO:2) compared to Ptch (SEQ ID NO:4). [0191]
  • 2. Northern blot analysis: [0192]
  • In order to determine the best tissue source for isolation of the complete full length Ptch-2 cDNA as well as to determine its expression profile, we probed human multiple tissue northern blots (Clontech) with a 752 bp fragment amplified from the 3′ untranslated region of Ptch-2 (SEQ ID NO:2) using the following primers: [0193]
    TM2: TM2 5-GCTTAGGCCCGAGGAGAT-3′ (SEQ ID NO:25)
    UTR2: 5′-AACTCACAACTTTCTCTCCA-3′. (SEQ ID NO:26)
  • The resulting fragment was gel purified and labeled by random priming. The blots were hybridized in ExpressHyb® hybridization solution (Clontech) in the presence of 1×10[0194] 6 cpm/ml 32P-labeled probe at 42° C. overnight. The blots were washed in 2×SSC at room temperature for 10 minutes and washed in 0.1×SSC/0.1% SDS at 42° C. for 30 minutes then exposed to x-ray film overnight. FIG. 4 shows that Ptch-2 message is expressed at high levels in only the testis.
  • 3. Chromosomal localization: [0195]
  • The primers TM2 (SEQ ID NO:25) and UTR2 (SEQ ID NO:26) described above were used to screen the Genome Systems (St. Louis, Mo.) BAC library. Two individual BAC clones were obtained from this library and chromosomal localization of both of the clones by FISH indicated that Ptch-2 (SEQ ID NO:2) maps to human chromosome 1p33-34 (FIG. 5). Loss of heterozyosity (LOH) for patched was reported to occur with high frequency in basal cell carcinoma . Loss of patched function is thought to lead to constitutive signaling by Smoothened (Smo (SEQ ID NO:17)), resulting in hyperproliferation of the basal layer of the dermis. A similar mechanism may lead to the formation of germ cell tumors. This model proposes that the first step in the progression of a germ cell tumor is an initial loss of DNA by a germ cell precursor, leading to a neoplastic germ cell which then forms a seminoma [De Jong et al., [0196] Cancer Genet. Cytogenet. 48: 143-167 (1990)]. From the invasive seminoma, all other forms of germ cell tumor types develop. Approximately 80% of all germ cell tumors correlate with an isochromosome 12p (i12p) and is found at a higher frequency in non-seminomas than seminomas [Rodriguez et al., Cancer Res 52: 2285-2291(1992)]. However, analysis of recurrent chromosomal abnormalities in testicular tumors including seminomas revealed a deletion of the region 1p32-36. Loss of this region was consistent in 36% of the germ cell tumor cases of in a recent study Summersgill et al., B. J. Cancer 57: 305-313 (1998)]. A similar deletion of chromosome 1p32-36 has been reported at a frequency of 28% in oligodendrogliomas Bello, et al., Int. J. Cancer 57: 172-175 (1994). While expression of patched-2 (SEQ ID NO:2) in the brain was not examined here in detail, patched-2 (SEQ ID NO:2) is thought to be the Dhh receptor (see below) and expression of Dhh by murine Schwann cells was previously reported [Bitgood et al, Develop. Biol. 172: 126-138 (1995)]. Since patched-2 (SEQ ID NO:2) localizes to chromosome 1p33-34 it is possible that patched-2 regulates Smo (SEQ ID NO:17) signaling in Dhh target cells and that loss of patched-2 function leads to abnormal Smo (SEQ ID NO:17) signaling in these cells and subsequent tumor formation.
  • 4. In situ hybridization: [0197]
  • Mouse testis sections were cut at 16 μm, and processed for in situ hybridization by the method described in Phillips et al., [0198] Science 250: 290-294 (1990). 33P-UTP labeled RNA probes were generated as described in Melton et al., Nucleic Acids Res. 12: 7035-7052 (1984). Sense and antisense probes were synthesized from the 3′ non coding region of the mouse Ptch or Ptch-2 and from a mouse FuRK cDNA fragment corresponding to the region encoding amino acid 317-486 of the human sequence using T3 and T7, respectively.
  • Ptch: [0199]
    Ptch:
    503 (Anti-sense)
    5′GGATTCTAATACGACTCACTATAGGGCCCAATGGCCTAAACCGACTGC3′ (SEQ ID NO:27)
    503 (Sense)
    5′CTATGAAATTAACCCTCACTAAAGGGACCCACGGCCTCTCCTCACA3′ (SEQ ID NO:28)
    Ptch2:
    504 (Anti-sense)
    5′GGATTCTAATACGACTCACTATAGGGCCCCTAAACTCCGCTGCTCCAC3′ (SEQ ID NO:12)
    504 (Sense)
    5′CTATGAAATTAACCCTCACTAAAGGGAGCTCCCGTGAGTCCCTATGTG3′ (SEQ ID NO:11)
  • FuRK sense and antisense were synthesized from a mouse fused DNA fragment using T3 and T7, respectively, corresponding to the region encoding amino acid residues 317-486 of the human sequence (Zhang et al., submitted, 1998; copending U.S. Ser. No. 09/031,563, filed Feb. 26, 1998). [0200]
  • FIG. 6 illustrates that, although both Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) are expressed in testis, their expression pattern does not overlap. Ptch (SEQ ID NO:4) is expressed in the Leydig cells of the interstitium while Ptch-2 (SEQ ID NO:2) is expressed in the primary and secondary spermatocytes. [0201]
  • The expression of Ptch-2 (SEQ ID NO:2) specifically in the developing spermatogonia suggest that Ptch-2 (SEQ ID NO:2) is the immediate target of Dhh (SEQ ID NO:13). Dhh (SEQ ID NO:13) is expressed by Sertoli cells and mice deficient in Dhh (SEQ ID NO:13) are sterile because of a defect in sperm production [Bitgood et al., [0202] Curr. Biol. 6: 298-304 (1996)]. Although this effect on germ cells was though to be indirect and mediated by Ptch present on Leydig cells, our data suggest that Dhh directly acts on germ cells through Ptch-2. This is further demonstrated by the localization of FuRK (SEQ ID NO:10), an intracellular kinase homologous to Drosophila Fused and involved in transducing the Hedgehog (Hh) signal. As shown in FIG. 6, FuRK (SEQ ID NO:10) is colocalizes with Ptch-2 (SEQ ID NO:2) in germ cells and not with Ptch (SEQ ID NO:4) in Leydig cells, suggesting that Ptch-2 and not Ptch will be able to transduce the Dhh signal. These results suggest that Ptch-2 is a Dhh receptor.
  • Ptch-2 mRNA levels in Smo-M2 (SEQ ID NO:16) transgenic mice [A Smo mutation which results in autonomous phenotypes similar to BCC, Xie et al., [0203] Nature 391: 90-92 (1998)] can be increased upon abnormal activation of the Hh signaling pathway. As indicated in FIG. 9, patch-2 levers were high in tumor cells (although lower than Ptch levels). This suggests that antibodies directed toward Ptch-2 may be useful in the treatments of BCC.
  • 5. Immunoprecipitation with Smo: [0204]
  • The binding of Ptch-2 to Smo (SEQ ID NO:17) was assessed by cotransfection using a transient transfection system of a myc-epitope tagged Smo (SEQ ID NO:15) and a FLAG-epitope tagged Ptch or Ptch2 expression construct in 293 cells using standard techniques (Gorman, C., [0205] DNA Cloning: A Practical Approach, Clover, D M ed., Vol. 11, pp. 143-190, IRL Press, Washington, D.C.). 36 hours after transfection, the cells were lysed in 1% NP-40 and immunoprecipitated overnight with the 9E 10 anti-myc antibody or with the M2 anti-FLAG antibody (IBI-Kodak) followed by protein A Sepharose, and then separated on a denatured 6% polyacrylamide gel. Proteins were detected by transfer to nitrocellulose and probing with antibodies to Flag or Myc epitopes, using the ECL detection system (Amersham). FIG. 7B indicates that both Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2) are expressed at the same level (IP Flag, Blot Flag) and that like Ptch (SEQ ID NO:4), Ptch-2 (SEQ ID NO:2) forms a physical complex with Smo (SEQ ID NO:17). These results suggest that like patched, patched-2 controls Hh signaling through its interaction with Smo (SEQ ID NO:17).
  • 6. Hh Binding: [0206]
  • To determine whether Ptch-2 is able to bind to the various hedgehog ligands, 293 cells were transfected with Ptch (SEQ ID NO:4) or Ptch-2 (SEQ ID NO:2) using standard procedures. Cells were incubated with 100 pM [0207] 125I-Shh (19 kD amino terminal fragment of murine Shh (SEQ ID NO:14)) in the presence or absence of excess unlabeled Shh (SEQ ID NO:14) or Dhh (SEQ ID NO:13) for 2 h at room temperature. After equilibrium was reached, the ligand bound cells were centrifuged through a continuous sucrose gradient to separate unincorporated and then counted in a scintillation counter. FIG. 7A shows that both Dhh (SEQ ID NO:13) and Shh (SEQ ID NO:14) bind to Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2). Varying concentrations of cold competitor indicate that the 2 ligands have similar affinity for Ptch (SEQ ID NO:4) and Ptch-2 (SEQ ID NO:2).
    • Example 2 Expression of patched-2 in E. coli
  • The DNA sequence encoding human patched-2 is initially amplified using selected PCR primers. The primers should contain restriction enzyme sites that correspond to the restriction enzyme sites on the selected expression vector. A variety of expression vectors may be employed. An example of a suitable vector is pBR322 (derived from [0208] E. coli; see Bolivar et al., Gene, 2:95 (1977)) which contains genes for ampicillin and tetracycline resistance. The vector is digested with restriction enzyme and dephosphorylated. The PCR amplified sequences are then ligated into the vector. The vector will preferably include sequences that encode for an antibiotic resistance gene, a trp promoter, a polyhis leader (including the first six STII codons, polyhis sequence, and enterokinase cleavage site), the vertebrate patched-2 coding region, lambda transcriptional terminator, and an argU gene.
  • The ligation mixture is then used to transform a selected [0209] E. coli strain using the methods described in Sambrook et al., supra. Transformants are identified by their ability to grow on LB plates and antibiotic resistant colonies are then selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing.
  • Selected clones can be grown overnight in liquid culture medium such as LB broth supplemented with antibiotics. The overnight culture may subsequently be used to inoculate a larger scale culture. The cells are then grown to a desired optical density, during which the expression promoter is turned on. [0210]
  • After culturing the cells for several more hours, the cells can be harvested by centrifugation. The cell pellet obtained by the centrifugation can be solubilized using various agents known in the art, and the solubilized vertebrate patched-2 protein can then be purified using a metal chelating column under conditions that allow tight binding of the protein. [0211]
    • Example 3 Expression of patched-2 in Mammalian Cells
  • The vector, pRK5 (see EP 307,247, published Mar. 15, 1989), is employed as the expression vector. Optionally, the vertebrate patched-2 DNA is ligated into pRK5 with selected restriction enzymes to allow insertion of the vertebrate patched-2 DNA using ligation methods such as described in Sambrook et al., supra. The resulting vector is called pRK5-patched-2. [0212]
  • In one embodiment, the selected host cells may be 293 cells. Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue culture plates in medium such as DMEM supplemented with fetal calf serum and optionally, nutrient components and/or antibiotics. About 10 μg pRK5-patched-2 DNA is mixed with about 1 μg DNA encoding the VA RNA gene [Thimmappaya et al., [0213] Cell, 31:543 (1982)] and dissolved in 500 μl of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCl2. To this mixture is added, dropwise, 500 μl of 50 mM HEPES (pH 7.35), 280 mM NaCl, 1.5 mM NaPO4, and a precipitate is allowed to form for 10 minutes at 25° C. The precipitate is suspended and added to the 293 cells and allowed to settle for about four hours at 37° C. The culture medium is aspirated off and 2 ml of 20% glycerol in PBS is added for 30 seconds. The 293 cells are then washed with serum free medium, fresh medium is added and the cells are incubated for about 5 days.
  • Approximately 24 hours after the transfections, the culture medium is removed and replaced with culture medium (alone) or culture medium containing 200 μCi/ml [0214] 35S-cysteine and 200 μCi/ml 35S-methionine. After a 12 hour incubation, the conditioned medium is collected, concentrated on a spin filter, and loaded onto a 15% SDS gel. The processed gel may be dried and exposed to film for a selected period of time to reveal the presence of vertebrate patched-2 polypeptide. The cultures containing transfected cells may undergo further incubation (in serum free medium) and the medium is tested in selected bioassays.
  • In an alternative technique, vertebrate patched-2 may be introduced into 293 cells transiently using the dextran sulfate method described by Somparyrac et al., [0215] Proc. Natl. Acad. Sci, 12:7575 (1981). 293 cells are grown to maximal density in a spinner flask and 700 μg pRK5-patched-2 DNA is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA-dextran precipitate is incubated on the cell pellet for four hours. The cells are treated with 20% glycerol for 90 seconds, washed with tissue culture medium, and re-introduced into the spinner flask containing tissue culture medium, 5 μg/ml bovine insulin and 0.1 μg/ml bovine transferrin. After about four days, the conditioned media is centrifuged and filtered to remove cells and debris. The sample containing expressed vertebrate patched-2 can then be concentrated and purified by any selected method, such as dialysis and/or column chromatography.
  • In another embodiment, vertebrate patched-2 can be expressed in CHO cells. The pSVi-patched-2 can be transfected into CHO cells using known reagents such as CaPO[0216] 4 or DEAE-dextran. As described above, the cell cultures can be incubated, and the medium replaced with culture medium (alone) or medium containing a radiolabel such as 35S-methionine. After determining the presence of vertebrate patched-2 polypeptide, the culture medium may be replaced with serum free medium. Preferably, the cultures are incubated for about 6 days, and then the conditioned medium is harvested. The medium containing the expressed vertebrate patched-2 can then be concentrated and purified by any selected method.
