Abstract:
The role of synaptic adhesion molecules in human cell development and function is largely unknown. This invention provides methods to study β-cell function in native tissue through the use of novel adhesion and migrations assays. Through the use of these assays, the inventors have been able to for the first time describe the contribution of SAMs to human β-cell adhesion, spreading, and motility. Furthermore, the inventors have used the results of these assays to develop methods for detection, treatment, and prevention of diseases related to the pancreas.

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
       [0001]    This application claims priority from U.S. Provisional Application Ser. No. 60/706,133 filed on Aug. 4, 2005, which is incorporated herein by reference in its entirety. 
     
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT 
       [0002]    This invention was made in part with Government support under National Institutes of Health Grant DK02944. The Government has certain rights in the invention. 
     
    
     INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ON A COMPACT DISC 
       [0003]    Not Applicable. 
       BACKGROUND OF THE INVENTION 
       [0004]    1. Field of the Invention 
         [0005]    The present invention relates generally to synaptic adhesion molecules and their role in pancreatic islet β-cells and, in particular, methods for imaging, isolating, and detecting the islets as well as inhibiting, treating and reversing diseases related to β-cell and pancreatic abnormalities. 
         [0006]    2. Description of Related Art 
         [0007]    Synaptic adhesion molecules are a disparate family of cell surface proteins involved in the adhesion of cells at synaptic junctions. The main constituents of synaptic adhesion molecules are members of the cadherin family and immunoglobulin superfamily. Synaptic adhesion molecules are thought to serve a plethora of functions, ranging from adhesion and cellular signaling to synaptic differentiation. Recent research has identified a synaptic adhesion molecule, SynCAM, as a molecule located at the synaptic junction. Two other known groups of synaptic adhesion molecules include neuroligins (e.g., neuroligin 1, neuroligin 2, neuroligin 3, neuroligin 4X and neuroligin 4Y) and neurexins (e.g., neurexin 1α, neurexin 2α, neurexin 3α, neurexin 1β, neurexin 2β, and neurexin 3β). The sequences of these polypeptides are known in the art and are available on the Internet at National Center for Biotechnology Information (“NCBI”), http://www.ncbi.nlm.nih.gov. 
         [0008]    As the incidence of diabetes increases, so too does the need for more improved diagnostic and treatment modalities. Islet β-cell transplantation has emerged as a key therapy in the treatment of type 1 diabetes. Although β-cell transplantation has met with some success, the treatment is fraught with numerous problems. Although, β-cell transplantation is initially effective for many patients, over time the recipient&#39;s ability to maintain insulin independence diminishes. The causes of this loss of independence are not known although a loss of β-cell mass is believed to be one cause. Because distinct β-cell specific cell surface proteins have not heretofore been identified, this has made determining the exact cause difficult. 
         [0009]    The ability to measure islet β-cell mass in vivo is of great interest to researchers and clinicians alike. Cell-surface proteins specific enough to be targeted for imaging and treatment have not heretofore been obtained which has hindered research in the areas of pancreatic cancer and, especially, diabetes mellitus. There are no known cell surface markers expressed in islet, β-cells of the pancreas that are specific enough to β-cells to be used for imaging or treatment. 
       BRIEF SUMMARY OF THE INVENTION 
       [0010]    Accordingly, it is an object of the invention to overcome these and other problems associated with the related art. These and other objects, features and technical advantages are achieved by targeting synaptic adhesion molecules expressed on islet β-cells, which include neuroligin 1, neuroligin 2, neuroligin 3, neuroligin 4X, neuroligin 4Y, neurexin 1α, neurexin 2α, neurexin 3α, neurexin 1β, neurexin 2β, neurexin 3β, SynCam, Thy-1, and neuronal pentraxin (hereinafter “SAMs”) and/or neuropilin 1 (sequences available at NCBI, supra) on the surface of β-cells, particularly pancreatic islet, β-cells. 
         [0011]    In accordance with a further aspect of the present invention, a method is provided for treating pancreatic disease such as diabetes mellitus or islet cell carcinoma by administering to a mammal in need thereof a therapeutically effective amount of an agent that selectively binds SAMs and/or neuropilin 1. The agent provided may be any of the classes of molecules and delivered by the various routes described herein. 
         [0012]    In accordance with yet another aspect of the present invention, a method is provided for treatment of autoimmune diabetes mellitus by administering to a mammal in need thereof a therapeutically effective amount of an agent capable of binding a component of the immunologic synapse. The component of the immunologic synapse targeted may be selected from the group consisting of SynCam, Thy-1 and neuropilin 1. 
         [0013]    This invention provides a method for imaging, targeting, detecting, identifying, and separating cells expressing SAMs and/or neuropilin 1, particularly pancreatic islet β-cells comprising treating cells with an agent capable of specifically binding to pancreatic islet β-cells. In one aspect of the present invention, the mammal is human. In accordance with a further aspect of the invention the agent is selected from the group consisting of an antibody, antibody fragment, polypeptide, polynucleotide, and aptamer. In one aspect of the present invention, the agent is an antibody. The antibody could be selected from the group consisting of a polyclonal, monoclonal, chimeric, or single chain antibody. The antibody fragments could consist of Fab fragments or Fab expression library. 
         [0014]    In yet another aspect of the current invention the agent can be a conjugate of a first compound and a second compound. For the purpose of detecting cells expressing SAMs and/or neuropilin 1 or treating a disease, the second agent can be a radioisotope or paramagnetic ion. In yet another aspect of the invention the disease to be treated can be diabetes, in particular diabetes mellitus, and more particularly autoimmune diabetes mellitus, pancreatic cancer, particularly metastatic pancreatic cancer. 
         [0015]    In accordance with a further aspect of the present invention, agents targeting SAMs and/or neuropilin 1 on the surface of islet, β-cells may be used to determine β-cell mass. β-cell mass may be monitored over time by repeated imaging using the methods of the present invention. 
         [0016]    In accordance with yet another aspect of the present invention, a method is provided for identifying agents capable of binding SAMs and/or neuropilin 1 by providing an immobilized SAMs and/or neuropilin 1 and incubating the immobilized molecule in the presence of a sample to be assayed. The immobilize molecule is subsequently removed from the sample and it is determined whether an agent is bound thereto. 
         [0017]    In accordance with yet another aspect of the present invention, a method is provided for detecting β-cell tumors by administering to a mammal in need thereof an effective amount of an agent capable of binding SAMs and/or neuropilin 1, imaging the β-cells of the mammal, and determining the presence or absence of tumors by use of the images generated. Over time, the progression or regression of a tumor may be monitored by this method. 
         [0018]    In yet another aspect of the present invention, kits are provided containing the necessary reagents to carry out the methods as described above and further herein. 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         [0019]      FIG. 1A . Depiction of neuroligin 2 and neurexin 1 staining to be, β-cell specific. 
           [0020]      FIG. 1B : Depiction of another view of neurexin 1 staining to be β-cell specific. 
           [0021]      FIG. 2 . Depiction of SynCam specificity islet specificity. 
           [0022]      FIG. 3 . NL-2 (neuroligin 2) is expressed in Beta cells. PCR data (human brain and islet cDNA, NT=negative control). INS-1 is a commonly used cell line used to study the biology of the pancreatic islet β cells. 
           [0023]      FIG. 4 . Western blot: neuroligin 1 in mouse brain, rat brain (on left) and two insulin-producing Beta cell lines (NIT and INS-1; on right) but not the alpha cell line alpha-TC6 (3rd lane). Antibody was monoclonal antibody (4C12) specific for neuroligin 1. 
           [0024]      FIG. 5 . NL-1 immunostaining. Neuroligin 1 is in the Beta cell line INS-1. 
           [0025]      FIG. 6 . An antibody to NL-1 stains islets in rat pancreas sections. 
           [0026]      FIG. 7 . Immunostaining for neurexin 1. Neurexin 1 is in pancreatic islets (on left; pancreas staining is islet-specific) and in the insulin-producing INS-1 Beta cell line. 
           [0027]      FIG. 8 . Immunostaining for SynCam. SynCam is present on the surface of the islet Beta cell line INS-1. 
           [0028]      FIG. 9 . Polymerase chain reaction using gene-specific primers shows that the neuroligins (NLs) and neurexins (Nrxn) are expressed in human islets (Is) and the rat-derived islet Beta cell line INS-1 (I) and the mouse-derived islet Beta cell line Nit-1 (N). As expected, the genes are also expressed in brain (Br). 
           [0029]      FIG. 10 . Neuroligins 1 and 2 are involved in insulin secretion. Increased insulin secretion is evident after overexpression (by gene transfection) of NL-1 and NL-2 in the Beta cell line INS-1. “Mock” is a control with no neuroligin overexpression. 
           [0030]      FIG. 11 . Neuroligins 3 and 4 are involved in insulin secretion. Increased insulin secretion is evident after overexpression (by gene transfection) of NL-1 and NL-2 in the Beta cell line INS-1. “Mock” is a control with no neuroligin overexpression. 
           [0031]      FIG. 12 . Expression of Neurexin 1 and Neuroligin 1 Protein in Islets and Islet cell lines. To determine whether neurexin and neuroligin proteins are expressed in islets, western blot analysis was performed using a goat polyclonal antibody to neurexin 1 and a mouse monoclonal antibody to neuroligin 1 (4C12). Neurexin 1b was detected in the b-cell lines Ins-1 and NIT, as well as in both human and rat islet extracts. Neuroligin 1 was only detected in INS-1 and NIT cells. In all experiments, protein extract from rat, mouse and human brains were used as positive controls. Since Neuroligin 1 was not detected in Human or Rat Islets, we suspected that the method used to isolate islets affected detection of it. It is notoriously difficult to detect cell surface proteins via WB analysis due to digestive enzymes produced in the pancreas. To determine of NL-1 was sensitive to some of these enzymes, we treated the beta-cell line NIT with trypsin. Here, we show that neuroligin is sensitive to trypsin. We also demonstrated that neurexin is not. In doing this experiment, we also confirmed that neurexin was expressed on the cell surface of NIT cells. 
           [0032]      FIG. 13 . Cell Surface Expression of Neurolign 1 in the NIT b-cell line. To determine if Neuroligin 1 is expressed on the cell surface, NIT cells were plated in flasks, cultured for 48 hours and either treated with or without trypsin. Protein was then extracted and western blot analysis was performed with equal amounts of protein using monoclonal neuroligin 1 antibody. Neuroligin 1 was decreased in cells treated with trypsin, suggesting that it is expressed on the cell surface of NIT cells. As a negative control, the same experiment was performed probing for the intracellular protein gephryin. As expected, gephyrin was not affected by treatment of cells with trypsin. (+, trypsin; −, not treated with trypsin). 
           [0033]      FIG. 14 . Expression of neurexin and neuroligin RNA in Human pancreatic Islets and Rat and Mouse b-cell lines. To determine whether neurexin and neuroligin messages are expressed in islets, RT-PCR analysis was performed on (A) human pancreatic islets, (B) INS-1 cells, (C) NIT cells and (D) human fetal pancreas using gene specific primers to all neurexin (Nrxn) and neuroligin (NL) family members. In all experiments, brain RNA from the appropriate species was used as a positive control. (Br, brain; Is; human islets; Nt, no template; I, INS-1 cells; N, NIT cells; P, human fetal pancreas; Nrxn, neurexin; NL, neuroligin). 