  • Epitope-tagged vertebrate patched-2 may also be expressed in host CHO cells. The vertebrate patched-2 may be subcloned out of the pRK5 vector. The subclone insert can undergo PCR to fuse in frame with a selected epitope tag such as a poly-his tag into an expression vector. The poly-his tagged vertebrate patched-2 insert can then be subcloned into a SV40 driven vector containing a selection marker such as DHFR for selection of stable clones. Finally, the CHO cells can be transfected (as described above) with the SV40 driven vector. Labeling may be performed, as described above, to verify expression. The culture medium containing the expressed poly-His tagged vertebrate patched-2 can then be concentrated and purified by any selected method, such as by Ni[0217] 2+-chelate affinity chromatography.
    • Example 4 Expression of Vertebrate patched-2 in Yeast
  • The following method describes recombinant expression of vertebrate patched-2 in yeast. [0218]
  • First, yeast expression vectors are constructed for intracellular production or secretion of vertebrate patched-2 from the ADH2/GAPDH promoter. DNA encoding vertebrate patched-2, a selected signal peptide and the promoter is inserted into suitable restriction enzyme sites in the selected plasmid to direct intracellular expression of vertebrate patched-2. For secretion, DNA encoding vertebrate patched-2 can be cloned into the selected plasmid, together with DNA encoding the ADH2/GAPDH promoter, the yeast alpha-factor secretory signal/leader sequence, and linker sequences (if needed) for expression of vertebrate patched-2. [0219]
  • Yeast cells, such as yeast strain AB110, can then be transformed with the expression plasmids described above and cultured in selected fermentation media. The transformed yeast supernatants can be analyzed by precipitation with 10% trichloroacetic acid and separation by SDS-PAGE, followed by staining of the gels with Coomassie Blue stain. [0220]
  • Recombinant vertebrate patched-2 can subsequently be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using selected cartridge filters. The concentrate containing vertebrate patched-2 may further be purified using selected column chromatography resins. [0221]
    • Example 5 Expression of Vertebrate patched-2 in Baculovirus-Infected Insect Cells
  • The following method describes recombinant expression of vertebrate patched-2 in Baculovirus-infected insect cells. [0222]
  • The vertebrate patched-2 is patched-2 upstream of an epitope tag contained within a baculovirus expression vector. Such epitope tags include poly-his tags and immunoglobulin tags (like Fc regions of IgG). A variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen). Briefly, the vertebrate patched-2 or the desired portion of the vertebrate patched-2 (such as the sequence encoding the extracellular domain of a transmembrane protein) is amplified by PCR with primers complementary to the 5′ and 3′ regions. The 5′ primer may incorporate flanking (selected) restriction enzyme sites. The product is then digested with those selected restriction enzymes and subcloned into the expression vector. [0223]
  • Recombinant baculovirus is generated by co-transfecting the above plasmid and BaculoGold™ virus DNA (Pharmingen) into [0224] Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL). After 4-5 days of incubation at 28° C., the released viruses are harvested and used for further amplifications. Viral infection and protein expression is performed as described by O'Reilley et al., Baculovirus expression vectors: A laboratory Manual, Oxford: Oxford University Press (1994).
  • Expressed poly-his tagged vertebrate patched-2 can then be purified, for example, by Ni[0225] 2+-chelate affinity chromatography as follows. Extracts are prepared from recombinant virus-infected Sf9 cells as described by Rupert et al., Nature, 362:175-179 (1993). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 mL Hepes, pH 7.9; 12.5 mM MgCl2; 0.1 mM EDTA; 10% Glycerol; 0.1% NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice. The sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl, 10% Glycerol, pH 7.8) and filtered through a 0.45 μm filter. A Ni2+-NTA agarose column (commercially available from Qiagen) is prepared with a bed volume of 5 mL, washed with 25 mL of water and equilibrated with 25 mL of loading buffer. The filtered cell extract is loaded onto the column at 0.5 mL per minute. The column is washed to baseline A280 with loading buffer, at which point fraction collection is started. Next, the column is washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% Glycerol, pH 6.0), which elutes nonspecifically bound protein. After reaching A280 baseline again, the column is developed with a 0 to 500 mM Imidazole gradient in the secondary wash buffer. One mL fractions are collected and analyzed by SDS-PAGE and silver staining or western blot with Ni2+-NTA-conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted His10-tagged vertebrate patched-2 are pooled and dialyzed against loading buffer.
  • Alternatively, purification of the IgG tagged (or Fc tagged) vertebrate patched-2 can be performed using known chromatography techniques, including for instance, Protein A or protein G column chromatography. [0226]
    • Example 6 Preparation of Antibodies that Bind Vertebrate patched-2
  • This example illustrates preparation of monoclonal antibodies, which can specifically bind vertebrate patched-2. [0227]
  • Techniques for producing the monoclonal antibodies are known in the art and are described, for instance, in Goding, supra. Immunogens that may be employed include purified vertebrate patched-2, fusion proteins containing vertebrate patched-2, and cells expressing recombinant vertebrate patched-2 on the cell surface. Selection of the immunogen can be made by the skilled artisan without undue experimentation. [0228]
  • Mice, such as Balb/c, are immunized with the vertebrate patched-2 immunogen (E.g., extracellular portions or cells expressed Ptch-2) emulsified in complete Freund's adjuvant and injected subcutaneously or intraperitoneally in an amount from 1-100 micrograms. Alternatively, the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, Mont.) and injected into the animal's hind foot pads. The immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice may also be boosted with additional immunization injections. Serum samples may be periodically obtained from the mice by retro-orbital bleeding for testing in ELISA assays to detect vertebrate patched-2 antibodies. [0229]
  • After a suitable antibody titer has been detected, the animals “positive” for antibodies can be injected with a final intravenous injection of vertebrate patched-2. Three to four days later, the mice are sacrificed and the spleen cells are harvested. The spleen cells are then patched-2 (using 35% polyethylene glycol) to a selected murine myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL 1597. The fusions generate hybridoma cells which can then be plated in 96 well tissue culture plates containing HAT (hypoxanthine, aminopterin, and thymidine) medium to inhibit proliferation of non-patched-2 cells, myeloma hybrids, and spleen cell hybrids. [0230]
  • The hybridoma cells will be screened in an ELISA for reactivity against vertebrate patched-2. Determination of “positive” hybridoma cells secreting the desired monoclonal antibodies against vertebrate patched-2 is within the skill in the art. [0231]
  • The positive hybridoma cells can be injected intraperitoneally into syngeneic Balb/c mice to produce ascites containing the anti-vertebrate patched-2 monoclonal antibodies. Alternatively, the hybridoma cells can be grown in tissue culture flasks or roller bottles. Purification of the monoclonal antibodies produced in the ascites can be accomplished using ammonium sulfate precipitation, followed by gel exclusion chromatography. Alternatively, affinity chromatography based upon binding of antibody to protein A or protein G can be employed. [0232]
    • Example 7 Gli Luciferase Assay
  • The following assay may be used to measure the activation of the transcription factor GLI, the mammalian homologue of the [0233] Drosophila cubitus interruptus (Ci). It has been shown that GLI is a transcription factor activated upon SHh stimulation of cells.
  • Nine (9) copies of a GLI binding site present in the HNF3β enhancer, (Sasaki et al., [0234] Development 124: 1313-1322 (1997)), are introduced in front of a thymidine kinase minimal promoter driving the luciferase reporter gene in the pGL3 plasmid (Promega). The sequence of the GLI binding sequence is: TCGACAAGCAGGGAACACCCAAGTAGAAGCTC (p9XGliLuc) (SEQ ID NO:31), while the negative control sequence is: TCGACAAGCAGGGAAGTGGGAAGTAGAAGCTC (p9XmGliLuc) (SEQ ID NO:32). These constructs are cotransfected with the full length Ptch-2 and Smo in C3H10T1/2 cells grown in F12, DMEM (50:50), 10% FCS heat inactivated. The day before transfection 1×105 cells per well was inoculated in 6 well plates, in 2 ml of media. The following day, 1 μg of each construct is cotransfected in duplicate with 0.025 mg ptkRenilla luciferase plasmid using lipofectamine (Gibco-BRL) in 100 μl OptiMem (with GlutaMAX) as per manufacturer's instructions for 3 hours at 37° C. Serum (20%, 1 ml) is then added to each well and the cells were incubated for 3 more hours at 37° C. Cells are then washed twice with PBS, then incubated for 48 hours at 37° C. in 2 ml of media. Each well is then washed with PBS, and the cells lysed in 0.5 ml Passive Lysis Buffer (Promega) for 15 min. at room temperature on a shaker. The lysate is transferred in eppendorf tubes on ice, spun in a refrigerated centrifuge for 30 seconds and the supernatant saved on ice. For each measure, 20 μl of cell lysate is added to 100 μl of LARII (luciferase assay reagent, Promega) in a polypropylene tube and the luciferase light activity measured. The reaction is stopped by the addition of Stop and Glow buffer (Promega), mixed by pipetting up and down 3 to 5 times and Renilla luciferase lights activity is measured on the luminometer.
    • Deposit of Material
  • The following materials have been deposited with the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Md., USA (ATCC): [0235]
    Designation: ATCC Dep. No. Deposit Date
    pRK7.hptc2.Flag-1405 209778 4/14/98
  • This deposit was made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purpose of Patent Procedure and the Regulations thereunder (Budapest Treaty). This assures maintenance of a viable culture of the deposit for 30 years from the date of deposit. The deposit will be made available by ATCC under the terms of the Budapest Treaty, and subject to an agreement between Genentech, Inc. and ATCC, which assures permanent and unrestricted availability of the progeny of the culture of the deposit to the public upon issuance of the pertinent U.S. patent or upon laying open to the public of any U.S. or foreign patent application, whichever comes first, and assures availability of the progeny to one determined by the U.S. Commissioner of Patents and Trademarks to be entitled thereto according to 35 USC §122 and the Commissioner's rules pursuant thereto (including 37 CFR §1.14 with particular reference to 886 OG 638). [0236]
  • The assignee of the present application has agreed that if a culture of the materials on deposit should die or be lost or destroyed when cultivated under suitable conditions, the materials will be promptly replaced on notification with another of the same. Availability of the deposited material is not to be construed as a license to practice the invention in contravention of the rights granted under the authority of any government in accordance with its patent laws. [0237]
  • The foregoing written specification is considered to be sufficient to enable one skilled in the art to practice the invention. The present invention is not to be limited in scope by the construct deposited, since the deposited embodiment is intended as a single illustration of certain aspects of the invention and any constructs that are functionally equivalent are within the scope of this invention. The deposit of material herein does not constitute an admission that the written description herein contained is inadequate to enable the practice of any aspect of the invention, including the best mode thereof, nor is it to be construed as limiting the scope of the claims to the specific illustrations that it represents. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims. [0238]
  • 1 32 1 4030 DNA Homo sapiens 1 gttatttcag gccatggtgt tgcgccgaat taattcccga tccagacatg 50 ataagataca ttgatgagtt tggacaaacc acaactagaa tgcagtgaaa 100 aaaatgcttt atttgtgaaa tttgtgatgc tattgcttta tttgtaacca 150 ttataagctg caataaacaa gttgggccat ggcggccaag cttctgcagg 200 tcgactctag aggatccccg gggaattccg gcatgactcg atcgccgccc 250 ctcagagagc tgcccccgag ttacacaccc ccagctcgaa ccgcagcacc 300 ccagatccta gctgggagcc tgaaggctcc actctggctt cgtgcttact 350 tccagggcct gctcttctct ctgggatgcg ggatccagag acattgtggc 400 aaagtgctct ttctgggact gttggccttt ggggccctgg cattaggtct 450 ccgcatggcc attattgaga caaacttgga acagctctgg gtagaagtgg 500 gcagccgggt gagccaggag ctgcattaca ccaaggagaa gctgggggag 550 gaggctgcat acacctctca gatgctgata cagaccgcac gccaggaggg 600 agagaacatc ctcacacccg aagcacttgg cctccacctc caggcagccc 650 tcactgccag taaagtccaa gtatcactct atgggaagtc ctgggatttg 700 aacaaaatct gctacaagtc aggagttccc cttattgaaa atggaatgat 750 tgagtggatg attgagaagc tgtttccgtg cgtgatcctc acccccctcg 800 actgcttctg ggagggagcc aaactccaag ggggctccgc ctacctgccc 850 ggccgcccgg atatccagtg gaccaacctg gatccagagc agctgctgga 900 ggagctgggt ccctttgcct cccttgaggg cttccgggag ctgctagaca 950 aggcacaggt gggccaggcc tacgtggggc ggccctgtct gcaccctgat 1000 gacctccact gcccacctag tgcccccaac catcacagca ggcaggctcc 1050 caatgtggct cacgagctga gtgggggctg ccatggcttc tcccacaaat 1100 tcatgcactg gcaggaggaa ttgctgctgg gaggcatggc cagagacccc 1150 caaggagagc tgctgagggc agaggccctg cagagcacct tcttgctgat 1200 gagtccccgc cagctgtacg agcatttccg gggtgactat cagacacatg 1250 acattggctg gagtgaggag caggccagca cagtgctaca agcctggcag 1300 cggcgctttg tgcagctggc ccaggaggcc ctgcctgaga acgcttccca 1350 gcagatccat gccttctcct ccaccaccct ggatgacatc ctgcatgcgt 1400 tctctgaagt cagtgctgcc cgtgtggtgg gaggctatct gctcatgctg 1450 gcctatgcct gtgtgaccat gctgcggtgg gactgcgccc agtcccaggg 1500 ttccgtgggc cttgccgggg tactgctggt ggccctggcg gtggcctcag 1550 gccttgggct ctgtgccctg ctcggcatca ccttcaatgc tgccactacc 1600 caggtgctgc ctttcttggc tctgggaatc ggcgtggatg acgtattcct 1650 gctggcgcat gccttcacag aggctctgcc tggcacccct ctccaggagc 1700 gcatgggcga gtgtctgcag cgcacgggca ccagtgtcgt actcacatcc 1750 atcaacaaca tggccgcctt cctcatggct gccctcgttc ccatccctgc 1800 gctgcgagcc ttctccctac aggcggccat agtggttggc tgcacctttg 1850 tagccgtgat gcttgtcttc ccagccatcc tcagcctgga cctacggcgg 1900 cgccactgcc agcgccttga tgtgctctgc tgcttctcca gtccctgctc 1950 tgctcaggtg attcagatcc tgccccagga gctgggggac gggacagtac 2000 cagtgggcat tgcccacctc actgccacag ttcaagcctt tacccactgt 2050 gaagccagca gccagcatgt ggtcaccatc ctgcctcccc aagcccacct 2100 ggtgccccca ccttctgacc cactgggctc tgagctcttc agccctggag 2150 ggtccacacg ggaccttcta ggccaggagg aggagacaag gcagaaggca 2200 gcctgcaagt ccctgccctg tgcccgctgg aatcttgccc atttcgcccg 2250 ctatcagttt gccccgttgc tgctccagtc acatgccaag gccatcgtgc 2300 tggtgctctt tggtgctctt ctgggcctga gcctctacgg agccaccttg 2350 gtgcaagacg gcctggccct gacggatgtg gtgcctcggg gcaccaagga 2400 gcatgccttc ctgagcgccc agctcaggta cttctccctg tacgaggtgg 2450 ccctggtgac ccagggtggc tttgactacg cccattccca acgcgccctc 2500 tttgatctgc accagcgctt cagttccctc aaggcggtgc tgcccccacc 2550 ggccacccag gcaccccgca cctggctgca ctattaccgc aactggctac 2600 agggaatcca ggctgccttt gaccaggact gggcttctgg gcgcatcacc 2650 cgccactcgt accgcaatgg ctctgaggat ggggccctgg cctacaagct 2700 gctcatccag actggagacg cccaggagcc tctggatttc agccagctga 2750 ccacaaggaa gctggtggac agagagggac tgattccacc cgagctcttc 2800 tacatggggc tgaccgtgtg ggtgagcagt gaccccctgg gtctggcagc 2850 ctcacaggcc aacttctacc ccccacctcc tgaatggctg cacgacaaat 2900 acgacaccac gggggagaac cttcgcatcc cgccagctca gcccttggag 2950 tttgcccagt tccccttcct gctgcgtggc ctccagaaga ctgcagactt 3000 tgtggaggcc atcgaggggg cccgggcagc atgcgcagag gccggccagg 3050 ctggggtgca cgcctacccc agcggctccc ccttcctctt ctgggaacag 3100 tatctgggcc tgcggcgctg cttcctgctg gccgtctgca tcctgctggt 3150 gtgcactttc ctcgtctgtg ctctgctgct cctcaacccc tggacggctg 3200 gcctcatagt gctggtcctg gcgatgatga cagtggaact ctttggtatc 3250 atgggtttcc tgggcatcaa gctgagtgcc atccccgtgg tgatccttgt 3300 ggcctctgta ggcattggcg ttgagttcac agtccacgtg gctctgggct 3350 tcctgaccac ccagggcagc cggaacctgc gggccgccca tgcccttgag 3400 cacacatttg cccccgtgac cgatggggcc atctccacat tgctgggtct 3450 gctcatgctt gctggttccc actttgactt cattgtaagg tacttctttg 3500 cggcgctgac agtgctcacg ctcctgggcc tcctccatgg actcgtgctg 3550 ctgcctgtgc tgctgtccat cctgggcccg ccgccagagg tgatacagat 3600 gtacaaggaa agcccagaga tcctgagtcc accagctcca cagggaggcg 3650 ggcttaggtg gggggcatcc tcctccctgc cccagagctt tgccagagtg 3700 actacctcca tgaccgtggc catccaccca ccccccctgc ctggtgccta 3750 catccatcca gcccctgatg agcccccttg gtcccctgct gccactagct 3800 ctggcaacct cagttccagg ggaccaggtc cagccactgg gtgaaagagc 3850 agctgaagca cagagaccat gtgtggggcg tgtggggtca ctgggaagca 3900 ctgggtctgg tgttagacgc aggacggacc cctggagggc cctgctgctg 3950 ctgcatcccc tctcccgacc cagctgtcat gggcctccct gatatcgaat 4000 tcaatcgata gaaccgaggt gcagttggac 4030 2 1203 PRT Homo sapiens 2 Met Thr Arg Ser Pro Pro Leu Arg Glu Leu Pro Pro Ser Tyr Thr 1 5 10 15 Pro Pro Ala Arg Thr Ala Ala Pro Gln Ile Leu Ala Gly Ser Leu 20 25 30 Lys Ala Pro Leu Trp Leu Arg Ala Tyr Phe Gln Gly Leu Leu Phe 35 40 45 Ser Leu Gly Cys Gly Ile Gln Arg His Cys Gly Lys Val Leu Phe 50 55 60 Leu Gly Leu Leu Ala Phe Gly Ala Leu Ala Leu Gly Leu Arg Met 65 70 75 Ala Ile Ile Glu Thr Asn Leu Glu Gln Leu Trp Val Glu Val Gly 80 85 90 Ser Arg Val Ser Gln Glu Leu His Tyr Thr Lys Glu Lys Leu Gly 95 100 105 Glu Glu Ala Ala Tyr Thr Ser Gln Met Leu Ile Gln Thr Ala Arg 110 115 120 Gln Glu Gly Glu Asn Ile Leu Thr Pro Glu Ala Leu Gly Leu His 125 130 135 Leu Gln Ala Ala Leu Thr Ala Ser Lys Val Gln Val Ser Leu Tyr 140 145 150 Gly Lys Ser Trp Asp Leu Asn Lys Ile Cys Tyr Lys Ser Gly Val 155 160 165 Pro Leu Ile Glu Asn Gly Met Ile Glu Trp Met Ile Glu Lys Leu 170 175 180 Phe Pro Cys Val Ile Leu Thr Pro Leu Asp Cys Phe Trp Glu Gly 185 190 195 Ala Lys Leu Gln Gly Gly Ser Ala Tyr Leu Pro Gly Arg Pro Asp 200 205 210 Ile Gln Trp Thr Asn Leu Asp Pro Glu Gln Leu Leu Glu Glu Leu 215 220 225 Gly Pro Phe Ala Ser Leu Glu Gly Phe Arg Glu Leu Leu Asp Lys 230 235 240 Ala Gln Val Gly Gln Ala Tyr Val Gly Arg Pro Cys Leu His Pro 245 250 255 Asp Asp Leu His Cys Pro Pro Ser Ala Pro Asn His His Ser Arg 260 265 270 Gln Ala Pro Asn Val Ala His Glu Leu Ser Gly Gly Cys His Gly 275 280 285 Phe Ser His Lys Phe Met His Trp Gln Glu Glu Leu Leu Leu Gly 290 295 300 Gly Met Ala Arg Asp Pro Gln Gly Glu Leu Leu Arg Ala Glu Ala 305 310 315 Leu Gln Ser Thr Phe Leu Leu Met Ser Pro Arg Gln Leu Tyr Glu 320 325 330 His Phe Arg Gly Asp Tyr Gln Thr His Asp Ile Gly Trp Ser Glu 335 340 345 Glu Gln Ala Ser Thr Val Leu Gln Ala Trp Gln Arg Arg Phe Val 350 355 360 Gln Leu Ala Gln Glu Ala Leu Pro Glu Asn Ala Ser Gln Gln Ile 365 370 375 His Ala Phe Ser Ser Thr Thr Leu Asp Asp Ile Leu His Ala Phe 380 385 390 Ser Glu Val Ser Ala Ala Arg Val Val Gly Gly Tyr Leu Leu Met 395 400 405 Leu Ala Tyr Ala Cys Val Thr Met Leu Arg Trp Asp Cys Ala Gln 410 415 420 Ser Gln Gly Ser Val Gly Leu Ala Gly Val Leu Leu Val Ala Leu 425 430 435 Ala Val Ala Ser Gly Leu Gly Leu Cys Ala