           [0034]      FIG. 15 . Data from fluorescent activated cell sorting (FACS) obtained using human pancreatic cells. Cells were labeled with antibodies to proinsulin and to the extracellular domain of SynCam (an antibody of chicken egg origin). Left panel: control chicken antibody (IgY) does not enable sorting for proinsulin-positive cells, Center panel: A large fraction of the cells with high labelling by the extracellular SynCam antibody (towards the right) also exhibit high proinsulin antibody labelling (towards the top). Right panel: Cell with high amylase expression (in other words, pancreatic acinar [non-islet] cells) did not label with SynCam (the acinar cells were towards the left). Conclusion: Sorting pancreatic cells with SynCam enables purification of the insulin-producing islet beta cells from the pancreatic acinar cells (which comprise most of the 98% of the pancreas that is non-islet). Sorting with SynCam yields a population of cells greatly enriched for beta cells. 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Abbreviations and Definitions 
       [0035]    Unless otherwise defined, all technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Commonly understood definitions of molecular biology terms can be found in Rieger et al., G LOSSARY OF  G ENETICS : C LASSICAL AND  M OLECULAR,  5 th  edition, Springer-Verlag; New York, 1991; and Lewin, GENES V, Oxford University Press; New York, 1994. To facilitate the understanding of the invention, a number of terms and abbreviations as used herein are defined below as follows: 
         [0036]    Bind(s) or Interacts With: As used herein, the terms “bind,” or “interacts with” refers to an activity wherein one molecule recognizes and adheres to a particular second molecule in a sample, but does not substantially recognize or adhere to other structurally-unrelated molecules in the sample. Generally, a first molecule that “specifically binds” to a second molecule has a binding affinity greater than about 10 5  to 10 6  moles/liter for that second molecule. 
         [0037]    Nucleic Acid or Nucleic Acid Molecule or polynucleotide: As used herein, the terms “nucleic acid” or “nucleic acid molecule” refer to a chain of two or more nucleotides such as RNA (ribonucleic acid) and DNA (deoxyribonucleic acid). 
         [0038]    Pharmaceutically Acceptable: As used herein, the term “pharmaceutically acceptable” means approved by a regulatory agency or authority, either national (e.g. the FDA), supra-national (e.g. the EMEA), or other regulatory agency, governmental entity, ethics board, or committee involved in the granting of Regulatory Approval, or a state government, or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals and, more particularly, in humans. 
         [0039]    Pharmaceutically Acceptable Carrier: As used herein, the term “pharmaceutically acceptable carrier” refers to a diluent, adjuvant, excipient, or vehicle with which an agent is administered. Such carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil, tocopherols and the like, polyethylene glycols, glycerine, propylene glycol, or other synthetic solvents. Water is a preferred carrier when an agent is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol, or and compound found in the  Handbook of Pharmaceutical Excipients  (4 th  edition, Pharmaceutical Press) and the like. An agent, if desired, can also contain minor amount of wetting or emulsifying agents, or pH buffering agents such as acetates, citrates, or phosphates. Antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; and agents for the adjustment of tonicity such as sodium chloride or dextrose may also be a carrier. 
         [0040]    Protein or Polypeptide: As used herein, the terms “protein” or “polypeptide” mean any peptide-linked chain of amino acids, regardless of length or post-translational modification, e.g. glycosylation or phosphorylation. 
         [0041]    Therapeutically Effective Amount: As used herein, the term “therapeutically effective amount” refers to those amounts that, when administered to a particular subject in view of the nature and severity of that subject&#39;s disease or condition, will have a desired therapeutic effect, e.g. an amount which will cure, prevent, inhibit, or at least partially arrest or partially prevent a target disease or condition. 
         [0042]    Methods for Treating and Detecting Beta-Cell Disease 
         [0043]    The present invention relates to a method for imaging, treating, separating and identifying islet β-cells using β-cell specific molecules present on the surface thereof. In one aspect of the present invention, a class of molecules known collectively as SAMs are utilized. SAMs have previously been thought to be expressed only in neurons. It has been surprisingly discovered, however, that such molecules are also expressed in pancreatic islet β-cells. In another aspect of the present invention, neuropilin 1, a member of the immunological synapse (but not a synaptic adhesion molecule) is used in the present method. 
         [0044]    The SAM and neuropilin sequences of the invention include: Neuroligin 1 (NCBI Accession No: NM — 014932, SEQ ID NO: 1); Neuroligin 2 (NCBI Accession Nos: NM — 020795 and AF376802, SEQ ID NOs: 2 and 3); Neuroligin 3 (NCBI Accession No: NM — 018977, SEQ ID NO: 4); Neuroligin 4Y (NCBI Accession No: AF376804, SEQ ID NO: 5); Neuroligin 4X (NCBI Accession No: AF376803, SEQ ID NO: 6); Neurexin 1 Alpha (NCBI Accession No: NM — 004801, SEQ ID NO: 7); Neurexin 1 Beta (NCBI Accession No: NM — 138735, SEQ ID NO: 8); Neurexin 2 alpha (NCBI Accession Nos: NM — 015080, NM — 138732, SEQ ID NOs: 9 and 10); Neurexin 2 beta (NCBI Accession No: NM — 138734, SEQ ID NO: 11); Neurexin 3 alpha (NCBI Accession Nos: NM — 004796, NM — 004796, SEQ ID NOs: 12 and 13); Neurexin 3 beta (NCBI Accession No: NM — 138970, SEQ ID NO: 14); Syncam (NCBI Accession No: NM — 014333, SEQ ID NO: 15); THY-1 (NCBI Accession No: BC065559, SEQ ID NO: 16); and Neuropilin 1 (NCBI Accession Nos: NM — 003873 NM — 001024628 NM — 001024629, SEQ ID NOs: 17, 18 and 19). The invention also includes SAM and neuropilin proteins including SAM and neurolipin variants, fragments, analogs and the like as described below. 
         [0045]    Previously published articles in the art claim that neuropilin 1 is not expressed in the pancreas. It has been surprisingly found that this molecule is, in fact, expressed in the β-cells of the pancreas. The presence of SAMs and/or neuropilin 1 on β-cells may be utilized to assess β-cell mass, location, presence, and depletion as they relate to certain diseases such as pancreatic cancer and diabetes mellitus. 
         [0046]    Because the blood brain barrier functions to prevent the transmission of macromolecules circulating in the body from entering the nervous tissue—an immune privileged site—the present method results specifically in the imaging, identification, treatment, and separation of SAMs on pancreatic islet β-cells. Thus, SAMs are a preferred target for imaging and treating pancreatic diseases. 
         [0047]    The current invention provides a method for detecting both in vitro and in vivo, and imaging pancreatic islets, β-cells in vitro and in vivo by administering to a mammal an agent capable of selectively binding to SAMs and/or neuropilin 1 molecules present on the surface of pancreatic islet β-cells. Experiments using the polymerase chain reaction have revealed that the SAMs expressed in islet β-cells include neuroligin 1, neuroligin 2, neuroligin 3, neuroligin 4X, neuroligin 4Y, neurexin 1α, neurexin 2α, neurexin 3α, neurexin 1β, neurexin 2β, neurexin 3β, SynCam, Thy-1, and neuronal pentraxin. In accordance with a further aspect of the invention the agent is selected from a group consisting of an antibody, antibody fragment, variable region of an antibody, protein, polypeptide, nucleic acids, probes, oligonucleotides, and ribozymes. The various aspects of the agent are described more fully below. 
         [0048]    Antibodies 
         [0049]    Antibodies that specifically recognize and bind to SAM and/or neuropilin 1 protein are useful in the invention. For example, such antibodies can be used for detection and modulation of SAM function. Antibodies within the scope of the invention include, for example, polyclonal antibodies, monoclonal antibodies, and antibody fragments. Engineering, production, purification, fragmentation, and use of various types of antibodies is well known in the art. See generally, Carter (2006) Nat Rev Immunol. 6(5), 343-357; Teillaud (2005) Expert Opin Biol Ther. 5 (Supp. 1) S15-27; Subramanian, ed. (2004) Antibodies: Volume 1: Production and Purification, Springer, ISBN 0306482452; Lo, ed. (2003) Antibody Engineering Methods and Protocols, Humana Press, ISBN 1588290921; Ausubel et al., ed. (2002) Short Protocols in Molecular Biology 5th Ed., Current Protocols, ISBN 0471250929; Brent et al., ed. (2003) Current Protocols in Molecular Biology, John Wiley &amp; Sons Inc, ISBN 047150338X; Coligan (2005) Short Protocols in Immunology, John Wiley &amp; Sons, ISBN 0471715786. 
         [0050]    Polyclonal Antibodies 
         [0051]    Polyclonal antibodies are heterogeneous populations of antibody molecules that are obtained from immunized animals, usually from sera. Polyclonal antibodies may be readily generated by one of ordinary skill in the art from a variety of warm-blooded animals, as well known in the art and described in the numerous references listed above. Further, polyclonal antibodies can be obtained from a variety of commercial sources. 
         [0052]    Monoclonal Antibodies 
         [0053]    Monoclonal antibodies are homogeneous populations of antibodies to a particular antigen. In contrast to polyclonal antibodies that may be specific for several epitopes of an antigen, monoclonal antibodies are usually specific for a single epitope. Generally, monoclonal antibodies are produced by removing B-cells from the spleen of an antigen-challenged animal (wherein the antigen includes the proteins described herein) and then fusing with myeloma tumor cells that can grow indefinitely in culture. The fused hybrid cells, or hybridomas, multiply rapidly and indefinitely and can produce large amounts of antibodies. The hybridomas can be sufficiently diluted and grown so as to obtain a number of different colonies, each producing only one type of antibody. The antibodies from the different colonies can then be tested for their ability to bind to the antigen, followed by selection of the most effective. 
         [0054]    In particular, monoclonal antibodies can be obtained by any technique that provides for the production of antibody molecules by continuous cell lines in culture such as those described in references listed above. Further, monoclonal antibodies can be obtained from a variety of commercial sources. 
         [0055]    Such antibodies can be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. Preferably, the antibody is of the IgG immunoglobulin class. A hybridoma producing a mAb of the invention may be cultivated in vitro or in vivo. The ability to produce high titers of mAbs in vivo makes this a particularly useful method of production. MAbs generally have a longer terminal half life than many antibody fragments, translating into greater uptake, that can be desirable for therapeutic applications. 
         [0056]    MAbs can be selected on the basis of their (a) specificity, (b) high binding affinity, (c) isotype, and (d) stability. MAbs can be screened or tested for specificity using any of a variety of standard techniques, including Western Blotting (Koren, E. et al., Biochim. Biophys. Acta 876:91-100 (1986)) and enzyme-linked immunosorbent assay (ELISA) (Koren et al., Biochim. Biophys. Acta 876:91-100 (1986)). 
         [0057]    These monoclonal antibodies will usually bind with at least a KD of about 1 mM, more usually at least about 300 μM, typically at least about 10 μM, more typically at least about 30 μM, preferably at least about 10 μM, and more preferably at least about 3 μM or better. 