Leu Leu Gly Ile Thr 440 445 450 Phe Asn Ala Ala Thr Thr Gln Val Leu Pro Phe Leu Ala Leu Gly 455 460 465 Ile Gly Val Asp Asp Val Phe Leu Leu Ala His Ala Phe Thr Glu 470 475 480 Ala Leu Pro Gly Thr Pro Leu Gln Glu Arg Met Gly Glu Cys Leu 485 490 495 Gln Arg Thr Gly Thr Ser Val Val Leu Thr Ser Ile Asn Asn Met 500 505 510 Ala Ala Phe Leu Met Ala Ala Leu Val Pro Ile Pro Ala Leu Arg 515 520 525 Ala Phe Ser Leu Gln Ala Ala Ile Val Val Gly Cys Thr Phe Val 530 535 540 Ala Val Met Leu Val Phe Pro Ala Ile Leu Ser Leu Asp Leu Arg 545 550 555 Arg Arg His Cys Gln Arg Leu Asp Val Leu Cys Cys Phe Ser Ser 560 565 570 Pro Cys Ser Ala Gln Val Ile Gln Ile Leu Pro Gln Glu Leu Gly 575 580 585 Asp Gly Thr Val Pro Val Gly Ile Ala His Leu Thr Ala Thr Val 590 595 600 Gln Ala Phe Thr His Cys Glu Ala Ser Ser Gln His Val Val Thr 605 610 615 Ile Leu Pro Pro Gln Ala His Leu Val Pro Pro Pro Ser Asp Pro 620 625 630 Leu Gly Ser Glu Leu Phe Ser Pro Gly Gly Ser Thr Arg Asp Leu 635 640 645 Leu Gly Gln Glu Glu Glu Thr Arg Gln Lys Ala Ala Cys Lys Ser 650 655 660 Leu Pro Cys Ala Arg Trp Asn Leu Ala His Phe Ala Arg Tyr Gln 665 670 675 Phe Ala Pro Leu Leu Leu Gln Ser His Ala Lys Ala Ile Val Leu 680 685 690 Val Leu Phe Gly Ala Leu Leu Gly Leu Ser Leu Tyr Gly Ala Thr 695 700 705 Leu Val Gln Asp Gly Leu Ala Leu Thr Asp Val Val Pro Arg Gly 710 715 720 Thr Lys Glu His Ala Phe Leu Ser Ala Gln Leu Arg Tyr Phe Ser 725 730 735 Leu Tyr Glu Val Ala Leu Val Thr Gln Gly Gly Phe Asp Tyr Ala 740 745 750 His Ser Gln Arg Ala Leu Phe Asp Leu His Gln Arg Phe Ser Ser 755 760 765 Leu Lys Ala Val Leu Pro Pro Pro Ala Thr Gln Ala Pro Arg Thr 770 775 780 Trp Leu His Tyr Tyr Arg Asn Trp Leu Gln Gly Ile Gln Ala Ala 785 790 795 Phe Asp Gln Asp Trp Ala Ser Gly Arg Ile Thr Arg His Ser Tyr 800 805 810 Arg Asn Gly Ser Glu Asp Gly Ala Leu Ala Tyr Lys Leu Leu Ile 815 820 825 Gln Thr Gly Asp Ala Gln Glu Pro Leu Asp Phe Ser Gln Leu Thr 830 835 840 Thr Arg Lys Leu Val Asp Arg Glu Gly Leu Ile Pro Pro Glu Leu 845 850 855 Phe Tyr Met Gly Leu Thr Val Trp Val Ser Ser Asp Pro Leu Gly 860 865 870 Leu Ala Ala Ser Gln Ala Asn Phe Tyr Pro Pro Pro Pro Glu Trp 875 880 885 Leu His Asp Lys Tyr Asp Thr Thr Gly Glu Asn Leu Arg Ile Pro 890 895 900 Pro Ala Gln Pro Leu Glu Phe Ala Gln Phe Pro Phe Leu Leu Arg 905 910 915 Gly Leu Gln Lys Thr Ala Asp Phe Val Glu Ala Ile Glu Gly Ala 920 925 930 Arg Ala Ala Cys Ala Glu Ala Gly Gln Ala Gly Val His Ala Tyr 935 940 945 Pro Ser Gly Ser Pro Phe Leu Phe Trp Glu Gln Tyr Leu Gly Leu 950 955 960 Arg Arg Cys Phe Leu Leu Ala Val Cys Ile Leu Leu Val Cys Thr 965 970 975 Phe Leu Val Cys Ala Leu Leu Leu Leu Asn Pro Trp Thr Ala Gly 980 985 990 Leu Ile Val Leu Val Leu Ala Met Met Thr Val Glu Leu Phe Gly 995 1000 1005 Ile Met Gly Phe Leu Gly Ile Lys Leu Ser Ala Ile Pro Val Val 1010 1015 1020 Ile Leu Val Ala Ser Val Gly Ile Gly Val Glu Phe Thr Val His 1025 1030 1035 Val Ala Leu Gly Phe Leu Thr Thr Gln Gly Ser Arg Asn Leu Arg 1040 1045 1050 Ala Ala His Ala Leu Glu His Thr Phe Ala Pro Val Thr Asp Gly 1055 1060 1065 Ala Ile Ser Thr Leu Leu Gly Leu Leu Met Leu Ala Gly Ser His 1070 1075 1080 Phe Asp Phe Ile Val Arg Tyr Phe Phe Ala Ala Leu Thr Val Leu 1085 1090 1095 Thr Leu Leu Gly Leu Leu His Gly Leu Val Leu Leu Pro Val Leu 1100 1105 1110 Leu Ser Ile Leu Gly Pro Pro Pro Glu Val Ile Gln Met Tyr Lys 1115 1120 1125 Glu Ser Pro Glu Ile Leu Ser Pro Pro Ala Pro Gln Gly Gly Gly 1130 1135 1140 Leu Arg Trp Gly Ala Ser Ser Ser Leu Pro Gln Ser Phe Ala Arg 1145 1150 1155 Val Thr Thr Ser Met Thr Val Ala Ile His Pro Pro Pro Leu Pro 1160 1165 1170 Gly Ala Tyr Ile His Pro Ala Pro Asp Glu Pro Pro Trp Ser Pro 1175 1180 1185 Ala Ala Thr Ser Ser Gly Asn Leu Ser Ser Arg Gly Pro Gly Pro 1190 1195 1200 Ala Thr Gly 1203 3 228 DNA Homo sapiens unknown 20, 27, 135, 156, 210 unknown base 3 gctggggtgc acgcctaccn cagcggntcc cccttcctct tctgggaaca 50 gtatctgggc ctgcggcgct gcttcctgct ggccgtctgc atcctgctgg 100 tgtgcacttt cctcgtctgt gctctgctgc tcctnaaccc ctggacggct 150 ggcctnatag tgctggtcct ggcgatgatg acagtggaac tctttggtat 200 catgggtttn ctgggcatca agctgagt 228 4 76 PRT Homo sapiens 4 Leu Gly Leu Ser Ser Tyr Pro Asn Gly Tyr Pro Phe Leu Phe Trp 1 5 10 15 Glu Gln Tyr Ile Gly Leu Arg His Trp Leu Leu Leu Phe Ile Ser 20 25 30 Val Val Leu Ala Cys Thr Phe Leu Val Cys Ala Val Phe Leu Leu 35 40 45 Asn Pro Trp Thr Ala Gly Ile Ile Val Met Val Leu Ala Leu Met 50 55 60 Thr Val Glu Leu Phe Gly Met Met Gly Leu Ile Gly Ile Lys Leu 65 70 75 Ser 76 5 125 DNA Homo sapiens unknown 115 unknown base 5 gctggggtgc acgcctaccc cagcggctcc cccttcctct tctgggaaca 50 gtatctgggc ctgcggcgct gcttcctgct ggccgtctgc atcctgctgg 100 tgtgcacttt cctcntctgt gctct 125 6 50 DNA Homo sapiens unknown 13-14 unknown base 6 ccgggcggca tgnngcgaag cggaccacgc tggggggtgg ctcaggggag 50 7 1182 PRT Mus musculus 7 Met Val Arg Pro Leu Ser Leu Gly Glu Leu Pro Pro Ser Tyr Thr 1 5 10 15 Pro Pro Ala Arg Ser Ser Ala Pro His Ile Leu Ala Gly Ser Leu 20 25 30 Gln Ala Pro Leu Trp Leu Arg Ala Tyr Phe Gln Gly Leu Leu Phe 35 40 45 Ser Leu Gly Cys Arg Ile Gln Lys His Cys Gly Lys Val Leu Phe 50 55 60 Leu Gly Leu Val Ala Phe Gly Ala Leu Ala Leu Gly Leu Arg Val 65 70 75 Ala Val Ile Glu Thr Asp Leu Glu Gln Leu Trp Val Glu Val Gly 80 85 90 Ser Arg Val Ser Gln Glu Leu His Tyr Thr Lys Glu Lys Leu Gly 95 100 105 Glu Glu Ala Ala Tyr Thr Ser Gln Met Leu Ile Gln Thr Ala His 110 115 120 Gln Glu Gly Gly Asn Val Leu Thr Pro Glu Ala Leu Asp Leu His 125 130 135 Leu Gln Ala Ala Leu Thr Ala Ser Lys Val Gln Val Ser Leu Tyr 140 145 150 Gly Lys Ser Trp Asp Leu Asn Lys Ile Cys Tyr Lys Ser Gly Val 155 160 165 Pro Leu Ile Glu Asn Gly Met Ile Glu Arg Met Ile Glu Lys Leu 170 175 180 Phe Pro Cys Val Ile Leu Thr Pro Leu Asp Cys Phe Trp Glu Gly 185 190 195 Ala Lys Leu Gln Gly Gly Ser Ala Tyr Leu Pro Gly Arg Pro Asp 200 205 210 Ile Gln Trp Thr Asn Leu Asp Pro Gln Gln Leu Leu Glu Glu Leu 215 220 225 Gly Pro Phe Ala Ser Leu Glu Gly Phe Arg Glu Leu Leu Asp Lys 230 235 240 Ala Gln Val Gly Gln Ala Tyr Val Gly Arg Pro Cys Leu Asp Pro 245 250 255 Asp Asp Pro His Cys Pro Pro Ser Ala Pro Asn Arg His Ser Arg 260 265 270 Gln Ala Pro Asn Val Ala Gln Glu Leu Ser Gly Gly Cys His Gly 275 280 285 Phe Ser His Lys Phe Met His Trp Gln Glu Glu Leu Leu Leu Gly 290 295 300 Gly Thr Ala Arg Asp Leu Gln Gly Gln Leu Leu Arg Ala Glu Ala 305 310 315 Leu Gln Ser Thr Phe Leu Leu Met Ser Pro Arg Gln Leu Tyr Glu 320 325 330 His Phe Arg Gly Asp Tyr Gln Thr His Asp Ile Gly Trp Ser Glu 335 340 345 Glu Gln Ala Ser Met Val Leu Gln Ala Trp Gln Arg Arg Phe Val 350 355 360 Gln Leu Ala Gln Glu Ala Leu Pro Ala Asn Ala Ser Gln Gln Ile 365 370 375 His Ala Phe Ser Ser Thr Thr Leu Asp Asp Ile Leu Arg Ala Phe 380 385 390 Ser Glu Val Ser Thr Thr Arg Val Val Gly Gly Tyr Leu Leu Met 395 400 405 Leu Ala Tyr Ala Cys Val Thr Met Leu Arg Trp Asp Cys Ala Gln 410 415 420 Ser Gln Gly Ala Val Gly Leu Ala Gly Val Leu Leu Val Ala Leu 425 430 435 Ala Val Ala Ser Gly Leu Gly Leu Cys Ala Leu Leu Gly Ile Thr 440 445 450 Phe Asn Ala Ala Thr Thr Gln Val Leu Pro Phe Leu Ala Leu Gly 455 460 465 Ile Gly Val Asp Asp Ile Phe Leu Leu Ala His Ala Phe Thr Lys 470 475 480 Ala Pro Pro Asp Thr Pro Leu Pro Glu Arg Met Gly Glu Cys Leu 485 490 495 Arg Ser Thr Gly Thr Ser Val Ala Leu Thr Ser Val Asn Asn Met 500 505 510 Val Ala Phe Phe Met Ala Ala Leu Val Pro Ile Pro Ala Leu Arg 515 520 525 Ala Phe Ser Leu Gln Ala Ala Ile Val Val Gly Cys Asn Phe Ala 530 535 540 Ala Val Met Leu Val Phe Pro Ala Ile Leu Ser Leu Asp Leu Arg 545 550 555 Arg Arg His Arg Gln Arg Leu Asp Val Leu Cys Cys Phe Ser Ser 560 565 570 Pro Cys Ser Ala Gln Val Ile Gln Met Leu Pro Gln Glu Leu Gly 575 580 585 Asp Arg Ala Val Pro Val Gly Ile Ala His Leu Thr Ala Thr Val 590 595 600 Gln Ala Phe Thr His Cys Glu Ala Ser Ser Gln His Val Val Thr 605 610 615 Ile Leu Pro Pro Gln Ala His Leu Leu Ser Pro Ala Ser Asp Pro 620 625 630 Leu Gly Ser Glu Leu Tyr Ser Pro Gly Gly Ser Thr Arg Asp Leu 635 640 645 Leu Ser Gln Glu Glu Gly Thr Gly Pro Gln Ala Ala Cys Arg Pro 650 655 660 Leu Leu Cys Ala His Trp Thr Leu Ala His Phe Ala Arg Tyr Gln 665 670 675 Phe Ala Pro Leu Leu Leu Gln Thr Arg Ala Lys Ala Leu Val Leu 680 685 690 Leu Phe Phe Gly Ala Leu Leu Gly Leu Ser Leu Tyr Gly Ala Thr 695 700 705 Leu Val Gln Asp Gly Leu Ala Leu Thr Asp Val Val Pro Arg Gly 710 715 720 Thr Lys Glu His Ala Phe Leu Ser Ala Gln Leu Arg Tyr Phe Ser 725 730 735 Leu Tyr Glu Val Ala Leu Val Thr Gln Gly Gly Phe Asp Tyr Ala 740 745 750 His Ser Gln Arg Ala Leu Phe Asp Leu His Gln Arg Phe Ser Ser 755 760 765 Leu Lys Ala Val Leu Pro Pro Pro Ala Thr Gln Ala Pro Arg Thr 770 775 780 Trp Leu His Tyr Tyr Arg Ser Trp Leu Gln Gly Ile Gln Ala Ala 785 790 795 Phe Asp Gln Asp Trp Ala Ser Gly Arg Ile Thr Cys His Ser Tyr 800 805 810 Arg Asn Gly Ser Glu Asp Gly Ala Leu Ala Tyr Lys Leu Leu Ile 815 820 825 Gln Thr Gly Asn Ala Gln Glu Pro Leu Asp Phe Ser Gln Leu Thr 830 835 840 Thr Arg Lys Leu Val Asp Lys Glu Gly Leu Ile Pro Pro Glu Leu 845 850 855 Phe Tyr Met Gly Leu Thr Val Trp Val Ser Ser Asp Pro Leu Gly 860 865 870 Leu Ala Ala Ser Gln Ala Asn Phe Tyr Pro Pro Pro Pro Glu Trp 875 880 885 Leu His Asp Lys Tyr Asp Thr Thr Gly Glu Asn Leu Arg Ile Pro 890 895 900 Ala Ala Gln Pro Leu Glu Phe Ala Gln Phe Pro Phe Leu Leu His 905 910 915 Gly Leu Gln Lys Thr Ala Asp Phe Val Glu Ala Ile Glu Gly Ala 920 925 930 Arg Ala Ala Cys Thr Glu Ala Gly Gln Ala Gly Val His Ala Tyr 935 940 945 Pro Ser Gly Ser Pro Phe Leu Phe Trp Glu Gln Tyr Leu Gly Leu 950 955 960 Arg Arg Cys Phe Leu Leu Ala Val Cys Ile Leu Leu Val Cys Thr 965 970 975 Phe Leu Val Cys Ala Leu Leu Leu Leu Ser Pro Trp Thr Ala Gly 980 985 990 Leu Ile Val Leu Val Leu Ala Met Met Thr Val Glu Leu Phe Gly 995 1000 1005 Ile Met Gly Phe Leu Gly Ile Lys Leu Ser Ala Ile Pro Val Val 1010 1015 1020 Ile Leu Val Ala Ser Ile Gly Ile Gly Val Glu Phe Thr Val His 1025 1030 1035 Val Ala Leu Gly Phe Leu Thr Ser His Gly Ser Arg Asn Leu Arg 1040 1045 1050 Ala Ala Ser Ala Leu Glu Gln Thr Phe Ala Pro Val Thr Asp Gly 1055 1060 1065 Ala Val Ser Thr Leu Leu Gly Leu Leu Met Leu Ala Gly Ser Asn 1070 1075 1080 Phe Asp Phe Ile Ile Arg Tyr Phe Phe Val Val Leu Thr Val Leu 1085 1090 1095 Thr Leu Leu Gly Leu Leu His Gly Leu Leu Leu Leu Pro Val Leu 1100 1105 1110 Leu Ser Ile Leu Gly Pro Pro Pro Gln Val Val Gln Val Tyr Lys 1115 1120 1125 Glu Ser Pro Gln Thr Leu Asn Ser Ala Ala Pro Gln Arg Gly Gly 1130 1135 1140 Leu Arg Trp Asp Arg Pro Pro Thr Leu Pro Gln Ser Phe Ala Arg 1145 1150 1155 Val Thr Thr Ser Met Thr Val Ala Leu His Pro Pro Pro Leu Pro 1160 1165 1170 Gly Ala Tyr Val His Pro Ala Ser Glu Glu Pro Thr 1175 1180 1182 8 4004 DNA Homo sapiens 8 cccacgcgtc cgggagaagc tgggggagga ggctgcatac acctctcaga 50 tgctgataca gaccgcacgc caggagggag agaacatcct cacacccgaa 100 gcacttggcc tccacctcca ggcagccctc actgccagta aagtccaagt 150 atcactctat gggaagtcct gggatttgaa caaaatctgc tacaagtcag 200 gagttcccct tattgaaaat ggaatgattg agcggatgat tgagaagctg 250 tttccgtgcg tgatcctcac ccccctcgac tgcttctggg agggagccaa 300 actccaaggg ggctccgcct acctgccgct cccaatgtgg ctcacgagct 350 gagtgggggc tgccatggct tctcccacaa attcatgcac tggcaggagg 400 aattgctgct gggaggcatg gccagagacc cccaaggaga gctgctgagg 450 gcagaggccc tgcagagcac cttcttgctg atgagtcccc gccagctgta 500 cgagcatttc cggggtgact atcagacaca tgacattggc tggagtgagg 550 agcaggccag cacagtgcta caagcctggc agcggcgctt tgtgcaggtc 600 ggtatggaca aggacagggg ggtgccctga ggccattccc tcctcctgcc 650 ccctcctatc caccctgttt ctccagctgg cccaggaggc cctgcctgag 700 aacgcttccc agcagatcca tgccttctcc tccaccaccc tggatgacat 750 cctgcatgcg ttctctgaag tcagtgctgc ccgtgtggtg ggaggctatc 800 tgctcatggt gggtcttgca cctggcacct tgcccccacc ccacctccaa 850 ccagtgccca ccctggggag cccctgagac tgccctttcc ccccacagct 900 ggcctatgcc tgtgtgacca tgctgcggtg ggactgcgcc cagtcccagg 950 gttccgtggg ccttgccggg gtactgctgg tggccctggc ggtggcctca 1000 ggccttgggc tctgtgccct gctcggcatc accttcaatg ctgccactac 1050 ccaggtacgc caggactgca gggcagactc agtgccagtc accaggcttc 1100 acgggtcctc agctgcccgc tcctctgccc ctccaggtgc tgcccttctt 1150 gactctggga atcggcgtgg atgacgtatt cctgctggcg catgccttca 1200 cagaggctct gcctggcacc cctctccagg tggggccttg tcccccaggg 1250 ctcatctgag gcagctcagc ttactggtta agagcctctt ggttcaagtg 1300 accttgggct gctaatgaac ctcggtgcct cttgtcccca tgtgtaaaca 1350 ggggaaataa tagtgctgtg tcctaagggt tattgtttgg atcagtgaag 1400 taactcaagt tgaatgctta gaacagccca tcatacgtac atggtaccca 1450 ataaatgcta gccactgtgt tatgactgcc ccacctctgc accccaagtt 1500 cctgagcctc cccttcactc cactttgaca cggcccctcc cttgtgacct 1550 gagggcaggt ccccactctg tcctggcagg agcgcatggg cgagtgtctg 1600 cagcgcacgg gcaccagtgt tgtactcaca tccatcaaca acatggccgc 1650 cttcctcatg gctgccctcg ttcccatccc tgcgctgcga gccttctccc 1700 tacagcctgg acctacggcg gcgccactgc cagcgccttg atgtgctctg 1750 ctgcttctcc aggtactgcc tgcgccccag ccccttcctc ccgtgaccca 1800 cgccagcctg tcccctcacc agcatttcaa ggcacagacc tgtcatccac 1850 tctctacctc ttccagtccc tgctctgctc aggtgattca gatcctgccc 1900 caggagctgg gggacgggac agtaccagtg ggcattgccc acctcactgc 1950 cacagttcaa gcctttaccc actgtgaagc cagcagccag catgtggtca 2000 ccatcctgcc tccccaagcc cacctggtgc ccccaccttc tgacccactg 2050 ggctctgagc tcttcagccc tggagggtcc acacgggacc ttctaggcca 2100 ggaggaggag acaaggcaga aggcagcctg caagtccctg ccctgtgccc 2150 gctggaatct tgcccatttc gcccgctatc agtttgcccc gttgctgctc 2200 cagtcacatg ccaaggccat cgtgctggtg ctctttggtg ctcttctggg 2250 cctgagcctc tacggagcca ccttggtgca agacggcctg gccctgacgg 2300 atgtggtgcc tcggggcacc aaggagcatg ccttcctgag cgcccagctc 2350 aggtacttct ccctgtacga ggtggccctg gtgacccagg gtggctttga 2400 ctacgcccac tcccaacgcg ccctctttga tctgcaccag cgcttcagtt 2450 ccctcaaggc ggtgctgccc ccaccggcca cccaggcacc ccgcacctgg 2500 ctgcactatt accgcaactg gctacaggga atccaggctg cctttgacca 2550 ggactgggct tctgggcgca tcacccgcca ctcgtaccgc aatggctctg 2600 aggatggggc cctggcctac aagctgctca tccagactgg agacgcccag 2650 gagcctctgg atttcagcca ggttgggaga gggctggagg ggtccactag 2700 tacaggggct gcaggcctcc tgggcccagg ccttcagccc tctctgcctc 2750 tgcagctgac cacaaggaag ctggtggaca gagagggact gattccaccc 2800 gagctcttct acatggggct gaccgtgtgg gtgagcagtg accccctggg 2850 tctggcagcc tcacaggcca acttctaccc cccacctcct gaatggctgc 2900 acgacaaata cgacaccacg ggggagaacc ttcgcagtga gtcttggggg 2950 gagctcggca agagcctcag cctcgcccac acaagccctg agcctgaggc 3000 cctgcccact ctgccccgtg ctcaccgccc tgtccctctc cctcttctcc 3050 cttcccctcc cctccacagt cccgccagct cagcccttgg agtttgccca 3100 gttccccttc ctgctgcgtg gcctccagaa gactgcagac tttgtggagg 3150 ccatcgaggg ggcccgggca gcatgcgcag aggccggcca ggctggggtg 3200 cacgcctacc ccagcggctc ccccttcctc ttctgggaac agtatctggg 3250 cctgcggcgc tgcttcctgc tggccgtctg catcctgctg gtgtgcactt 3300 tcctcgtctg tgctctgctg ctcctcaacc cctggacggc tggcctcata 3350 gtgagtgctt gcaggagtgg ggacagagac accccaccct tccctgccca 3400 gcctgtcatc cctcctgcca ggagccctct gtgagccctg tctccctcag 3450 gtgctggtcc tggcgatgat gacagtggaa ctctttggta tcatgggttt 3500 cctgggcatc aagctgagtg ccatccccgt ggtgatcctt gtggcctctg 3550 taggcattgg cgttgagttc acagtccacg tggctctggt gagcacgggc 3600 accccgggga gggaccaatc agctgattca gtattcaaca catattgttc 3650 aagcccctac tatgtgctag gtactattta agaatttggg ctgggtggac 3700 gtggtggctc attcctgtaa tcccagcact ttgggaggcc gaggcgggtg 3750 gatcacctga ggtcgggagt tcgaaaccag cctggccaac atggtgaaac 3800 cctgtcttta ctaaaaatac aaaaaattag ccaggcgtgg tggcacatgc 3850 cagtagtccc agctactttg gaggctgagg cagaattgct tgaacctggg 3900 aggcgaaggt tgcagtgagc tgagatcgtg ccattgcact ccagcctggg 3950 caacaagagt gcaactctcc gtctcaaaaa aaaaaaaaaa aagggcggcc 4000 gcga 4004 9 2082 DNA Homo sapiens 9 ttccggcatg actcgatcgc cgcccctcag agagctgccc ccgagttaca 50 cacccccagc tcgaaccgca gcaccccaga tcctagctgg gagcctgaag 100 gctccactct ggcttcgtgc ttacttccag ggcctgctct tctctctggg 150 atgcgggatc cagagacatt gtggcaaagt gctctttctg ggactgttgg 200 cctttggggc cctggcatta ggtctccgca tggccattat tgagacaaac 250 ttggaacagc tctgggtaga agtgggcagc cgggtgagcc aggagctgca 300 ttacaccaag gagaagctgg gggaggaggc tgcatacacc tctcagatgc 350 tgatacagac cgcacgccag gagggagaga acatcctcac acccgaagca 400 cttggcctcc acctccaggc agccctcact gccagtaaag tccaagtatc 450 actctatggg aagtcctggg atttgaacaa aatctgctac aagtcaggag 500 ttccccttat tgaaaatgga atgattgagt ggatgattga gaagctgttt 550 ccgtgcgtga tcctcacccc cctcgactgc ttctgggagg gagccaaact 600 ccaagggggc tccgcctacc tgcccggccg cccggatatc cagtggacca 650 acctggatcc agagcagctg ctggaggagc tgggtccctt tgcctccctt 700 gagggcttcc gggagctgct agacaaggca caggtgggcc aggcctacgt 750 ggggcggccc tgtctgcacc ctgatgacct ccactgccca cctagtgccc 800 ccaaccatca cagcaggcag gctcccaatg tggctcacga gctgagtggg 850 ggctgccatg gcttctccca caaattcatg cactggcagg aggaattgct 900 gctgggaggc atggccagag acccccaagg agagctgctg agggcagagg 950 ccctgcagag caccttcttg ctgatgagtc cccgccagct gtacgagcat 1000 ttccggggtg actatcagac acatgacatt ggctggagtg aggagcaggc 1050 cagcacagtg ctacaagcct ggcagcggcg ctttgtgcag ctggcccagg 1100 aggccctgcc tgagaacgct tcccagcaga tccatgcctt ctcctccacc 1150 accctggata acatcctgca tgcgttctct gaagtcagtg ctgcccgtgt 1200 ggtgggaggc tatctgctca tgctggccta tgcctgtgtg accatgctgc 1250 ggtgggactg cgcccagtcc cagggttccg tgggccttgc cggggtactg 1300 ctggtggccc tggcggtggc ctcaggcctt gggctctgtg ccctgctcgg 1350 catcaccttc aatgctgcca ctacccaggt gctgcccttc ttggctctgg 1400 gaatcggcgt ggatgacgta ttcctgctgg cgcatgcctt cacagaggct 1450 ctgcctggca cccctctcca ggagcgcatg ggcgagtgtc tgcagcgcac 1500 gggcaccagt gtcgtactca catccatcaa caacatggcc gccttcctca 1550 tggctgccct cgttcccatc cctgcgctgc gagccttctc cttacagcca 1600 tcctcagcct ggacctacgg cggcgccact gccagcgcct tgatgtgctc 1650 tgctgcttct ccagtccctg ctctgctcag gtgattcaga tcctgcccca 1700 ggagctgggg gacgggacag taccagtggg cattgcccac ctcactgcca 1750 cagttcaagc ctttacccac tgtgaagcca gcagccagca tgtggtcacc 1800 atcctgcctc cccaagccca cctggtgccc ccaccttctg acccactggg 1850 ctctgagctc ttcagccctg gagggtccac acgggacctt ctaggccagg 1900 aggaggagac aaggcagaag gcagcctgca agtccctgcc ctgtgcccgc 1950 tggaatcttg cccatttcgc cccggaattc ctgcagcccg ggggatccac 2000 tagttctaga gcggccgcca ccgcggtgga gctccagctt ttgttccctt 2050 tagtgagggt taattgcgcg cttgggtatc tt 2082 10 1315 PRT Homo sapiens 10 Met Glu Lys Tyr His Val Leu Glu Met Ile Gly Glu Gly Ser Phe 1 5 10 15 Gly Arg Val Tyr Lys Gly Arg Arg Lys Tyr Ser Ala Gln Val Val 20 25 30 Ala Leu Lys Phe Ile Pro Lys Leu Gly Arg Ser Glu Lys Glu Leu 35 40 45 Arg Asn Leu Gln Arg Glu Ile Glu Ile Met Arg Gly Leu Arg His 50 55 60 Pro Asn Ile Val His Met Leu Asp Ser Phe Glu Thr Asp Lys Glu 65 70 75 Val Val Val Val Thr Asp Tyr Ala Glu Gly Glu Leu Phe Gln Ile 80 85 90 Leu Glu Asp Asp Gly Lys Leu Pro Glu Asp Gln Val Gln Ala Ile 95 100 105 Ala Ala Gln Leu Val Ser Ala Leu Tyr Tyr Leu His Ser His Arg 110 115 120 Ile Leu His Arg Asp Met Lys Pro Gln Asn Ile Leu Leu Ala Lys 125 130 135 Gly Gly Gly Ile Lys Leu Cys Asp Phe Gly Phe Ala Arg Ala Met 140 145 150 Ser Thr Asn Thr Met Val Leu Thr Ser Ile Lys Gly Thr Pro Leu 155 160 165 Tyr Met Ser Pro Glu Leu Val Glu Glu Arg Pro Tyr Asp His Thr 170 175 180 Ala Asp Leu Trp Ser Val Gly Cys Ile Leu Tyr Glu Leu Ala Val 185 190 195 Gly Thr Pro Pro Phe Tyr Ala Thr Ser Ile Phe Gln Leu Val Ser 200 205 210 Leu Ile Leu Lys Asp Pro Val Arg Trp Pro Ser Thr Ile Ser Pro 215 220 225 Cys Phe Lys Asn Phe Leu Gln Gly Leu Leu Thr Lys Asp Pro Arg 230 235 240 Gln Arg Leu Ser Trp Pro Asp Leu Leu Tyr His Pro Phe Ile Ala 245 250 255 Gly His Val Thr Ile Ile Thr Glu Pro Ala Gly Pro Asp Leu Gly 260 265 270 Thr Pro Phe Thr Ser Arg Leu Pro Pro Glu Leu Gln Val Leu Lys 275 280 285 Asp Glu Gln Ala His Arg Leu Ala Pro Lys Gly Asn Gln Ser Arg 290 295 300 Ile Leu Thr Gln Ala Tyr Lys Arg Met Ala Glu Glu Ala Met Gln 305 310 315 Lys Lys His Gln Asn Thr Gly Pro Ala Leu Glu Gln Glu Asp Lys 320 325 330 Thr Ser Lys Val Ala Pro Gly Thr Ala Pro Leu Pro Arg Leu Gly 335 340 345 Ala Thr Pro Gln Glu Ser Ser Leu Leu Ala Gly Ile Leu Ala Ser 350 355 360 Glu Leu Lys Ser Ser Trp Ala Lys Ser Gly Thr Gly Glu Val Pro 365 370 375 Ser Ala Pro Arg Glu