         [0058]    Antibody Fragments 
         [0059]    It may be desirable to produce and use functional antibody fragments, for example Fab, F(ab′)2, F(ab′)2, F(ab′)3, Fc, single chain Fv (scFv), scFV-Fc, (scFv)2, dsFv, Vh, Vl, Minibody, Diabody, Triabody, Tetrabody. Generally, these alternative antibody formats can span a molecular-weight range of 12-150 kDa; a valency (n) range from monomeric (n=1), dimeric (n=2), trimeric (n=3), tetrameric, or even higher; and antigen-binding specificities from 1 to more than three antigens or epitopes on the same antigen. 
         [0060]    These fragments will generally include hypervariable regions containing stretches of amino acid sequences known as complementarity determining regions, which are responsible for the antibody&#39;s specificity for one particular site on an antigen molecule. A building block that can be used to create various antibody formats is the single-chain variable (V)-domain antibody fragment (scFv), which comprises V domains from the heavy and light chain (VH and VL domain) joined by a peptide linker of up to about 15 amino-acid residues. Preferably, the scFV antibody fragment is composed of the VL-domain-peptide-linker-VH-domain topology or the VH-domain-peptide-linker-VL-domain topology. 
         [0061]    Techniques for designing, producing, purifying, screening, antibody fragments are well known in the art as described in the numerous references cited above. For example, filamentous phage display expressing large combinatorial libraries of human VH and VL make it possible to select for specific fragments (see e.g., Hoogenboom (2002) Methods Mol. Biol. 178, 1-37, providing a review of antibody phage display technology). Phage-display selection technology can also be utilized to, for example, optimize binding affinity; select for specific binding properties, such as species cross-reactivity; or obtain large (e.g., over 1,000) collections of specific antibodies to identify combinatorial properties or very high potency. Antibody fragments produced via phage display can be reformatted through high-throughput methods into various other forms of antibodies, such as IgG, as known in the art. As another example, generation and isolation of high-affinity antibodies can be based upon the use of hypermutating B cell lines and on a selection process initiated at a very low affinity threshold (see e.g., Cumber et al. (2002) Nat. Biotechnol. 20, 1129-1134). As a further example, antibody fragments can be produced by ribosome display library screening, involving selection, recovery, amplification, and expression of antibody fragment mRNAs, optionally followed by reformatting of VH and VL (see e.g., Hanes et al. (2000) Nat. Biotechnol. 18, 1287-1292). As yet another example, using multiplex yeast library screening involving C-terminus fusion to the mating adhesion receptor of  Saccharomyces cerevisiae , antibody fragments from a randomly mutated library can be selected and isolated (see e.g., Feldhaus et al. (2003) Nat. Biotechnol. 21, 163-170). 1 
         [0062]    Also, the antibody fragments described herein can be reformatted through high-throughput methods to, for example, IgG molecules. See e.g., Carter et al. (2006) Nat Rev Immunol. 6(5), 343-357, 347. Antibody fragments can be desirable to avoid Fc-dependent effector functions. And, after PEGylation, antibody fragments can show a broad range of pharmacokinetic properties. Because of more efficient tumor penetration and faster clearance, antibody fragments can be desirable for imaging applications. And a monovalent antibody fragment can be more desirable than a bivalent form, such as IgG, for use as a receptor antagonist that can block ligand binding to a receptor without crosslinking and potentially activate the receptor. 
         [0063]    Antibody-Based Fusion Molecules 
         [0064]    Antibody-based fusion molecules exhibiting at least two different modules with bifunctional activities can be produced from molecular engineering techniques known in the art. Engineered fusion molecules contain a flexible linker between the two modules. The linker can be, for example, derived from the hinge region of an IgG isotope, a small stretch of hydrophobic amino acids such as the (Gly4Ser)3 motif, or a few amino acids corresponding to a DNA enzyme restriction site. 
         [0065]    Generally, two types of antibody-based fusion molecules can be engineered. The first type of antibody-based fusion molecules are molecules that retain antibody specificity fused to enzymes, toxins, growth factors, chemokines, cytokines, etc. The target recognition module can be antibody fragments or whole antibodies. For example, the target module can be fused to a toxin module such as  Pseudomonas  toxin, ricin, diphtheria toxin, or other toxins known to the art. As another example, the target module can be fused to an enzyme, preferably an enzyme used to generate a toxic product from a prodrug. This strategy, termed ADPET (antibody-directed enzyme prodrug therapy) is based on the pretargeting of, for example, tumor cells by the fusion molecule, which is injected systemically and allowed to clear from normal tissue. Glycosolation can improve control and clearance from non-target tissue sites. A nontoxic prodrug is then infused and transformed by the enzyme to a bioactive agent at the target site. As another example, fusion reagents for various ELISAs can be generated by fusing an antibody with alkaline phosphatase. 
         [0066]    An alternative to bifunctional molecules include bispecific antibodies (BsAbs) that crosslink effector and target cells (see e.g., Weiner and Adams (2000) Oncogene 19, 6144-6151). BsAbs facilitate pretargetting strategies where a BsAb is first infused, followed by injection of molecules such as radiolabelled haptens, drugs, or cytokines, which allows concentrating effector molecules in the vicinity of the cells to which the BsAb is bound (see e.g., Chang et al. (2002) Mol. Cancer. Ther. 1, 553-563). 
         [0067]    The second type of antibody-based fusion molecules act as competitors of surface molecules for ligand binding or as soluble decoy receptors for capturing soluble ligands (see e.g., Teillaud (2005) Expert Opin Biol Ther. 5(Suppl 1) S15-27). Generally, these fusion molecules contain an Fc region (e.g., Fc derived from IgG1 or IgG4) and are secreted under dimeric forms by mammalian cells, such as CHO or NS1 cells, due to formation of a disulfide bridge between each of the expressed single-strand fusion protein via the three cysteines present in the Fc region. This dimeric recombinant form can bind the target molecule with an avidity higher than the monovalent equivalent. Furthermore, the Fc region increases the serum-half life and tissue diffusion, facilitates clearance of the immune complexes, and/or stabilizes interactions of the fusion molecule with its target antigen by interacting also with FcγRs expressed by immune cells. 
         [0068]    Engineering Antibodies for Reduced Immunogenicity 
         [0069]    Chimeric, humanized, and fully human MAbs can effectively overcome potential limitations on the use of antibodies derived from non-human sources, this providing decreased immunogenicity with optimized effector functions. Such agents can be produced through protein engineering (e.g., complementarity-determining region grafting), through library technologies (e.g., phage, yeast, or ribsome display), or by MAb generation in transgenic mice. 
         [0070]    Generally, chimeric and humanized antibodies will contain an Fc region derived from human IgG1, because this subclass exhibits characteristics (FcγRs binding, serum half-life) and functional properties (ADCC, phagocytosis, endocytosis, complement activation) adequate for immune intervention. To avoid triggering of effector functions (i.e., complement activation and functional properties triggered by FcγRs binding) and to decrease nonspecific binding to normal tissues, it is preferable to use the Fc region of human IgG2 or IgG4. Antibody fragments for use in developing chimeric and humanized antibodies can be produced by any of the methods discussed above, including but not limited to, phage display library screening, hypermutating B cell lines, ribosome display library screening, and yeast display library screening. 
         [0071]    Chimeric antibodies can be obtained by joining the variable domains of, for example, a mouse monoclonal antibody to the constant domains of human heavy and light chains. Such an approach can address the sometimes high immunogenicity of foreign proteins in humans, the weak interactions and inefficient effector functions that non-human antibodies can have with human complement and FcγRs, and the reduced terminal half-life of non-human antibodies that can occur in human system. Expression vectors can be built to contain appropriate cloning sites allowing the in-frame cloning of the rodent leader heavy-chain variable domain (VH) cDNA and leader-light chain variable domain (VL) cDNA, 5′ of DNA sequences coding human IgG Fc region and Cκ domain, respectively. Thus, reshaped VH and VL cDNA together with leader sequences can be cloned into expression vectors that contain human constant regions. 
         [0072]    Humanized antibodies can be obtained by grafting complementarity determining regions (CDRs) derived from murine antibodies with desired specificity onto human VH and VL frameworks (FRs) (see e.g., Teillaud (2005) Expert Opin. Biol. Ther. 5(1), S15-S27). Further, transfer of one or more framework-region residues from the parent mouse antibody can result in the generation of humanized antibodies with a high binding affinity for antigen. Antibody humanization generally requires analysis of the primary amino acid sequences of the mouse variable domains to identify the residues involved in the antigen-binding site formation. Alternatively, in variable domain resurfacing, humanization of murine mAbs can be based on systematic analysis of known antibody structures to determine the solvent accessibility distributions of amino acid residues in murine and human variable regions (see e.g., Roguska et al. (1994) Proc. Natl. Acad. Ci. USA 91, 969-973; Delagrave et al. (1999) Protein Eng. 12, 357-362). The identified murine surface residues pattern can be converted to a human pattern with only a few amino acid changes. 
         [0073]    It can often desirable to obtain species-cross reactive antibodies, allowing the biological function of the antibodies to be evaluated and/or utilized in animal models of disease. Selection of humanized antibodies with species cross-reactivity can be accomplished with, for example, phage-display libraries. 
         [0074]    Fully human antibodies can be derived by several means known to the art. For example, phage display As another example, gene inactivation and insertion of large human DNA fragments from yeast artificial chromosome or human chromosome fragments in mouse germline can produce transgenic mice capable of producing fully human antibodies following immunization (see e.g., Tomizuka et al. (2000) Proc. Nat. Acad. Sci. USA 97, 722-727). Such mice can generate a repertoire of human sequence immunoglobulins and, additionally, their spleen cells can be fused to mouse myeloma cells for generating hybridomas secreting human IgG antigen-specific antibodies exhibiting high affinity. Alternatively, transgenic mice such as double trans-chromosomic/double knockout mice can mount an antigen-specific human antibody response following immunization, and human-specific mAbs can be generated (see e.g., Tomizuka et al. (2000) Proc. Nat. Acad. Sci. USA 97, 722-727). Other examples for generation of human antibodies include phage-, ribosome-, mRNA- and yeast-display libraries, as well as human hybridomas from patients and antibody-cDNA cloning from single lymphocytes selected on antigen (see e.g., Carter et al. (2006) Nat Rev Immunol. 6(5), 343-357, 346-347. 
         [0075]    Different Ig isotypes can be generated, other than then commonly used IgG1, with the humanized mice so as to tailor the produced antibody to different applications. For example, human IgG4 has limited capacity to activate effector functions of immune cells, and so, can be preferably used to block targets with limited immune activation. Radiolabelled IgG4 mAbs are particularly preferred for radioimmunotherapy and imaging, as a reduced nonspecific binding to normal tissue can be achieved with this isotope due to its poor binding to FcγRs. As another example, IgAs are preferred anti-infective reagents and, in addition, are potent activators of immune functions such as ADCC and phagocytosis. 
         [0076]    Optimization of FcγRs Function of Antibodies 
         [0077]    Various antibodies elicit effector functions following interactions between their Fc region and different Fc receptors (FcRs). The therapeutic efficacy of antibodies containing the Fc region can be optimized or diminished by engineering the interactions between the Fc region and various FcRs (e.g., FcγRs). For example, cytotoxic mAbs with enhanced engagement of activating FcγR and reduced binding to inhibitory FcγR can elicit increased antitumor and/or antiviral efficacy. As another example, mAbs that recruit and activate preferentially inhibitory FcγR can be used in the treatment of autoimmune diseases. As a further example, Fc-containing fusion molecules can be engineered for minimum interactions with some FcγRs and increased binding to some other FcR. As yet another example, an Fc fusion protein can be mutated so that the cellular toxicity and cell lysis triggered by FcγRs engagement does not occur. 
         [0078]    The Fc-FcRs interaction can be tailored by, for example, substituting amino acids residues and/or altering the glycosylation pattern of Fc. It is known in the art that a number of specific amino acid residues of Fc (of for example, human IgG1) are critical for FcγR interaction (see e.g., Shields et al. (2001) J. Biol. Chem. 276, 6591-6604). These amino acids residues can be substituted to achieve a desired FcRs binding profile. The glycosylation pattern of the Fc region is important for effector functions of the molecule. Alteration of this Fc region glycosylation pattern can increase or decrease the efficacy of the molecule (see e.g., Teillaud (2005) Expert Opin Biol Ther. 5(Suppl 1) S15-27). For example, deglycosylation of the conserved Asn297 of each CH2 domain in the Fc region causes a domain conformation change that prevents FcγR binding. 
         [0079]    Aptamer 
         [0080]    Aptamers are oligonucleic acid or peptide molecules selected from a large random sequence pool to bind to specific target molecule. The small size of aptamers makes them easier to synthesize and chemically modify and enables them to access epitopes that otherwise might be blocked or hidden. And aptamers are generally nontoxic and weak antigens because of their close resemblance to endogenous molecules. 
         [0081]    DNA or RNA aptamers consist of (usually short) strands of oligonucleotides. Oligonucleotide aptamers are DNA or RNA molecules that have been, for example, selected from vast populations of random sequences, through a combinatorial approach known as systematic evolution of ligands by exponential enrichment (SELEX). The selected sequences have the ability to recognize specific ligands by forming binding pockets and can bind to nucleic acids, proteins or small organic compounds. Generation, selection, and delivery of aptamers is within the skill of the art (see e.g., Lee et al. (2006) Curr Opin Chem. Biol. 10, 1-8). For example, capillary electrophoreses can be used to select aptamers with extremely well-defined affinity profiles. Aptamers can be selected not only against purified targets or antigens, but also against heterogeneous targets, such as whole cells (see e.g., Yan et al. (2005) Front Biosci 10, 1802-1827). Selection against complex targets, such as cell surfaces, allows the identification of aptamers even in the absence of known biomarkers. Furthermore, negative selection procedures with whole cells can yield aptamers that can finely discriminate between different cell types, for example transformed and normal cells. Incorporation of modified nucleotides into aptamers allows the selection of aptamers with increased affinities and reduced labilities. 
         [0082]    Peptide aptamers are proteins that are designed to interfere with, for example, other protein interactions inside cells (see e.g., Hoppe-Seyler and Butz (2000) J Mol. Med. 78(8), 426-430, reviewing peptide aptamers). Peptide aptamers consist of a short variable peptide domain, attached at both end to a protein scaffold. They consist of a variable peptide loop attached at both ends to a protein scaffold. This double structural constraint can greatly increases the binding affinity of the peptide aptamer to levels comparable to an antibody&#39;s (nanomolar range). The variable loop length is typically comprised of 10 to 20 amino acids, and the scaffold can be any protein which have good solubility and compacity properties. For example, the bacterial protein Thioredoxin-A can be used as a scaffold protein, the variable loop being inserted within the reducing active site, which is a -Cys-Gly-Pro-Cys- loop in the wild protein, the two Cysteins lateral chains being able to form a disulfide bridge. Peptide aptamers selection can be made using various systems, including the yeast two-hybrid system. Protein aptamers can also be used to temporally and spatially regulate protein function in cells and organisms. For example, the ligand-regulated peptide (LiRP) system provides a general method where the binding activity of intracellular peptides is controlled by a cell-permeable small molecule (see e.g., Binkowski (2005) Chem &amp; Biol. 12(7), 847-55). 
         [0083]    Antibody Production 
         [0084]    Engineering, generation, and screening of various types of antibodies is well known in the art. See e.g., Carter (2006) Nat Rev Immunol. 6(5), 343-357; Teillaud (2005) Expert Opin Biol Ther. 5(Suppl 1) S15-27; Subramanian, ed. (2004) Antibodies: Volume 1: Production and Purification, Springer, ISBN 0306482452; Subramanian, ed. (2001) Manufacturing of Gene Therapeutics—Methods, Processing, Regulation and Validation, Springer, ISBN 0306466805; Lo, ed. (2003) Antibody Engineering Methods and Protocols, Humana Press, ISBN 1588290921. These methods can generally be used for the generation of antibodies having similar affinity and specificity and which are functionally equivalent to those used in the working examples. 
         [0085]    While antibody therapeutics are conventionally produced in mammalian cells—commonly Chinese hamster ovary cells, NS0 mouse myeloma cells or hybridoma cells—alternative hosts for production can also be employed (e.g.,  E. coli , other microorganisms, insect cells, and transgenic plants and animals). See generally Carter et al. (2006) Nat Rev Immunol. 6(5), 343-357. For example, antibody fragments can be produced at gram-per-liter titres by  E. coli  fermentation. 
         [0086]    Once produced, immunopeptides can be tested for SAM and/or neuropilin 1 recognition by various procedures including Western blot or immunoprecipitation analysis by standard methods, as described in the references above. Preferred antigen-binding affinity ranges from a Kd of, for example, 0.001 to 100 nM, 0.01 to 50 nM, and 0.08 nM to 32 nM. 
         [0087]    Numerous interdependent properties of the antibodies described herein can be tuned to improve their clinical and/or diagnostic efficacy. These properties include, but are not limited to, immunogenicity, antigen binding specificity and affinity, effector functions and other biological activities, pharmacokinetics, molecular architecture, internalization after cell binding, and biophysical properties. For example, display libraries and structure-based design (i.e., rational design) can be used, either individually or in combination, for the optimization of antibody therapeutics. See e.g., Carter et al. (2006) Nat Rev Immunol. 6(5), 343-357, 348; Wu et al. (2005) Nature Biotech 23(9), 1137-1146. Such optimization can include, for example, minimizing adverse-immunogenicity risk; improving antigen selectivity; increasing species cross-reactivity; increasing or decreasing antigen binding affinity; increasing potency; increasing or decreasing effector functions; increasing or decreasing plasma half-life; increasing or decreasing internalization efficiency; increase chemical, proteolytic, and thermodynamic stability; and improve solubility and folding kinetics. As a specific example, phage-display libraries can be used to select antibody fragments optimized for robust expression, high stability, and solubility. As another specific example, phage-display libraries can be used for affinity maturation of antibodies and increased in vitro biological potency. See e.g., Carter et al. (2006) Nat Rev Immunol. 6(5), 343-357, 350. Such increases can increase efficacy as well as reduce dosage or frequency of administration. 
         [0088]    The terminal half-life of antibodies in plasma can be tuned over a wide range to fit clinical goals. The antibody half-life can be engineered to be between several minutes to several weeks. It can also be desirable to increase the terminal half-life of an antibody to improve efficacy, to reduce the dose or frequency of administration, or to improve localization to the target. Alternatively, it can be advantageous to do the converse—that is, to decrease the terminal half-life of an antibody—to reduce whole body exposure or to improve the target-to-non-target binding ratios. 
         [0089]    Monoclonal antibody fragments can be engineered to tailor pharmacokinetics and allow selection of optimized versions for various applications, such as imaging or therapeutics. See e.g., Wu et al. (2005) Nature Biotech 23(9) 1137-1146. For example, scFVs (around 25 kDa) are diabodies (around 55 kDa) below the threshold for first-pass renal clearance and can show terminal half-lives on the order of, for example, several hours. Larger fragments such as minibodies or small immunoproteins (e.g., scFVs fused to single constant domains of IgG, 80 kDa) show intermediate clearance rate and reach higher tissue uptake levels. Still larger fragments include scFVs fused to intact Fc domains (scFVs-Fcs, 110-120 kDa) have similar pharmokinetics to intact monoclonal antibodies because of the Fc region, including the neonatal Fc receptor bidning site. 
         [0090]    Decreasing antibody terminal half-life can, for example, allow tumor imaging by positron emission tomography. For example, the terminal half-life of IgG can be increased or decreased by tailoring the interaction between IgG and its salvage receptor, FcRn. See e.g., Carter et al. (2006) Nat Rev Immunol. 6(5), 343-357, 353. The terminal half-life of antibody fragments, usually shorter than non-fragments, can be extended by binding to longer-lived molecules, such as IgG and serum albumin, or conjugation to molecules such as polyethylene glycol (i.e., PEGylation). PEGylated antibody fragments provide the advantage of, for example, lack of undesirable Fc-mediated effects, reduction in the risk of immunogenicity, and a moderate reduction in cost. 
         [0091]    Antibodies can be altered or selected so as to achieve efficient antibody internalization. Further, antibody-drug conjugates can increase the efficiency of antibody internalization. Efficient antibody internalization can be desirable for certain applications, such as for delivery of cytotoxic drugs and immunoliposomes. Removal of the target antigen from the cell surface prevents the further binding of any ligands and can therefore be a desirable outcome when using a receptor antagonist, in for example, antibody therapeutics. By contrast, rapid antibody internalization after cell binding can be undesirable where the therapeutic strategy requires effector functions. 
         [0092]    Conjugation of antibodies to a variety of agents, including drugs, toxins, and radionuclides, is well known in the art. See generally, Wu et al. (2005) Nat. Biotechnol. 23(9), 1137-1146; McCarron et al. (2005) Mol Interv 5(6), 368-380; Niemeyer (2004) Bioconjugation Protocols, Strategies and Methods, Humana Press, ISBN 1588290980; Hermanson (1996) Bioconjugate Techniques, Academic Press, ISBN 0123423368. 
         [0093]    Antibody Uses 
         [0094]    Among the various uses for antibodies described herein are, for example, function inhibitor, expression inhibitor, detector agent, diagnostic agent, purification agent, therapeutic agent, and imaging agent. 
         [0095]    Antibodies of this invention can be used as inhibitors of SAM and/or neuropilin 1 function and expression. For example, antibody inhibitors of the insulin secretion pathway can target, directly or indirectly, any factor or component involved in the biological cascade which results in promoting pancreatic islet hormone release. Inhibitors of SAM and/or neuropilin 1 include inhibitors targeting neuroligin 1, neuroligin 2, neuroligin 3, neuroligin 4X, neuroligin 4Y, neurexin 1α, neurexin 2α, neurexin 3α, neurexin 1β, neurexin 2β, neurexin 3β, SynCam, Thy-1, and neuronal pentraxin and/or neuropilin 1. Standard methods using antibodies can be used to detect and quantitate SAM and/or neuropilin 1 expression, including but not limited to: radioimmunoassays, receptor assays, enzyme immunoassays, cytochemical bioassays, ligand assays, immunoradiometric assays, fluoroimmunoassays, and enzyme-linked immunosorbent assays. 