Asn Arg Thr Thr Pro Asp Cys Glu Arg Ala 380 385 390 Phe Pro Glu Glu Arg Pro Glu Val Leu Gly Gln Arg Ser Thr Asp 395 400 405 Val Val Asp Leu Glu Asn Glu Glu Pro Asp Ser Asp Asn Glu Trp 410 415 420 Gln His Leu Leu Glu Thr Thr Glu Pro Val Pro Ile Gln Leu Lys 425 430 435 Ala Pro Leu Thr Leu Leu Cys Asn Pro Asp Phe Cys Gln Arg Ile 440 445 450 Gln Ser Gln Leu His Glu Ala Gly Gly Gln Ile Leu Lys Gly Ile 455 460 465 Leu Glu Gly Ala Ser His Ile Leu Pro Ala Phe Arg Val Leu Ser 470 475 480 Ser Leu Leu Ser Ser Cys Ser Asp Ser Val Ala Leu Tyr Ser Phe 485 490 495 Cys Arg Glu Ala Gly Leu Pro Gly Leu Leu Leu Ser Leu Leu Arg 500 505 510 His Ser Gln Glu Ser Asn Ser Leu Gln Gln Gln Ser Trp Tyr Gly 515 520 525 Thr Phe Leu Gln Asp Leu Met Ala Val Ile Gln Ala Tyr Phe Ala 530 535 540 Cys Thr Phe Asn Leu Glu Arg Ser Gln Thr Ser Asp Ser Leu Gln 545 550 555 Val Phe Gln Glu Ala Ala Asn Leu Phe Leu Asp Leu Leu Gly Lys 560 565 570 Leu Leu Ala Gln Pro Asp Asp Ser Glu Gln Thr Leu Arg Arg Asp 575 580 585 Ser Leu Met Cys Phe Thr Val Leu Cys Glu Ala Met Asp Gly Asn 590 595 600 Ser Arg Ala Ile Ser Lys Ala Phe Tyr Ser Ser Leu Leu Thr Thr 605 610 615 Gln Gln Val Val Leu Asp Gly Leu Leu His Gly Leu Thr Val Pro 620 625 630 Gln Leu Pro Val His Thr Pro Gln Gly Ala Pro Gln Val Ser Gln 635 640 645 Pro Leu Arg Glu Gln Ser Glu Asp Ile Pro Gly Ala Ile Ser Ser 650 655 660 Ala Leu Ala Ala Ile Cys Thr Ala Pro Val Gly Leu Pro Asp Cys 665 670 675 Trp Asp Ala Lys Glu Gln Val Cys Trp His Leu Ala Asn Gln Leu 680 685 690 Thr Glu Asp Ser Ser Gln Leu Arg Pro Ser Leu Ile Ser Gly Leu 695 700 705 Gln His Pro Ile Leu Cys Leu His Leu Leu Lys Val Leu Tyr Ser 710 715 720 Cys Cys Leu Val Ser Glu Gly Leu Cys Arg Leu Leu Gly Gln Glu 725 730 735 Pro Leu Ala Leu Glu Ser Leu Phe Met Leu Ile Gln Gly Lys Val 740 745 750 Lys Val Val Asp Trp Glu Glu Ser Thr Glu Val Thr Leu Tyr Phe 755 760 765 Leu Ser Leu Leu Val Phe Arg Leu Gln Asn Leu Pro Cys Gly Met 770 775 780 Glu Lys Leu Gly Ser Asp Val Ala Thr Leu Phe Thr His Ser His 785 790 795 Val Val Ser Leu Val Ser Ala Ala Ala Cys Leu Leu Gly Gln Leu 800 805 810 Gly Gln Gln Gly Val Thr Phe Asp Leu Gln Pro Met Glu Trp Met 815 820 825 Ala Ala Ala Thr His Ala Leu Ser Ala Pro Ala Glu Val Arg Leu 830 835 840 Thr Pro Pro Gly Ser Cys Gly Phe Tyr Asp Gly Leu Leu Ile Leu 845 850 855 Leu Leu Gln Leu Leu Thr Glu Gln Gly Lys Ala Ser Leu Ile Arg 860 865 870 Asp Met Ser Ser Ser Glu Met Trp Thr Val Leu Trp His Arg Phe 875 880 885 Ser Met Val Leu Arg Leu Pro Glu Glu Ala Ser Ala Gln Glu Gly 890 895 900 Glu Leu Ser Leu Ser Ser Pro Pro Ser Pro Glu Pro Asp Trp Thr 905 910 915 Leu Ile Ser Pro Gln Gly Met Ala Ala Leu Leu Ser Leu Ala Met 920 925 930 Ala Thr Phe Thr Gln Glu Pro Gln Leu Cys Leu Ser Cys Leu Ser 935 940 945 Gln His Gly Ser Ile Leu Met Ser Ile Leu Lys His Leu Leu Cys 950 955 960 Pro Ser Phe Leu Asn Gln Leu Arg Gln Ala Pro His Gly Ser Glu 965 970 975 Phe Leu Pro Val Val Val Leu Ser Val Cys Gln Leu Leu Cys Phe 980 985 990 Pro Phe Ala Leu Asp Met Asp Ala Asp Leu Leu Ile Val Val Leu 995 1000 1005 Ala Asp Leu Arg Asp Ser Glu Val Ala Ala His Leu Leu Gln Val 1010 1015 1020 Cys Cys Tyr His Leu Pro Leu Met Gln Val Glu Leu Pro Ile Ser 1025 1030 1035 Leu Leu Thr Arg Leu Ala Leu Met Asp Pro Thr Ser Leu Asn Gln 1040 1045 1050 Phe Val Asn Thr Val Ser Ala Ser Pro Arg Thr Ile Val Ser Phe 1055 1060 1065 Leu Ser Val Ala Leu Leu Ser Asp Gln Pro Leu Leu Thr Ser Asp 1070 1075 1080 Leu Leu Ser Leu Leu Ala His Thr Ala Arg Val Leu Ser Pro Ser 1085 1090 1095 His Leu Ser Phe Ile Gln Glu Leu Leu Ala Gly Ser Asp Glu Ser 1100 1105 1110 Tyr Arg Pro Leu Arg Ser Leu Leu Gly His Pro Glu Asn Ser Val 1115 1120 1125 Arg Ala His Thr Tyr Arg Leu Leu Gly His Leu Leu Gln His Ser 1130 1135 1140 Met Ala Leu Arg Gly Ala Leu Gln Ser Gln Ser Gly Leu Leu Ser 1145 1150 1155 Leu Leu Leu Leu Gly Leu Gly Asp Lys Asp Pro Val Val Arg Cys 1160 1165 1170 Ser Ala Ser Phe Ala Val Gly Asn Ala Ala Tyr Gln Ala Gly Pro 1175 1180 1185 Leu Gly Pro Ala Leu Ala Ala Ala Val Pro Ser Met Thr Gln Leu 1190 1195 1200 Leu Gly Asp Pro Gln Ala Gly Ile Arg Arg Asn Val Ala Ser Ala 1205 1210 1215 Leu Gly Asn Leu Gly Pro Glu Gly Leu Gly Glu Glu Leu Leu Gln 1220 1225 1230 Cys Glu Val Pro Gln Arg Leu Leu Glu Met Ala Cys Gly Asp Pro 1235 1240 1245 Gln Pro Asn Val Lys Glu Ala Ala Leu Ile Ala Leu Arg Ser Leu 1250 1255 1260 Gln Gln Glu Pro Gly Ile His Gln Val Leu Val Ser Leu Gly Ala 1265 1270 1275 Ser Glu Lys Leu Ser Leu Leu Ser Leu Gly Asn Gln Ser Leu Pro 1280 1285 1290 His Ser Ser Pro Arg Pro Ala Ser Ala Lys His Cys Arg Lys Leu 1295 1300 1305 Ile His Leu Leu Arg Pro Ala His Ser Met 1310 1315 11 48 DNA Artificial sequence Artificial sequence 1-48 11 ctatgaaatt aaccctcact aaagggagct cccgtgagtc cctatgtg 48 12 48 DNA Artificial sequence Artificial sequence 1-48 12 ggattctaat acgactcact atagggcccc taaactccgc tgctccac 48 13 396 PRT Mus musculus 13 Met Ala Leu Pro Ala Ser Leu Leu Pro Leu Cys Cys Leu Ala Leu 1 5 10 15 Leu Ala Leu Ser Ala Gln Ser Cys Gly Pro Gly Arg Gly Pro Val 20 25 30 Gly Arg Arg Arg Tyr Val Arg Lys Gln Leu Val Pro Leu Leu Tyr 35 40 45 Lys Gln Phe Val Pro Ser Met Pro Glu Arg Thr Leu Gly Ala Ser 50 55 60 Gly Pro Ala Glu Gly Arg Val Thr Arg Gly Ser Glu Arg Phe Arg 65 70 75 Asp Leu Val Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu 80 85 90 Glu Asn Ser Gly Ala Asp Arg Leu Met Thr Glu Arg Cys Lys Glu 95 100 105 Arg Val Asn Ala Leu Ala Ile Ala Val Met Asn Met Trp Pro Gly 110 115 120 Val Arg Leu Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His His 125 130 135 Ala Gln Asp Ser Leu His Tyr Glu Gly Arg Ala Leu Asp Ile Thr 140 145 150 Thr Ser Asp Arg Asp Arg Asn Lys Tyr Gly Leu Leu Ala Arg Leu 155 160 165 Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Arg Asn 170 175 180 His Ile His Val Ser Val Lys Ala Asp Asn Ser Leu Ala Val Arg 185 190 195 Ala Gly Gly Cys Phe Pro Gly Asn Ala Thr Val Arg Leu Arg Ser 200 205 210 Gly Glu Arg Lys Gly Leu Arg Glu Leu His Arg Gly Asp Trp Val 215 220 225 Leu Ala Ala Asp Ala Ala Gly Arg Val Val Pro Thr Pro Val Leu 230 235 240 Leu Phe Leu Asp Arg Asp Leu Gln Arg Arg Ala Ser Phe Val Ala 245 250 255 Val Glu Thr Glu Arg Pro Pro Arg Lys Leu Leu Leu Thr Pro Trp 260 265 270 His Leu Val Phe Ala Ala Arg Gly Pro Ala Pro Ala Pro Gly Asp 275 280 285 Phe Ala Pro Val Phe Ala Arg Arg Leu Arg Ala Gly Asp Ser Val 290 295 300 Leu Ala Pro Gly Gly Asp Ala Leu Gln Pro Ala Arg Val Ala Arg 305 310 315 Val Ala Arg Glu Glu Ala Val Gly Val Phe Ala Pro Leu Thr Ala 320 325 330 His Gly Thr Leu Leu Val Asn Asp Val Leu Ala Ser Cys Tyr Ala 335 340 345 Val Leu Glu Ser His Gln Trp Ala His Arg Ala Phe Ala Pro Leu 350 355 360 Arg Leu Leu His Ala Leu Gly Ala Leu Leu Pro Gly Gly Ala Val 365 370 375 Gln Pro Thr Gly Met His Trp Tyr Ser Arg Leu Leu Tyr Arg Leu 380 385 390 Ala Glu Glu Leu Met Gly 395 396 14 437 PRT Mus musculus 14 Met Leu Leu Leu Leu Ala Arg Cys Phe Leu Val Ile Leu Ala Ser 1 5 10 15 Ser Leu Leu Val Cys Pro Gly Leu Ala Cys Gly Pro Gly Arg Gly 20 25 30 Phe Gly Lys Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr 35 40 45 Lys Gln Phe Ile Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser 50 55 60 Gly Arg Tyr Glu Gly Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys 65 70 75 Glu Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu 80 85 90 Glu Asn Thr Gly Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp 95 100 105 Lys Leu Asn Ala Leu Ala Ile Ser Val Met Asn Gln Trp Pro Gly 110 115 120 Val Arg Leu Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His His 125 130 135 Ser Glu Glu Ser Leu His Tyr Glu Gly Arg Ala Val Asp Ile Thr 140 145 150 Thr Ser Asp Arg Asp Arg Ser Lys Tyr Gly Met Leu Ala Arg Leu 155 160 165 Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Lys Ala 170 175 180 His Ile His Cys Ser Val Lys Ala Glu Asn Ser Val Ala Ala Lys 185 190 195 Ser Gly Gly Cys Phe Pro Gly Ser Ala Thr Val His Leu Glu Gln 200 205 210 Gly Gly Thr Lys Leu Val Lys Asp Leu Arg Pro Gly Asp Arg Val 215 220 225 Leu Ala Ala Asp Asp Gln Gly Arg Leu Leu Tyr Ser Asp Phe Leu 230 235 240 Thr Phe Leu Asp Arg Asp Glu Gly Ala Lys Lys Val Phe Tyr Val 245 250 255 Ile Glu Thr Leu Glu Pro Arg Glu Arg Leu Leu Leu Thr Ala Ala 260 265 270 His Leu Leu Phe Val Ala Pro His Asn Asp Ser Gly Pro Thr Pro 275 280 285 Gly Pro Ser Ala Leu Phe Ala Ser Arg Val Arg Pro Gly Gln Arg 290 295 300 Val Tyr Val Val Ala Glu Arg Gly Gly Asp Arg Arg Leu Leu Pro 305 310 315 Ala Ala Val His Ser Val Thr Leu Arg Glu Glu Glu Ala Gly Ala 320 325 330 Tyr Ala Pro Leu Thr Ala His Gly Thr Ile Leu Ile Asn Arg Val 335 340 345 Leu Ala Ser Cys Tyr Ala Val Ile Glu Glu His Ser Trp Ala His 350 355 360 Arg Ala Phe Ala Pro Phe Arg Leu Ala His Ala Leu Leu Ala Ala 365 370 375 Leu Ala Pro Ala Arg Thr Asp Gly Gly Gly Gly Gly Ser Ile Pro 380 385 390 Ala Ala Gln Ser Ala Thr Glu Ala Arg Gly Ala Glu Pro Thr Ala 395 400 405 Gly Ile His Trp Tyr Ser Gln Leu Leu Tyr His Ile Gly Thr Trp 410 415 420 Leu Leu Asp Ser Glu Thr Met His Pro Leu Gly Met Ala Val Lys 425 430 435 Ala Ser 437 15 803 PRT Artificial sequence Artificial sequence 1-803 15 Met Ala Ala Gly Arg Pro Val Arg Gly Pro Glu Leu Ala Pro Arg 1 5 10 15 Arg Leu Leu Gln Leu Leu Leu Leu Val Leu Leu Gly Gly Arg Gly 20 25 30 Arg Gly Ala Ala Leu Ser Gly Asn Val Thr Gly Pro Gly Pro Arg 35 40 45 Ser Ala Gly Gly Ser Ala Arg Arg Asn Ala Pro Val Thr Ser Pro 50 55 60 Pro Pro Pro Leu Leu Ser His Cys Gly Arg Ala Ala His Cys Glu 65 70 75 Pro Leu Arg Tyr Asn Val Cys Leu Gly Ser Ala Leu Pro Tyr Gly 80 85 90 Ala Thr Thr Thr Leu Leu Ala Gly Asp Ser Asp Ser Gln Glu Glu 95 100 105 Ala His Ser Lys Leu Val Leu Trp Ser Gly Leu Arg Asn Ala Pro 110 115 120 Arg Cys Trp Ala Val Ile Gln Pro Leu Leu Cys Ala Val Tyr Met 125 130 135 Pro Lys Cys Glu Asn Asp Arg Val Glu Leu Pro Ser Arg Thr Leu 140 145 150 Cys Gln Ala Thr Arg Gly Pro Cys Ala Ile Val Glu Arg Glu Arg 155 160 165 Gly Trp Pro Asp Phe Leu Arg Cys Thr Pro Asp His Phe Pro Glu 170 175 180 Gly Cys