         [0096]    The antibodies described herein can be used to detect the presence and quantity of the substance against which they were raised. For example, the antibodies of the invention can be used to detect SAM and/or neuropilin 1 protein in a biological sample. Various protocols well known in the art can be utilized for these purposes, including but not limited to, a Western blot test (to detect a substance in a solution) or an immunofluorescence test (to detect a substance in a whole cell). For example, antibodies described herein can be used in an immunoassay to monitor the level of a SAM and/or neuropilin 1 protein produced by a mammal (e.g., to determine the amount or subcellular location of an SAM and/or neuropilin 1 protein). 
         [0097]    In biochemical applications, antibodies can be used for immunological identification of proteins, using, for example, the Western blot method. A similar technique is used in ELISPOT and ELISA assays, in which detection antibodies are used to detect cell secretions such as cytokines or antibodies. Antibodies can also be used to separate proteins (and anything bound to them) from the other molecules in a cell lysate. Antibodies can also be used in immunohistochemical staining. 
         [0098]    Antibodies of the invention can also be used to purify a substance with techniques such as immunoprecipitation and affinity chromatography. 
         [0099]    Antibodies described herein can be used as therapeutic agents, either alone or conjugated to another active agent. Therapeutic use of antibodies is known in the art. See e.g., Carter (2006) Nat Rev Immunol. 6(5), 343-357; Subramanian, ed. (2004) Antibodies vol. 2 Novel Technologies and Therapeutic Use, Springer, ISBN 0306483157. Antibodies can be used therapeutically by nature of their ability to bind to cell-specific antigens and induce an immunological response against the target cell, for example an islet Beta cell. Such antibodies can also be modified for delivery of, for example, a toxin, radioisotope, cytokine or other active conjugate. Bispecific antibodies can also be designed to bind with their Fab regions both to a target antigen and to a conjugate or effector cell. 
         [0100]    The antibodies of the invention can be used in a variety of imaging and/or localization applications. 
         [0101]    The methods discussed above are well known and will be understood by those skilled in the art to require a reasonable amount of experimentation to optimize the interaction between antibodies and antigens and the detection of the antigens by the antibodies. See e.g., Wild (2005) The Immunoassay Handbook, 3d ed., Elsevier Science, ISBN 0080445268; Coligan (2005) Short Protocols in Immunology, John Wiley &amp; Sons, ISBN 0471715786; Brent et al., ed. (2003) Current Protocols in Molecular Biology, John Wiley &amp; Sons Inc, ISBN 047150338X; Ausubel et al., ed. (2002) Short Protocols in Molecular Biology 5th Ed., Current Protocols, ISBN 0471250929. 
         [0102]    Radioimaging and Radioimmunotherapy 
         [0103]    Radionucleotides can be coupled to the antibodies described herein, thus facilitating a variety of imaging and therapeutic protocols. See e.g., Wu et al. (2005) Nature Biotech 23(9), 1137-1146. As an imaging example, radioimmunoscintigraphy using gamma cameras or single photon emmission tomography requires coupling of gamma emitting isotopes (e.g., 99 mTc, 123I, 111In) to an antibody. Positron emission tomogrpahy (PET) relies on attachment of positron emitters (e.g., 18F, 64Cu, 68Ga, 86Y, 124I) to antibodies. Targeted delivery of beta emitters (e.g., 131I, 90Y, 177Lu, 67Cu) or alpha-emitting radionucleotides (e.g., 213Bi, 211At) through conjugation to an antibody is a touchstone for effective radioimmunotherapy procedures. Radioimmunoimaging can be used in conjunction with radioimmunotherapy as a means for evaluating targeting and dosimetry. Generally, antibody fragments are desirable for immunoimaging applications due to their relatively shorter circulating half-life, tissue penetration, and more homogenous distribution within tissues. 
         [0104]    Antibodies can be coupled to radionuclides for radioimmunotherapy applications. Generally, dose delivered to the target is balanced against exposure of normal organs and tissues to radiation. Both alpha and beta emitters with a variety of energy transfer properties, half-lives and emission rates can be used for radioimmunotherapy. See e.g., Milenic et al. (2004) Nat Rev Drug Discov 3, 488-499. Examples of toxic radionuclides that can be coupled to the antibody include 131I, 90Y, and 177Lu. 
         [0105]    Coupling radionucleotides and proteins is well known in the art and can be accomplished, for example, through conjugation to existing or genetically introduced cysteine residues in the antibody. See e.g., Wu et al. (2005) Nature Biotech 23(9), 1137-1146.; McCarron et al. (2005) Mol Interv 5(6), 368-380; Niemeyer (2004) Bioconjugation Protocols, Strategies and Methods, Humana Press, ISBN 1588290980; Hermanson (1996) Bioconjugate Techniques, Academic Press, ISBN 0123423368. Other examples include labeling of hexahistidine-tagged recombinant proteins and covalent modification of monoclonal antibody binding sites for ligand binding. A further coupling example is incorporation of enyzmatically labile linkers between radiometal and antibody that allow release and clearance of the conjugated radiometal from circulating conjugates, with cleavage by exogenous or endogenous enzymes. 
         [0106]    It can also be desirable to utilize pretargeting radioimmunotherapy. Under this approach, antibody-directed localization and radionuclide delivery are separated physically and temporally. First, the antibody conjugate is administered so as to bind the target. A clearing agent can be applied to clear the blood. Then, a low molecular weight radioactive ligand that binds the antibody conjugate is administered. This approach effectively separates the slow distribution of the antibody moiety from rapid binding and elimination of the radioisotope-tagged ligand. For example, an antibody-streptavidin conjugate can be employed in the first step, followed by a radiolabeled biotin derivative. See e.g., Sharkey et al. (2005) Clin Cancer Res 11, 7109s-7121s. 
         [0107]    It can also be desirable to utilize antibody-directed enzyme prodrug therapy (ADEPT). See e.g., Wu et al. (2005) Nature Biotech 23(9), 1137-1146. This alternate form of pretargeting is a two-step process in which, first, an antibody-enzyme conjugate is administered that localizes on or in the target and clears from systemic circulation over time. Once the target/nontarget ration is sufficiently high, a prodrug is given that is converted to an active drug by the targeted enzyme. One advantage of this approach is the ability to use prodrugs that would be too toxic in untargeted form. 
         [0108]    Antibody Administration 
         [0109]    The biomolecules described herein can be used therapeutically either as exogenous materials or as endogenous materials. Exogenous agents are those produced or manufactured outside of the body and administered to the body. Endogenous agents are those produced or manufactured inside the body by some type of device (biologic or other) for delivery to within or to other organs in the body. 
         [0110]    Administration of biomolecules by a variety of methods is well known in the arts. Administration can include, for example, methods involving direct injection (eg, systemic or stereotactic), implantation of cells engineered to secrete the factor of interest, drug-releasing biomaterials, implantable matrix devices, implantable pumps, injectable gels and hydrogels, liposomes, micelles (e.g., up to 30 μm), microspheres (e.g., 1-100 μm), reservoir devices, etc. 
         [0111]    A safe and effective amount of an anti-SAM and/or neuropilin 1 antibody is, for example, that amount that would cause the desired therapeutic effect in a patient while minimizing undesired side effects. The dosage regimen will be determined by skilled clinicians, based on factors such as the exact nature of the condition being treated, the severity of the condition, the age and general physical condition of the patient, and so on. 
         [0112]    The compositions of the present invention can include one or more pharmaceutically acceptable vehicles for said compound(s). Such pharmaceutical formulations are discussed in depth below. 
         [0113]    Adverse reactions to antibody administration in a subject can be attenuated in a variety of ways known in the art. For example, infusion reactions (e.g., fever, chills, headaches, vomiting, and diarrhoea) can be attenuated by humanization, attentuating effector functions (e.g., antibody-dependent cell-mediated cytotoxicity and complement dependent cytotoxicity), premedication, and by incremental increase in the rate of infusion of antibody formulation. See e.g. Carter et al. (2006) Nat Rev Immunol. 6(5), 343-357. As another example, Fc-mediated reactions, such as acute and severe influenza-like syndrome, can be largely overcome by attenuating the interaction between the Fc region of the antibody and the receptors for the antibody (e.g., IgG receptors; FcγRs) expressed by the patient. In general, increasing the potency of the antibody or extending its half-life in plasma can allow the dose or frequency of administration to be reduced, with the associated benefits of improved quality of life and/or convenience for the patient, and/or reduced cost of the drug. 
         [0114]    Parenteral 
         [0115]    The biomolecules described herein can be administered parenterally, including intravenous, intramuscular, subcutaneous, and intraperitoneal injections. 
         [0116]    Excipients, commonly used in the parenteral delivery of small drug molecules, including solubility enhancers, osmotic agents, buffers, and preservatives, can also be included in biomolecule formulations. Inclusion of antiaggregation and antiadsorption agents, such as surfactants and albumin, when formulating and delivering biomolecules can add increased stability and decrease the risk of the active biomolecule interacting with an interface, which can lead to unfolding, aggregation, and/or precipitation. The biomolecule can be lyophilized for added stability during storage, and re-processed before parenteral administration. 
         [0117]    For example, antibody delivery can be by intravenous infusion, usually entailing multiple doses. Local, controlled release methods for antibody delivery are also known in the art (see e.g., See e.g., Raza et al. (2005) Expert Opin Biol Ther. 5(4), 477-494; Stayton et al. (2005) Orthod Craniofacial Res 8, 219-225; Grainger (2004 Expert Opin Biol Ther. 4(7), 1029-44; Varde and Pack (2004) Expert Opin Biol Ther. 4(1), 35-51; Whittlesey and Shea (2004) Exp Neurol. 190(1), 1-16). 
         [0118]    Antibodies can be administered in an amount of, for example, about [[0.05 mg to about 2.5 mg]] per injection. As another example, antibodies can be injected at a concentration of about [[0.1 mg to about 1 mg]] per injection. Preferably, immunopeptide inhibitors are injected at a concentration of about [[0.3 mg to about 0.5 mg]] per injection. 
         [0119]    Cell Implantation 
         [0120]    Antibodies described above can be delivered by implanting antibody-producing hybridoma cells (see e.g., Bromsamle et al. (2000) J. Neuroscience 20, 8061-8068). 
         [0121]    Oral 
         [0122]    Oral administration of the biomolecular agents described herein provides ease of administration as well as the ability to achieve systemic distribution of the agent. A variety of means to avoid degradation of the relatively fragile bioagents of the present invention are known to the art. Carrier-based systems for biomolecule delivery can be used in conjunction with oral delivery. For example, bioadhesive systems that adhere to the intestinal epithelium are available (see e.g., Ramdas et al. (1999) J. Biomater. Appl. 13, 290-296, describing alginate encapsulated bioadhesive chitosan microspheres for intestinal drug delivery). As another example, certain devices that can release formulations in the intestine for several days or several weeks are available. 
         [0123]    Pulmonary 
         [0124]    Pulmonary delivery of macromoles and/or drugs, such as the biomolecules described herein, provide for relatively easy, non-invasive administration to the circulatory system for systemic circulation, airway surface, and/or airway cells (see e.g., Cryan (2004) AAPS J. 7(1) article 4, E20-41, providing a review of pulmonary delivery technology). Advantages of pulmonary delivery include noninvasiveness, large surface area for absorption (˜75 m2), thin (˜0.1 to 0.5 μm) alveolar epitheliuem permitting rapid absorption, absence of first pass metabolism, decreased proteolytic activity, rapid onset of action, and high bioavailablity. Drug formulations for pulmonary delivery, with or without excipients and/or a dispersible liquid, are known to the art. Carrier-based systems for biomolecule delivery, such as polymeric delivery systems, liposomes, and micronized carbohydrates, can be used in conjunction with pulmonary delivery. Penetration enhancers (e.g., surfactants, bile salts, cyclodextrins, enzyme inhibitors (e.g., chymostatin, leupeptin, bacitracin), and carriers (e.g., microspheres and liposomes) can be used to enhance uptake across the alveolar epithelial cells for systemic distribution. 
         [0125]    Various inhalation delivery devices, such as metered-dose inhalers, nebulizers, and dry-powder inhalers, that can be used to deliver the biomolecules described herein are known to the art (e.g., AErx (Aradigm, Calif.); Respimat (Boehringer, Germany); AeroDose (Aerogen Inc., CA)). As known in the art, device selection can depend upon the state of the biomolecule (e.g., solution or dry powder) to be used, the method and state of storage, the choice of excipients, and the interactions between the formulation and the device. 
         [0126]    Dry powder inhalation devices are particularly preferred for pulmonary delivery of protein-based agents (e.g., Spinhaler (Fisons Pharmaceuticals, NY); Rotohaler (GSK, NC); Diskhaler (GSK, NC); Spiros (Dura Pharmaceuticals, CA); Nektar (Nektar Pharmaceuticals, CA)). Dry powder formulation of the active biological ingredient to provide good flow, dispersability, and stability is known to those skilled in the art. 
         [0127]    Pumps 
         [0128]    The biomolecules described herein can be delivered, for example, via a surgically implanted osmotic pump or cannula system. 
         [0129]    Carrier Delivery Systems 
         [0130]    Carrier delivery systems encapsulate the biomolecule of interest and provide controlled release of the agent over extended periods of time. Generally a carrier includes molecules conjugated to, mixed with, or used for encapsulating biomolecular agents. Carrier-based systems for biomolecular agent delivery can: tailor biomolecule/agent release rates; increase the proportion of biomolecule that reaches its site of action; improve the transport of the drug to its site of action; allow colocalized deposition with other agents or excipients; improve the stability of the agent in vivo; prolong the residence time of the agent at its site of action by reducing clearance; decrease the nonspecific delivery of the agent to nontarget tissues; decrease irritation caused by the agent; decrease toxicity due to high initial doses of the agent; alter the immunogenicity of the agent; decrease dosage frequency, improve taste of the product; and/or improve shelf life of the product. 
         [0131]    Polymeric release systems can be used to deliver small molecule drugs, pharmocologic agents, proteins, enzymes, peptides, polypeptides, nucleotides, polynucleotides, oligonucleotides, antisense oligonucleotides, nucleosides, antibodies, viral and nonviral vectors, etc. for a variety of purposes discussed above (see Whittlesey and Shea (2004) Experimental Neurology 190, 1-16). Polymeric systems can also be designed to deliver multiple biomolecules that can act synergistically or sequentially on cellular processes. Polymeric delivery systems can maintain therapeutic levels of the biomolecular agents described herein, reduce harmful side effects, decrease the amount of biomolecule required, decrease the number of dosages, facilitate delivery of agents with short in vivo half-lives, and overcome barriers associated with low oral and transdermal bioavailabilities. Release rates can be controlled by altering the pore size, structure, and polymer contents of synthetic polymers such as the nondegradable synthetic polymer EVAc and the degradable synthetic polymer polyester PLGA. Furthermore, the degradation of the material itself serves to govern release profiles, providing an additional level of control over release rate. Polymeric delivery systems described herein can be tailored for release durations of, for example, minutes, hours, days, weeks, and even years depending upon the physical and chemical properties of the delivered molecule, the polymer employed, and the processing conditions used during fabrication. 
         [0132]    Both natural (e.g., collagen) and synthetic polymers (e.g., silicone, poly-lactide-co-glycolide (PLGA), and polyethylene vinyl-co-acetate (EVAc)) can be utilized for the local and systemic delivery of biomolecules. Biodegradable polymers are preferable for biomolecule delivery because the device can disappear over time, eliminating the need for surgical retrieval. PLGA is a widely used biopolymer due to its commercial availabilty, controllable degradation rate, proven biocompatibility, and FDA approval (see e.g., Lu et al. (2000) Biomaterials 21, 1837-1845). Polyanhydrides are a similar class of degradeable polymer that can be used for biomolecule delivery. 
         [0133]    Microspheres 
         [0134]    Polymeric microspheres can facilitate delivery of the biomolecules described herein. For example, sustained delivery microspheres can be stereotactically injected to over express an encoded protein or release a biomolecular inhibitor of that protein at a target site. Microspheres are produced using naturally occurring or synthetic polymers to produce particulate systems in the size range of 0.1 to 500 μm. Generally, microspheres are physically and chemically more stable than liposomes and allow for higher agent loading. Polymeric micelles and polymeromes are polymeric delivery vehicles with similar characteristics to microspheres and can also facilitate encapsulation and delivery of the biomolecules described herein. 
         [0135]    Fabrication, encapsulation, and stabilization of microspheres for a variety of biomolecule payloads are within the skill of the art (see e.g., Varde &amp; Pack (2004) Expert Opin. Biol. 4(1)35-51). Polymer materials useful for forming microspheres include PLA, PLGA, PLGA coated with DPPC, DPPC, DSPC, EVAc, gelatin, albumin, chitosan, dextran, DL-PLG, SDLMs, PEG (e.g., ProMaxx), sodium hyaluronate, diketopiperazine derivatives (e.g., Technosphere), calcium phosphate-PEG particles, and oligosaccharide derivative DPPG (e.g., Solidose). Encapsulation can be accomplished, for example, using a water/oil single emulsion method, a water-oil-water double emulsion method, or lyophilization. Several commercial encapsulation technologies are available (e.g., ProLease®, Alkerme). 
         [0136]    Release rate of microspheres can be tailored by type of polymer, polymer molecular weight, copolymer composition, excipients added to the microsphere formulation, and microsphere size. 
         [0137]    The type of polymer and the way in which it degrades affects agent release kinetics. Bulk-eroding polymers, such as PLGA, readily allow permeation of water into the polymer matrix with polymer degradation throughout the matrix. Bulk erosion typically results in biphasic or triphasic release profiles. In contrast, surface eroding polymers, such as polyanhydrides, are composed of relatively hydrophobic monomers linked by labile bonds, resulting in resistance to water permeation into the polymer bulk but rapid degradation at the polymer/water interface via hydrolysis. Typically, the encapsulated agent is released from the surface degradation, with the largest rate of release at the beginning and, as the surface area decreases, asymptotically decreasing. 
         [0138]    Generally, encapsulated agent release rate decreases with increased polymer molecular weight in bulk-eroding polymers but has little effect in surface-eroding polymers. Microsphere size also affects release rate, with the rate of flux of the biomolecule out of the matrix increasing with decreased particle size. Microspheres can be formulated to contain one or more polymers and the relative ratio of each monomeric unit can affect the release rate. 
         [0139]    Excipients can be added to the microsphere formulation to stabilize the emulsion during fabrication and to stabilize the biomolecule during fabrication and/or release. In the case of microsphere encapsulated proteins, addition of excipients, such as PEG, carbohydrates, and buffering salts (e.g., magnesium hydroxide), can prevent aggregation and stabilize the folded protein structure. As another example, encapsulated protein biomolecules in PLGA microspheres in the presence of the hydrophilic excipient mannitol can enhance biomolecular stability. Excipients can also impact release rate. For example, PVA in the biomolecule solution can stabilize the primary emulsion and provide more uniform distribution throughout the matrix, prevent coalescence of inner aqueous-phase droplets, and decrease initial release burst and overall release rate. Coating of microspheres can be used to alter in vivo properties. For example, coating PLGA microspheres with DPPC can decrease uptake of the biomolecule cargo into macrophages. As another example, coating particles with mucoadhesive polymers such as chitosan and hydroxypropylcellulose can increase residency time of pulmonary carriers. 
         [0140]    Microspheres encapsulating the biomolecules described herein can be administered in a variety of means including parenteral, oral, pulmonary, implantation, and pumping device. For single walled polymeric microspheres, the biphasic release rate of the bioactive molecule depends on the ratio of surface-associated to encapsulated drug. Typically an initial “burst release” (resulting from of the incorporated biomolecule being left on the surface of the microsphere) is followed by a more prolonged release (i.e., biphasic release), with rates dictated by the polymer used. Double-walled polymeric micropsheres exhibit a more linear release rate (see e.g., Yang et al. (2003) J. Controlled Release 88, 201-213). 
         [0141]    Hydrogels 
         [0142]    Polymeric hydrogels, composed of hydrophillic polymers such as collagen, fibrin, and alginate, can also be used for the sustained release of incorporated biomolecules (see e.g., Sakiyama et al. (2001) FASEB J. 15, 1300-1302). Biomolecules incorporated into the hydrogel can stimulate cellular function directly from the matrix or following release. 
         [0143]    Polymeric Implants 
         [0144]    Three-dimensional polymeric implants, on the millimeter to centimeter scale, can be loaded with biomolecules (see e.g., Teng et al (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 3024-3029). These polymeric implants can serve as structural for cell adhesion and tissue formation while also providing controlled release of biomolecules. A polymeric implant typically provides a larger depot of the bioactive factor. The implants can also be fabricated into structural supports, tailoring the geometry (e.g., shape, size, porosity) to the application. The porosity of the scaffold can influence cell seeding and cell infiltration from the surrounding tissue. Extracellular matrix proteins can be incorporated in or on the scaffold to influence cell adhesion and migration. For example, polymeric delivery vehicles shaped into structural supports, such as guidance channels or bridges, can provide architectural organization and biochemical factors to stimulate tissue formation. As another example, polymeric delivery systems can provide support structures for stem cell adhesion coupled with release of one or more proteins or other biomolecules to stimulate differentiation to a specific cell fate. Three-dimensional polymeric implants can be formed, for example, by direct casting of the polymer and drug or by processing loaded microspheres into a three-dimensional structure. Three-dimensional polymeric implants for biomolecule delivery can be formulated in a variety of means known to the art including, but not limited to, emulsion methods, solvent casting, and carbon dioxide foaming process (see e.g., Whittlesey and Shea (2004) Experimental Neurology 190, 1-16). Implantable matrix-based delivery systems are also commercially available in a variety of sizes and delivery profiles (e.g., Innovative Research of America, Sarasota, Fla.). 