Pro Asn Glu Val Gln Asn Ile Lys Phe Asn Ser Ser Gly 185 190 195 Gln Cys Glu Ala Pro Leu Val Arg Thr Asp Asn Pro Lys Ser Trp 200 205 210 Tyr Glu Asp Val Glu Gly Cys Gly Ile Gln Cys Gln Asn Pro Leu 215 220 225 Phe Thr Glu Ala Glu His Gln Asp Met His Ser Tyr Ile Ala Ala 230 235 240 Phe Gly Ala Val Thr Gly Leu Cys Thr Leu Phe Thr Leu Ala Thr 245 250 255 Phe Val Ala Asp Trp Arg Asn Ser Asn Arg Tyr Pro Ala Val Ile 260 265 270 Leu Phe Tyr Val Asn Ala Cys Phe Phe Val Gly Ser Ile Gly Trp 275 280 285 Leu Ala Gln Phe Met Asp Gly Ala Arg Arg Glu Ile Val Cys Arg 290 295 300 Ala Asp Gly Thr Met Arg Phe Gly Glu Pro Thr Ser Ser Glu Thr 305 310 315 Leu Ser Cys Val Ile Ile Phe Val Ile Val Tyr Tyr Ala Leu Met 320 325 330 Ala Gly Val Val Trp Phe Val Val Leu Thr Tyr Ala Trp His Thr 335 340 345 Ser Phe Lys Ala Leu Gly Thr Thr Tyr Gln Pro Leu Ser Gly Lys 350 355 360 Thr Ser Tyr Phe His Leu Leu Thr Trp Ser Leu Pro Phe Val Leu 365 370 375 Thr Val Ala Ile Leu Ala Val Ala Gln Val Asp Gly Asp Ser Val 380 385 390 Ser Gly Ile Cys Phe Val Gly Tyr Lys Asn Tyr Arg Tyr Arg Ala 395 400 405 Gly Phe Val Leu Ala Pro Ile Gly Leu Val Leu Ile Val Gly Gly 410 415 420 Tyr Phe Leu Ile Arg Gly Val Met Thr Leu Phe Ser Ile Lys Ser 425 430 435 Asn His Pro Gly Leu Leu Ser Glu Lys Ala Ala Ser Lys Ile Asn 440 445 450 Glu Thr Met Leu Arg Leu Gly Ile Phe Gly Phe Leu Ala Phe Gly 455 460 465 Phe Val Leu Ile Thr Phe Ser Cys His Phe Tyr Asp Phe Phe Asn 470 475 480 Gln Ala Glu Trp Glu Arg Ser Phe Arg Asp Tyr Val Leu Cys Gln 485 490 495 Ala Asn Val Thr Ile Gly Leu Pro Thr Lys Lys Pro Ile Pro Asp 500 505 510 Cys Glu Ile Lys Asn Arg Pro Ser Leu Leu Val Glu Lys Ile Asn 515 520 525 Leu Phe Ala Met Phe Gly Thr Gly Ile Ala Met Ser Thr Trp Val 530 535 540 Trp Thr Lys Ala Thr Leu Leu Ile Trp Arg Arg Thr Trp Cys Arg 545 550 555 Leu Thr Gly His Ser Asp Asp Glu Pro Lys Arg Ile Lys Lys Ser 560 565 570 Lys Met Ile Ala Lys Ala Phe Ser Lys Arg Arg Glu Leu Leu Gln 575 580 585 Asn Pro Gly Gln Glu Leu Ser Phe Ser Met His Thr Val Ser His 590 595 600 Asp Gly Pro Val Ala Gly Leu Ala Phe Glu Leu Asn Glu Pro Ser 605 610 615 Ala Asp Val Ser Ser Ala Trp Ala Gln His Val Thr Lys Met Val 620 625 630 Ala Arg Arg Gly Ala Ile Leu Pro Gln Asp Val Ser Val Thr Pro 635 640 645 Val Ala Thr Pro Val Pro Pro Glu Glu Gln Ala Asn Leu Trp Leu 650 655 660 Val Glu Ala Glu Ile Ser Pro Glu Leu Glu Lys Arg Leu Gly Arg 665 670 675 Lys Lys Lys Arg Arg Lys Arg Lys Lys Glu Val Cys Pro Leu Gly 680 685 690 Pro Ala Pro Glu Leu His His Ser Ala Pro Val Pro Ala Thr Ser 695 700 705 Ala Val Pro Arg Leu Pro Gln Leu Pro Arg Gln Lys Cys Leu Val 710 715 720 Ala Ala Asn Ala Trp Gly Thr Gly Glu Pro Cys Arg Gln Gly Ala 725 730 735 Trp Thr Val Val Ser Asn Pro Phe Cys Pro Glu Pro Ser Pro His 740 745 750 Gln Asp Pro Phe Leu Pro Gly Ala Ser Ala Pro Arg Val Trp Ala 755 760 765 Gln Gly Arg Leu Gln Gly Leu Gly Ser Ile His Ser Arg Thr Asn 770 775 780 Leu Met Glu Ala Glu Leu Leu Asp Ala Asp Ser Asp Phe Glu Gln 785 790 795 Lys Leu Ile Ser Glu Glu Asp Leu 800 803 16 793 PRT Artificial sequence Artificial sequence 1-793 16 Met Ala Ala Gly Arg Pro Val Arg Gly Pro Glu Leu Ala Pro Arg 1 5 10 15 Arg Leu Leu Gln Leu Leu Leu Leu Val Leu Leu Gly Gly Arg Gly 20 25 30 Arg Gly Ala Ala Leu Ser Gly Asn Val Thr Gly Pro Gly Pro Arg 35 40 45 Ser Ala Gly Gly Ser Ala Arg Arg Asn Ala Pro Val Thr Ser Pro 50 55 60 Pro Pro Pro Leu Leu Ser His Cys Gly Arg Ala Ala His Cys Glu 65 70 75 Pro Leu Arg Tyr Asn Val Cys Leu Gly Ser Ala Leu Pro Tyr Gly 80 85 90 Ala Thr Thr Thr Leu Leu Ala Gly Asp Ser Asp Ser Gln Glu Glu 95 100 105 Ala His Ser Lys Leu Val Leu Trp Ser Gly Leu Arg Asn Ala Pro 110 115 120 Arg Cys Trp Ala Val Ile Gln Pro Leu Leu Cys Ala Val Tyr Met 125 130 135 Pro Lys Cys Glu Asn Asp Arg Val Glu Leu Pro Ser Arg Thr Leu 140 145 150 Cys Gln Ala Thr Arg Gly Pro Cys Ala Ile Val Glu Arg Glu Arg 155 160 165 Gly Trp Pro Asp Phe Leu Arg Cys Thr Pro Asp His Phe Pro Glu 170 175 180 Gly Cys Pro Asn Glu Val Gln Asn Ile Lys Phe Asn Ser Ser Gly 185 190 195 Gln Cys Glu Ala Pro Leu Val Arg Thr Asp Asn Pro Lys Ser Trp 200 205 210 Tyr Glu Asp Val Glu Gly Cys Gly Ile Gln Cys Gln Asn Pro Leu 215 220 225 Phe Thr Glu Ala Glu His Gln Asp Met His Ser Tyr Ile Ala Ala 230 235 240 Phe Gly Ala Val Thr Gly Leu Cys Thr Leu Phe Thr Leu Ala Thr 245 250 255 Phe Val Ala Asp Trp Arg Asn Ser Asn Arg Tyr Pro Ala Val Ile 260 265 270 Leu Phe Tyr Val Asn Ala Cys Phe Phe Val Gly Ser Ile Gly Trp 275 280 285 Leu Ala Gln Phe Met Asp Gly Ala Arg Arg Glu Ile Val Cys Arg 290 295 300 Ala Asp Gly Thr Met Arg Phe Gly Glu Pro Thr Ser Ser Glu Thr 305 310 315 Leu Ser Cys Val Ile Ile Phe Val Ile Val Tyr Tyr Ala Leu Met 320 325 330 Ala Gly Val Val Trp Phe Val Val Leu Thr Tyr Ala Trp His Thr 335 340 345 Ser Phe Lys Ala Leu Gly Thr Thr Tyr Gln Pro Leu Ser Gly Lys 350 355 360 Thr Ser Tyr Phe His Leu Leu Thr Trp Ser Leu Pro Phe Val Leu 365 370 375 Thr Val Ala Ile Leu Ala Val Ala Gln Val Asp Gly Asp Ser Val 380 385 390 Ser Gly Ile Cys Phe Val Gly Tyr Lys Asn Tyr Arg Tyr Arg Ala 395 400 405 Gly Phe Val Leu Ala Pro Ile Gly Leu Val Leu Ile Val Gly Gly 410 415 420 Tyr Phe Leu Ile Arg Gly Val Met Thr Leu Phe Ser Ile Lys Ser 425 430 435 Asn His Pro Gly Leu Leu Ser Glu Lys Ala Ala Ser Lys Ile Asn 440 445 450 Glu Thr Met Leu Arg Leu Gly Ile Phe Gly Phe Leu Ala Phe Gly 455 460 465 Phe Val Leu Ile Thr Phe Ser Cys His Phe Tyr Asp Phe Phe Asn 470 475 480 Gln Ala Glu Trp Glu Arg Ser Phe Arg Asp Tyr Val Leu Cys Gln 485 490 495 Ala Asn Val Thr Ile Gly Leu Pro Thr Lys Lys Pro Ile Pro Asp 500 505 510 Cys Glu Ile Lys Asn Arg Pro Ser Leu Leu Val Glu Lys Ile Asn 515 520 525 Leu Phe Ala Met Phe Gly Thr Gly Ile Ala Met Ser Thr Leu Val 530 535 540 Trp Thr Lys Ala Thr Leu Leu Ile Trp Arg Arg Thr Trp Cys Arg 545 550 555 Leu Thr Gly His Ser Asp Asp Glu Pro Lys Arg Ile Lys Lys Ser 560 565 570 Lys Met Ile Ala Lys Ala Phe Ser Lys Arg Arg Glu Leu Leu Gln 575 580 585 Asn Pro Gly Gln Glu Leu Ser Phe Ser Met His Thr Val Ser His 590 595 600 Asp Gly Pro Val Ala Gly Leu Ala Phe Glu Leu Asn Glu Pro Ser 605 610 615 Ala Asp Val Ser Ser Ala Trp Ala Gln His Val Thr Lys Met Val 620 625 630 Ala Arg Arg Gly Ala Ile Leu Pro Gln Asp Val Ser Val Thr Pro 635 640 645 Val Ala Thr Pro Val Pro Pro Glu Glu Gln Ala Asn Leu Trp Leu 650 655 660 Val Glu Ala Glu Ile Ser Pro Glu Leu Glu Lys Arg Leu Gly Arg 665 670 675 Lys Lys Lys Arg Arg Lys Arg Lys Lys Glu Val Cys Pro Leu Gly 680 685 690 Pro Ala Pro Glu Leu His His Ser Ala Pro Val Pro Ala Thr Ser 695 700 705 Ala Val Pro Arg Leu Pro Gln Leu Pro Arg Gln Lys Cys Leu Val 710 715 720 Ala Ala Asn Ala Trp Gly Thr Gly Glu Pro Cys Arg Gln Gly Ala 725 730 735 Trp Thr Val Val Ser Asn Pro Phe Cys Pro Glu Pro Ser Pro His 740 745 750 Gln Asp Pro Phe Leu Pro Gly Ala Ser Ala Pro Arg Val Trp Ala 755 760 765 Gln Gly Arg Leu Gln Gly Leu Gly Ser Ile His Ser Arg Thr Asn 770 775 780 Leu Met Glu Ala Glu Leu Leu Asp Ala Asp Ser Asp Phe 785 790 793 17 793 PRT Homo sapiens 17 Met Ala Ala Gly Arg Pro Val Arg Gly Pro Glu Leu Ala Pro Arg 1 5 10 15 Arg Leu Leu Gln Leu Leu Leu Leu Val Leu Leu Gly Gly Arg Gly 20 25 30 Arg Gly Ala Ala Leu Ser Gly Asn Val Thr Gly Pro Gly Pro Arg 35 40 45 Ser Ala Gly Gly Ser Ala Arg Arg Asn Ala Pro Val Thr Ser Pro 50 55 60 Pro Pro Pro Leu Leu Ser His Cys Gly Arg Ala Ala His Cys Glu 65 70 75 Pro Leu Arg Tyr Asn Val Cys Leu Gly Ser Ala Leu Pro Tyr Gly 80 85 90 Ala Thr Thr Thr Leu Leu Ala Gly Asp Ser Asp Ser Gln Glu Glu 95 100 105 Ala His Ser Lys Leu Val Leu Trp Ser Gly Leu Arg Asn Ala Pro 110 115 120 Arg Cys Trp Ala Val Ile Gln Pro Leu Leu Cys Ala Val Tyr Met 125 130 135 Pro Lys Cys Glu Asn Asp Arg Val Glu Leu Pro Ser Arg Thr Leu 140 145 150 Cys Gln Ala Thr Arg Gly Pro Cys Ala Ile Val Glu Arg Glu Arg 155 160 165 Gly Trp Pro Asp Phe Leu Arg Cys Thr Pro Asp His Phe Pro Glu 170 175 180 Gly Cys Pro Asn Glu Val Gln Asn Ile Lys Phe Asn Ser Ser Gly 185 190 195 Gln Cys Glu Ala Pro Leu Val Arg Thr Asp Asn Pro Lys Ser Trp 200 205 210 Tyr Glu Asp Val Glu Gly Cys Gly Ile Gln Cys Gln Asn Pro Leu 215 220 225 Phe Thr Glu Ala Glu His Gln Asp Met His Ser Tyr Ile Ala Ala 230 235 240 Phe Gly Ala Val Thr Gly Leu Cys Thr Leu Phe Thr Leu Ala Thr 245 250 255 Phe Val Ala Asp Trp Arg Asn Ser Asn Arg Tyr Pro Ala Val Ile 260 265 270 Leu Phe Tyr Val Asn Ala Cys Phe Phe Val Gly Ser Ile Gly Trp 275 280 285 Leu Ala Gln Phe Met Asp Gly Ala Arg Arg Glu Ile Val Cys Arg 290 295 300 Ala Asp Gly Thr Met Arg Phe Gly Glu Pro Thr Ser Ser Glu Thr 305 310 315 Leu Ser Cys Val Ile Ile Phe Val Ile Val Tyr Tyr Ala Leu Met 320 325 330 Ala Gly Val Val Trp Phe Val Val Leu Thr Tyr Ala Trp His Thr 335 340 345 Ser Phe Lys Ala Leu Gly Thr Thr Tyr Gln Pro Leu Ser Gly Lys 350 355 360 Thr Ser Tyr Phe His Leu Leu Thr Trp Ser Leu Pro Phe Val Leu 365 370 375 Thr Val Ala Ile Leu Ala Val Ala Gln Val Asp Gly Asp Ser Val 380 385 390 Ser Gly Ile Cys Phe Val Gly Tyr Lys Asn Tyr Arg Tyr Arg Ala 395 400 405 Gly Phe Val Leu Ala Pro Ile Gly Leu Val Leu Ile Val Gly Gly 410 415 420 Tyr Phe Leu Ile Arg Gly Val Met Thr Leu Phe Ser Ile Lys Ser 425 430 435 Asn His Pro Gly Leu Leu Ser Glu Lys Ala Ala Ser Lys Ile Asn 440 445 450 Glu Thr Met Leu Arg Leu Gly Ile Phe Gly Phe Leu Ala Phe Gly 455 460 465 Phe Val Leu Ile Thr Phe Ser Cys His Phe Tyr Asp Phe Phe Asn 470 475 480 Gln Ala Glu Trp Glu Arg Ser Phe Arg Asp Tyr Val Leu Cys Gln 485 490 495 Ala Asn Val Thr Ile Gly Leu Pro Thr Lys Lys Pro Ile Pro Asp 500 505 510 Cys Glu Ile Lys Asn Arg Pro Ser Leu Leu Val Glu Lys Ile Asn 515 520 525 Leu Phe Ala Met Phe Gly Thr Gly Ile Ala Met Ser Thr Trp Val 530 535 540 Trp Thr Lys Ala Thr Leu Leu Ile Trp Arg Arg Thr Trp Cys Arg 545 550 555 Leu Thr Gly His Ser Asp Asp Glu Pro Lys Arg Ile Lys Lys Ser 560 565 570 Lys Met Ile Ala Lys Ala Phe Ser Lys Arg Arg Glu Leu Leu Gln 575 580 585 Asn Pro Gly Gln Glu Leu Ser Phe Ser Met His Thr Val Ser His 590 595 600 Asp Gly Pro Val Ala Gly Leu Ala Phe Glu Leu Asn Glu Pro Ser 605 610 615 