         [0145]    As an alternative to release, biomolecules can be immobilized on or in polymeric delivery systems. This approach includes substrate mediated delivery and solid-phase delivery. Generally, the polymeric substrate functions to support cell adhesion and place the biomolecular cargo directly in the cellular microenvironment (see e.g., Whittlesey and Shea (2004) Experimental Neurology 190, 1-16). Substrate mediated delivery can be used to deliver both nonviral and viral vectors. This approach is especially preferable for viral vector delivery as it mimics how many such vectors associate with the extracellular matrix as a means to facilitate cellular binding and internalization. For example, implantation of an adenovirus-modified collagen gel can result in transduction throughout the matrix with a differing delivery profile as compared to direct injection, thus localizing gene delivery and avoiding distal side effects (see e.g., Levy et al. (2001) Gene Ther. 8, 659-667). As another example, biomolecules can be delivered from polymer-coated stents and microcoils (se e.g., Abrahams et al. (2002) Stroke 33, 1376-132; Klugherz et al. (2002) Hum. Gene Ther. 13, 443-454. 
         [0146]    In formulating polymeric release systems, various additives can be included to stabilize the biomolecule to be delivered. Such additives and measures include, for example, carbohydrate sugars, polyethylene glycol, complexation with metal ions, and coencapsulation with a weak base to minimize the pH reduction during degradation. 
         [0147]    “Smart” Polymeric Carriers 
         [0148]    The biomolecular therapeutic agents described herein can be delivered to intracellular targets via so-called “smart” polymeric carriers. See e.g., Stayton et al. (2005) Orthod Craniofacial Res 8, 219-225; Wu et al. (2005) Nature Biotech (2005) 23(9), 1137-1146. Generally, carriers of this type utilize polymers that are hydrophilic and stealth-like at physiological pH, but become hydrophobic and membrane-destabilizing after uptake into the endosomal compartment (i.e., acidic stimuli from endosomal pH gradient) where they enhance the release of the cargo molecule into the cytoplasm. The design of the smart polymeric carrier can incorporate pH-sensing functionalities, hydrophobic membrane-destabilizing groups, versatile conjugation and/or complexation elements to allow the drug incorporation, and an optional cell targeting component. Potential therapeutic macromolecular cargo includes, but is not limited to, peptides, proteins, antibodies, polynucleotides, plasmid DNA (pDNA), aptamers, antisense oligodeoxynucleotides (ASODN), silencing RNA, and ribozymes. As an example, smart polymeric carriers can enhance the cytoplasmic delivery of antibody-targeted conjugates that are internalized through receptor mediated endocytosis. As another example, smart polymeric carriers can enhance cytoplasmic delivery of protein therapeutics. 
         [0149]    Polymeric carriers include, for example, the family of poly(alkylacrylic acid) polymers, specific examples including poly(methylacrylic acid), poly(ethylacrylic acid) (PEAA), poly(propylacrylic acid) (PPAA), and poly(butylacrylic acid) (PBAA), where the alkyl group progressively increased by one methylene group. 
         [0150]    Such polymeric carriers can be designed to provide a range of pH profiles and membrane-destabilizing activities, allowing their molecular properties to be matched to specific drugs and loading ranges. For example, the pH profile can be controlled by the choice of the alkylacrylic acid monomer and by ratio of the carboxylate-containing alkylacrylic acid monomer to alkylacrylate monomer. Similarly, the membrane destabilizing activity can be controlled by the lengths of the alkyl segment on the alkylacrylic acid monomer and the alkylacrylate monomer. 
         [0151]    Smart polymeric carriers with potent pH-responsive, membrane destabilizing activity can be designed to be below the renal excretion size limit. For example, poly(EAA-co-BA-co-PDSA) and poly(PAA-co-BA-co-PDSA) polymers exhibit high hemolytic/membrane destabilizing activity at the low molecular weights of 9 and 12 kDa, respectively. 
         [0152]    Various linker chemistries are available to provide degradable conjugation sites for proteins, nucleic acids, and/or targeting moieties. For example, pyridyl disulfide acrylate (PDSA) monomer allow efficient conjugation reactions through disulfide linkages that can be reduced in the cytoplasm after endosomal translocation of the therapeutics. 
         [0153]    Liposomes 
         [0154]    The drug carrying capacity and release rate of liposomes can depend on the lipid composition, size, charge, drug/lipid ratio, and method of delivery. Conventional liposomes are composed of neutral or anionic lipids (natural or synthetic). Commonly used lipids are lecithins such as (phosphatidylcholines), phosphatidylethanolamines (PE), sphingomyelins, phosphatidylserines, phosphatidylglycerols (PG), and phosphatidylinositols (PI). A commonly used method of encapsulation is rehydration of a lipid film with a biomolecule solution followed by freeze-thawing and extrusion. Other techniques for forming biomolecule liposomes include the proliposome technique (see e.g., Galovic et al. (2002) Eur. J. Pharm. Sci. 15, 441-448) and the crossflow injection technique (see e.g., Wagner et al. (2002) J. Liposome Res. 12, 259-270). Liposome encapsulation efficiency can be monitored and optimized through various procedures known to the art, including differential scanning calorimetry (see e.g., Lo et al. (199%) J. Pharm. Sci. 84, 805-814). 
         [0155]    Targeted liposomes and reactive liposomes can also be used to deliver the biomolecules of the invention. Targeted liposomes have targeting ligands, such as monoclonal antibodies or lectins, attached to their surface, allowing interaction with specific receptors and/or cell types. Reactive or polymorphic liposomes include a wide range of liposomes, the common property of which is their tendency to change their phase and structure upon a particular interaction (eg, pH-sensitive liposomes) (see e.g., Lasic (1997) Liposomes in Gene Delivery, CRC Press, FL). 
         [0156]    SAM and Neuropilin 1 Proteins 
         [0157]    In other aspects, the present invention utilizes a purified SAM and Neuropilin 1 proteins encoded by a SAM and Neuropilin 1 nucleic acid or gene. A preferred form of SAM and Neuropilin 1 is a purified native SAM and Neuropilin 1 protein that has the deduced amino acid sequences of SEQ ID NOs. 1-19. Variants of native SAM and Neuropilin 1 proteins such as fragments, analogs and derivatives of native SAM and Neuropilin 1 proteins are also within the invention. Such variants include, e.g., a polypeptide encoded by a naturally occurring allelic variant of a native SAM or Neuropilin 1 gene, a polypeptide encoded by an alternative splice form of a native SAM or Neuropilin 1 gene, a polypeptide encoded by a homolog of a native SAM or Neuropilin 1 gene, and a polypeptide encoded by a non-naturally occurring variant of a native SAM or Neuropilin 1 gene. 
         [0158]    SAM and Neuropilin 1 protein variants have a peptide sequence that differs from a native SAM or Neuropilin 1 protein in one or more amino acids. The peptide sequence of such variants can feature a deletion, addition, or substitution of one or more amino acids of a native SAM or Neuropilin 1 polypeptide. Amino acid insertions are preferably of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 to 25 contiguous amino acids, and deletions are preferably of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 to 25 contiguous aminoacids. In some applications, variant SAM and Neuropilin 1 proteins substantially maintain a SAM or Neuropilin 1 protein functional activity (e.g., association with pancreatic disease including diabetes and pancreatic cancer). For other applications, variant SAM and Neuropilin 1 proteins lack or feature a significant reduction in an SAM and Neuropilin 1 protein functional activity. Where it is desired to retain a functional activity of native SAM or Neuropilin 1 protein, preferred SAM and Neuropilin 1 protein variants can be made by expressing nucleic acid molecules that feature silent or conservative changes. Variant SAM and Neuropilin 1 proteins with substantial changes in functional activity can be made by expressing nucleic acid molecules within the invention that feature less than conservative changes. 
         [0159]    SAM and Neuropilin 1 protein fragments corresponding to one or more particular motifs and/or domains or to arbitrary sizes, for example, at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 75, 100, 125, 150, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1150 and 1200 amino acids in length are intended to be within the scope of the present invention. Isolated portions of SAM and Neuropilin 1 proteins can be obtained by screening peptides recombinantly produced from the corresponding fragment of the nucleic acid encoding such peptides. In addition, fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry. For example, a SAM or Neuropilin 1 protein of the present invention may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or preferably divided into overlapping fragments of a desired length. The fragments can be produced (recombinantly or by chemical synthesis) and tested to identify those fragments which can function as either agonists or antagonists of a native SAM and Neuropilin 1 protein. 
         [0160]    Another aspect of the present invention concerns recombinant forms of the SAM and Neuropilin 1 proteins. Recombinant polypeptides preferred by the present invention, in addition to native SAM and Neuropilin 1 protein, are encoded by a nucleic acid that has at least 85% sequence identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99%) with gene sequences encoding proteins having SEQ ID NOs: 1-19. In a preferred embodiment, variant SAM and Neuropilin 1 proteins have one or more functional activities of native SAM or Neuropilin 1 protein. 
         [0161]    SAM and Neuropilin 1 protein variants can be generated through various techniques known in the art. For example, SAM and Neuropilin 1 protein variants can be made by mutagenesis, such as by introducing discrete point mutation(s), or by truncation. Mutation can give rise to a SAM or Neuropilin 1 protein variant having substantially the same, or merely a subset of the functional activity of a native SAM or Neuropilin 1 protein. Alternatively, antagonistic forms of the protein can be generated which are able to inhibit the function of the naturally occurring form of the protein, such as by competitively binding to another molecule that interacts with SAM and Neuropilin 1 protein. In addition, agonistic forms of the protein may be generated that constitutively express on or more SAM or Neuropilin 1 functional activities. Other variants of SAM and Neuropilin 1 proteins that can be generated include those that are resistant to proteolytic cleavage, as for example, due to mutations which alter protease target sequences. Whether a change in the amino acid sequence of a peptide results in a SAM or Neuropilin 1 protein variant having one or more functional activities of a native SAM or Neuropilin 1 protein can be readily determined by testing the variant for a native SAM and Neuropilin 1 protein functional activity. 
         [0162]    As another example, SAM or Neuropilin 1 protein variants can be generated from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be carried out in an automatic DNA synthesizer, and the synthetic genes then ligated into an appropriate expression vector. One purpose for a degenerate set of genes is to provide, in one mixture, all of the sequences encoding the desired set of potential SAM or Neuropilin 1 protein sequences. The synthesis of degenerate oligonucleotides is well known in the art (see, e.g., Narang, S A (1983) Tetrahedron 39:3; Itakura et al. (1981) R ECOMBINANT  DNA, P ROC  3 RD  C LEVELAND  S YMPOS . M ACROMOLECULES , ed. A G Walton, Amsterdam: Elsevier pp 273-289; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477. Such techniques have been employed in the directed evolution of other proteins (see, e.g., Scott et al. (1990) Science 249:386-390; Roberts et al. (1992) Proc. Natl. Acad. Sci. USA 89:2429-2433; Devlin et al. (1990) Science 249: 404-406; Cwirla et al. (1990) Proc. Natl. Acad. Sci. USA 87: 6378-6382; as well as U.S. Pat. Nos. 5,223,409; 5,198,346; and 5,096,815). 