Ala Asp Val Ser Ser Ala Trp Ala Gln His Val Thr Lys Met Val 620 625 630 Ala Arg Arg Gly Ala Ile Leu Pro Gln Asp Val Ser Val Thr Pro 635 640 645 Val Ala Thr Pro Val Pro Pro Glu Glu Gln Ala Asn Leu Trp Leu 650 655 660 Val Glu Ala Glu Ile Ser Pro Glu Leu Glu Lys Arg Leu Gly Arg 665 670 675 Lys Lys Lys Arg Arg Lys Arg Lys Lys Glu Val Cys Pro Leu Gly 680 685 690 Pro Ala Pro Glu Leu His His Ser Ala Pro Val Pro Ala Thr Ser 695 700 705 Ala Val Pro Arg Leu Pro Gln Leu Pro Arg Gln Lys Cys Leu Val 710 715 720 Ala Ala Asn Ala Trp Gly Thr Gly Glu Pro Cys Arg Gln Gly Ala 725 730 735 Trp Thr Val Val Ser Asn Pro Phe Cys Pro Glu Pro Ser Pro His 740 745 750 Gln Asp Pro Phe Leu Pro Gly Ala Ser Ala Pro Arg Val Trp Ala 755 760 765 Gln Gly Arg Leu Gln Gly Leu Gly Ser Ile His Ser Arg Thr Asn 770 775 780 Leu Met Glu Ala Glu Leu Leu Asp Ala Asp Ser Asp Phe 785 790 793 18 228 DNA Homo sapiens 18 ctggggctgt ccagttaccc caacggctac cccttcctct tctgggagca 50 gtacatcggc ctccgccact ggctgctgct gttcatcagc gtggtgttgg 100 cctgcacatt cctcgtgtgc gctgtcttcc ttctgaaccc ctggacggcc 150 gggatcattg tgatggtcct ggcgctgatg acggtcgagc tgttcggcat 200 gatgggcctc atcggaatca agctcagt 228 19 18 DNA Homo sapiens 19 aggcggggga tcacagca 18 20 18 DNA Homo sapiens 20 ataccaaaga gttccact 18 21 45 DNA Artificial sequence Artificial sequence 1-45 21 ctgcggcgct gcttcctgct ggccgtctgc atcctgctgg tgtgc 45 22 45 DNA Artificial sequence Artificial sequence 1-45 22 agagcacaga cgaggaaagt gcacaccagc aggatgcaga cggcc 45 23 21 DNA Artificial sequence Artificial sequence 1-21 23 actcctgact tgtagcagat t 21 24 21 DNA Artificial sequence Artificial sequence 1-21 24 aggctgcata cacctctcag a 21 25 18 DNA Artificial sequence Artificial sequence 1-18 25 gcttaggccc gaggagat 18 26 20 DNA Artificial sequence Artificial sequence 1-20 26 aactcacaac tttctctcca 20 27 48 DNA Artificial sequence Artificial sequence 1-48 27 ggattctaat acgactcact atagggccca atggcctaaa ccgactgc 48 28 46 DNA Artificial sequence Artificial sequence 1-46 28 ctatgaaatt aaccctcact aaagggaccc acggcctctc ctcaca 46 29 449 PRT Mus musculus 29 Met Glu Ser Pro Arg Ala Thr Gln Thr Pro Glu Ser Pro Lys Leu 1 5 10 15 Ser Gln Pro Arg Ala His Leu Ser Ala His Gln Ala Pro Ser Pro 20 25 30 Ala Ala Leu Pro Gly Tyr Pro Ala Met Ser Pro Ala Trp Leu Arg 35 40 45 Pro Arg Leu Arg Phe Cys Leu Phe Leu Leu Leu Leu Leu Leu Val 50 55 60 Pro Ala Ala Arg Gly Cys Gly Pro Gly Arg Val Val Gly Ser Arg 65 70 75 Arg Arg Pro Pro Arg Lys Leu Val Pro Leu Ala Tyr Lys Gln Phe 80 85 90 Ser Pro Asn Val Pro Glu Lys Thr Leu Gly Ala Ser Gly Arg Tyr 95 100 105 Glu Gly Lys Ile Ala Arg Ser Ser Glu Arg Phe Lys Glu Leu Thr 110 115 120 Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr 125 130 135 Gly Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp Arg Leu Asn 140 145 150 Ser Leu Ala Ile Ser Val Met Asn Gln Trp Pro Gly Val Lys Leu 155 160 165 Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His His Ser Glu Glu 170 175 180 Ser Leu His Tyr Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp 185 190 195 Arg Asp Arg Asn Lys Tyr Gly Leu Leu Ala Arg Leu Ala Val Glu 200 205 210 Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Lys Ala His Val His 215 220 225 Cys Ser Val Lys Ser Glu His Ser Ala Ala Ala Lys Thr Gly Gly 230 235 240 Cys Phe Pro Ala Gly Ala Gln Val Arg Leu Glu Asn Gly Glu Arg 245 250 255 Val Ala Leu Ser Ala Val Lys Pro Gly Asp Arg Val Leu Ala Met 260 265 270 Gly Glu Asp Gly Thr Pro Thr Phe Ser Asp Val Leu Ile Phe Leu 275 280 285 Asp Arg Glu Pro Asn Arg Leu Arg Ala Phe Gln Val Ile Glu Thr 290 295 300 Gln Asp Pro Pro Arg Arg Leu Ala Leu Thr Pro Ala His Leu Leu 305 310 315 Phe Ile Ala Asp Asn His Thr Glu Pro Ala Ala His Phe Arg Ala 320 325 330 Thr Phe Ala Ser His Val Gln Pro Gly Gln Tyr Val Leu Val Ser 335 340 345 Gly Val Pro Gly Leu Gln Pro Ala Arg Val Ala Ala Val Ser Thr 350 355 360 His Val Ala Leu Gly Ser Tyr Ala Pro Leu Thr Arg His Gly Thr 365 370 375 Leu Val Val Glu Asp Val Val Ala Ser Cys Phe Ala Ala Val Ala 380 385 390 Asp His His Leu Ala Gln Leu Ala Phe Trp Pro Leu Arg Leu Phe 395 400 405 Pro Ser Leu Ala Trp Gly Ser Trp Thr Pro Ser Glu Gly Val His 410 415 420 Trp Tyr Pro Gln Met Leu Tyr Arg Leu Gly Arg Leu Leu Leu Glu 425 430 435 Glu Ser Thr Phe His Pro Leu Gly Met Ser Gly Ala Gly Ser 440 445 449 30 228 DNA Homo sapiens 30 ctggggctgt ccagttaccc caacggctac cccttcctct tctgggagca 50 gtacatcggc ctccgccact ggctgctgct gttcatcagc gtggtgttgg 100 cctgcacatt cctcgtgtgc gctgtcttcc ttctgaaccc ctggacggcc 150 gggatcattg tgatggtcct ggcgctgatg acggtcgagc tgttcggcat 200 gatgggcctc atcggaatca agctcagt 228 31 32 DNA Artificial sequence Artificial sequence 1-32 31 tcgacaagca gggaacaccc aagtagaagc tc 32 32 32 DNA Artificial sequence Artificial sequence 1-32 32 tcgacaagca gggaagtggg aagtagaagc tc 32

Claims (28)

What is claimed is:
1. Isolated nucleic acid comprising DNA having at least a 95% sequence identity to (a) a DNA molecule encoding a patched-2 polypeptide comprising the sequence of amino acids 1 to about 1203 of FIG. 1 (SEQ ID NO:2), and encoding a polypeptide having patched-2 biological activity.
2. An isolated nucleic acid comprising DNA having at least a 95% sequence identity to (a) a DNA molecule encoding the same mature polypeptide encoded by the cDNA in ATCC Deposit No. 209778 designation:, or (b) the complement of the DNA molecule of (a).
3. The isolated nucleic acid of claim 5 comprising human patched-2 encoding sequence of the cDNA in ATCC deposit No. 209778 designation:, or a sequence which hybridizes thereto under stringent conditions.
4. A vector comprising the nucleic acid of claim 1.
5. The vector of claim 4 operably linked to control sequences recognized by a host cell transformed with the vector.
6. A host cell transformed with the vector of claim 4.
7. The host cell of claim 6 which is mammalian.
8. The host cell of claim 7 wherein said cell is a CHO cell.
9. The host cell of claim 6 which is prokaryotic.
10. The host cell of claim 9 wherein said cell is an E. coli.
11. The host cell of claim 7 wherein said cell is a yeast cell.
12. The host cell of claim 11 which is Saccharomyces cerevisiae.
13. A process for producing patched-2 polypeptides comprising culturing the host cell of claim 9 under conditions suitable for expression of vertebrate patched-2 and recovering patched-2 from the cell culture.
14. Isolated native sequence human patched-2 polypeptide comprising amino acid residues 1 to 1203 of FIG. 1 (SEQ ID NO:2).
15. Isolated native sequence human patched-2 polypeptide encoded by the nucleotide deposited under accession number ATCC 209778 Designation having patched-2 biological activity.
16. A chimeric molecule comprising vertebrate patched-2 polypeptide patched-2 to a heterologous amino acid sequence.
17. The chimeric molecule of claim 16 wherein said heterologous amino acid sequence is an epitope tag sequence.
18. The chimeric molecule of claim 17 wherein said heterologous amino acid sequence is a constant region of an immunoglobulin.
19. An antagonist of patched-2 which blocks, prevents, inhibits and/or neutralizes the Dhh function in the Dhh signaling pathway.
20. The antagonist of claim 19 which is a small bioorganic molecule.
21. The antagonist of claim 19 which is an antisense nucleotide.
22. An agonist of patched-2 with stimulates or enhances the normal functioning of patched-2 in the Dhh signaling pathway.
23. The agonist of claim 22 which prevents Smo (SEQ ID NO:17) inactivation of Ptch-2 (SEQ ID NO:2).
24. The agonist of claim 22 which is a small bioorganic molecule.
25. The agonist of claim 24 which is a small bioorganic molecule.
26. A method of screening for antagonists or agonists of patched-2 biological activity comprising:
(a) exposing patched-2 expressing target cells in culture to a candidate compound and Dhh; and
(b) analyzing cells for binding of Dhh to patched-2; or
(c) scoring phenotypic or functional changes in the treated cells;
and comparing the results to control cells which were not exposed to the candidate compound.
27. A method of screening for antagonist or agonist molecule of patched-2 biological activity comprising:
(a) exposing a patched-2 ligand and a compound having patched-2 biological activity to a candidate antagonist or agonist; and
(b) analyzing the substrate for binding of the ligand to the compound; and
comparing the results to control reactions which were not exposed to the candidate molecule.
28. A method of diagnosing to determine whether a particular disorder is modulated by Dhh signaling, comprising:
(a) culturing test cells or tissues;
(b) administering a compound which can inhibit patched-2 modulated Dhh signaling; and
(c) analyzing the level of Dhh binding to patched-2 or Dhh mediated phenotypic effects in the test cells.
US09/990,046 1998-04-15 2001-11-20 Patched-2 antibodies Abandoned US20020156245A1 (en)

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US5225539A (en) 1986-03-27 1993-07-06 Medical Research Council Recombinant altered antibodies and methods of making altered antibodies
US5789543A (en) * 1993-12-30 1998-08-04 President And Fellows Of Harvard College Vertebrate embryonic pattern-inducing proteins and uses related thereto
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US6261786B1 (en) * 1993-12-30 2001-07-17 Imperial Cancer Res. Technology Screening assays for hedgehog agonists and antagonists
AU4001195A (en) 1994-10-07 1996-05-02 Board Of Trustees Of The Leland Stanford Junior University Patched genes and their use
US6027882A (en) 1994-10-07 2000-02-22 The Regents Of The University Of California Patched genes and their use for diagnostics
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US6309879B1 (en) * 1997-12-08 2001-10-30 Curis, Inc. Human patched genes and proteins, and uses related thereto

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