         [0163]    Similarly, a library of coding sequence fragments can be provided for a SAM or Neuropilin 1 gene clone in order to generate a variegated population SAM or Neuropilin 1 protein fragments for screening and subsequent selection of fragments having one or more native SAM or Neuropilin 1 protein functional activities. A variety of techniques are known in the art for generating such libraries, including chemical synthesis. In one embodiment, a library of coding sequence fragments can be generated by (i) treating a double-stranded PCR fragment of a SAM or Neuropilin 1 gene coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule; (ii) denaturing the double-stranded DNA; (iii) renaturing the DNA to form double-stranded DNA which can include sense/antisense pairs from different nicked products; (iv) removing single-stranded portions from reformed duplexes by treatment with S1 nuclease; and (v) ligating the resulting fragment library into an expression vector. By this exemplary method, an expression library can be derived which codes for N-terminal, C-terminal and internal fragments of various sizes. 
         [0164]    A wide range of techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a certain property. Such techniques will be generally adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of SAM or Neuropilin 1 gene variants. The most widely used techniques for screening large gene libraries typically involve cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates relatively easy isolation of the vector encoding the gene whose product was detected. 
         [0165]    Combinatorial mutagenesis has a potential to generate very large libraries of mutant proteins. To screen a large number of protein mutants, techniques that allow one to avoid the very high proportion of non-functional proteins in a random library and simply enhance the frequency of functional proteins (thus decreasing the complexity required to achieve a useful sampling of sequence space) can be used. For example, recursive ensemble mutagenesis (REM), an algorithm that enhances the frequency of functional mutants in a library when an appropriate selection or screening method is employed, might be used. Arkin and Yourvan (1992) Proc. Natl. Acad. Sci. USA 89:7811-7815; Yourvan et al. (1992) Parallel Problem Solving from Nature, Maenner and Manderick, eds., Elsevier Publishing Co., Amsterdam, pp. 401-410; Delgrave et al. (1993) Protein Engineering 6(3): 327-331. 
         [0166]    The invention also provides for reduction of SAM or Neuropilin 1 proteins to generate mimetics, e.g. peptide or non-peptide agents, that are able to disrupt binding of SAM or Neuropilin 1 protein to other proteins or molecules with which the native SAM or Neuropilin 1 protein interacts. Thus, the techniques described herein can also be used to map which determinants of SAM or Neuropilin 1 protein participate in the intermolecular interactions involved in, e.g., binding of SAM or Neuropilin 1 protein to other proteins which may function upstream (e.g., activators or repressors of SAM or Neuropilin 1 functional activity) of the SAM or Neuropilin 1 protein or to proteins or nucleic acids which may function downstream of the SAM or Neuropilin 1 protein, and whether such molecules are positively or negatively regulated by the SAM or Neuropilin 1 protein. To illustrate, the critical residues of an SAM or Neuropilin 1 protein, similar to the RGD motif described above, which are involved in molecular recognition of, e.g., SAM or Neuropilin 1 protein or other components upstream or downstream of the SAM or Neuropilin 1 protein can be determined and used to generate SAM or Neuropilin 1 protein-derived peptidomimetics which competitively inhibit binding of the SAM or Neuropilin 1 protein to that moiety. By employing scanning mutagenesis to map the amino acid residues of a SAM or Neuropilin 1 protein that are involved in binding other extracellular proteins, peptidomimetic compounds can be generated which mimic those residues of a native SAM or Neuropilin 1 protein. Such mimetics may then be used to interfere with the normal function of an SAM or Neuropilin 1 protein. 
         [0167]    For example, non-hydrolyzable peptide analogs of such residues can be generated using benzodiazepine (see, e.g., Freidinger et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings (Garvey et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), keto-methylene pseudopepitides (Ewenson et al. (1986) J. Med. Chem. 29:295; and Ewenson et al. in Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium) Pierce Chemical Co. Rockland, Ill., 1985), beta-turn dipeptide cores (Nagai et al. (1985) Tetrahedron Lett 26:647; and Sato et al. (1986) J. Chem. Soc. Perkin. Trans. 1: 1231), and beta-aminoalcohols (Gordon et al. (1985) Biochem. Biophys. Res. Commun. 126:419; and Dann et al. (1986) Biochem. Biophys. Res. Commun. 134:71). SAM or Neuropilin 1 proteins may also be chemically modified to create SAM or Neuropilin 1 protein derivatives by forming covalent or aggregate conjugates with other chemical moieties, such as glycosyl groups, lipids, phosphate, acetyl groups and the like. Covalent derivatives of SAM or Neuropilin 1 protein can be prepared by linking the chemical moieties to functional groups on amino acid side chains of the protein or at the N-terminus or at the C-terminus of the polypeptide. 
         [0168]    The present invention further pertains to methods of producing the subject SAM or Neuropilin 1 proteins. For example, a host cell transfected with a nucleic acid vector directing expression of a nucleotide sequence encoding the subject polypeptides can be cultured under appropriate conditions to allow expression of the peptide to occur. The cells may be harvested, lysed, and the protein isolated. A recombinant SAM or Neuropilin 1 protein can be isolated from host cells using techniques known in the art for purifying proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for such protein. 
         [0169]    For example, after a SAM or Neuropilin 1 protein has been expressed in a cell, it can be isolated using any immuno-affinity chromatography. More specifically, an anti-SAM or Neuropilin 1 antibody (e.g., produced as described below) can be immobilized on a column chromatography matrix, and the matrix can be used for immuno-affinity chromatography to purify the SAM or Neuropilin 1 protein from cell lysates by standard methods (see, e.g., Ausubel et al., supra). After immuno-affinity chromatography, the SAM or Neuropilin 1 protein can be further purified by other standard techniques, e.g., high performance liquid chromatography (see, e.g., Fisher, Laboratory Techniques In Biochemistry And Molecular Biology, Work and Burdon, eds., Elsevier, 1980). In another embodiment, an SAM or Neuropilin 1 protein is expressed as a fusion protein containing an affinity tag (e.g., GST) that facilitates its purification. 
         [0170]    Proteins that Associate with Sam or Neuropilin 1 Proteins 
         [0171]    The invention also features methods for identifying polypeptides that can associate with SAM or Neuropilin 1 protein. Any method that is suitable for detecting protein-protein interactions can be employed to detect polypeptides that associate with SAM or Neuropilin 1 protein. Examples of such methods include co-immunoprecipitation, crosslinking, and co-purification through gradients or chromatographic columns of cell lysates or proteins obtained from cell lysates and the use of SAM or Neuropilin 1 protein to identify proteins in the lysate that interact with the SAM or Neuropilin 1 protein. For these assays, the SAM or Neuropilin 1 protein can be a full length SAM or Neuropilin 1 protein, a particular domain of SAM or Neuropilin 1 protein, or some other suitable fragment of SAM or Neuropilin 1 protein. Once isolated, such an interacting protein can be identified and cloned and then used, in conjunction with standard techniques, to alter the activity of the protein with which it interacts. For example, at least a portion of the amino acid sequence of a protein that interacts with SAM or Neuropilin 1 protein can be ascertained using techniques well known to those of skill in the art, such as via the Edman degradation technique. The amino acid sequence obtained can be used as a guide for the generation of oligonucleotide mixtures that can be used to screen for gene sequences encoding the interacting protein. Screening can be accomplished, for example, by standard hybridization or PCR techniques. Techniques for the generation of oligonucleotide mixtures and the screening are well-known (Ausubel et al., supra; and PCR Protocols: A Guide to Methods and Applications, Innis et al., eds. Academic Press, Inc., NY, 1990). 
         [0172]    Additionally, methods can be employed that result directly in the identification of genes that encode proteins that interact with SAM or Neuropilin 1 protein. These methods include, e.g., screening expression libraries, in a manner similar to the well known technique of antibody probing of Igt11 libraries, using labeled SAM or Neuropilin 1 protein or SAM or Neuropilin 1 fusion protein, e.g., SAM or Neuropilin 1 protein or domain fused to a marker such as an enzyme, fluorescent dye, a luminescent protein, or to an IgFc domain. 
         [0173]    There are also methods available that can detect protein-protein interaction in vivo. For example, as described herein the two-hybrid system can be used to detect such interactions in vivo. See, e.g., Chien et al., Proc. Natl. Acad. Sci. USA 88:9578, 1991. Briefly, as one example of utilizing such a system, plasmids are constructed that encode two hybrid proteins: one plasmid includes a nucleotide sequence encoding the DNA-binding domain of a transcription activator protein fused to a nucleotide sequence encoding SAM or Neuropilin 1 protein, SAM or Neuropilin 1 protein variant or fragment, or SAM or Neuropilin 1 fusion protein, and the other plasmid includes a nucleotide sequence encoding the transcription activator protein&#39;s activation domain fused to a cDNA encoding an unknown protein which has been recombined into this plasmid as part of a cDNA library. The DNA-binding domain fusion plasmid and the cDNA library are transformed into a strain of the yeast  Saccharomyces cerevisiae  that contains a reporter gene (e.g., HBS or lacZ) whose regulatory region contains the transcription activator&#39;s binding site. Either hybrid protein alone cannot activate transcription of the reporter gene: the DNA-binding domain hybrid cannot because it does not provide activation function, and the activation domain hybrid cannot because it cannot localize to the activator&#39;s binding sites. Interaction of the two hybrid proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product. 
         [0174]    The two-hybrid system or related methodology can be used to screen activation domain libraries for proteins that interact with the “bait” gene product. By way of example, and not by way of limitation, SAM or Neuropilin 1 protein may be used as the bait. Total genomic or cDNA sequences are fused to the DNA encoding an activation domain. This library and a plasmid encoding a hybrid of bait SAM or Neuropilin 1 protein fused to the DNA-binding domain are co-transformed into a yeast reporter strain, and the resulting transformants are screened for those that express the reporter gene. For example, a bait SAM or Neuropilin 1 gene sequence, such as that encoding SAM or Neuropilin 1 protein or a domain of SAM or Neuropilin 1 protein can be cloned into a vector such that it is translationally fused to the DNA encoding the DNA-binding domain of the GAL4 protein. These colonies are purified and the library plasmids responsible for reporter gene expression are isolated. DNA sequencing is then used to identify the proteins encoded by the library plasmids. 
         [0175]    A cDNA library of the cell line from which proteins that interact with bait SAM or Neuropilin 1 protein are to be detected can be made using methods routinely practiced in the art. According to the particular system described herein, e.g., the cDNA fragments can be inserted into a vector such that they are translationally fused to the transcriptional activation domain of GAL4. This library can be co-transformed along with the SAM or Neuropilin 1 or SAM or Neuropilin 1-GAL4 encoding fusion plasmid into a yeast strain which contains a lacZ gene driven by a promoter which contains GAL4 activation sequence. A cDNA encoded protein, fused to GAL4 transcriptional activation domain, that interacts with bait SAM or Neuropilin 1 protein will reconstitute an active GAL4 protein and thereby drive expression of the HIS3 gene. Colonies that express HIS3 can then be purified from these strains and used to produce and isolate bait SAM or Neuropilin 1 protein-interacting proteins using techniques routinely practiced in the art. 
         [0176]    Diabetes Mellitus 
         [0177]    Diabetes mellitus is characterized by a progressive loss of islet β-cells with concomitant loss of the body&#39;s ability to maintain normoglycemia. The current invention provides a method to monitor, detect, and identify diabetes mellitus. An agent capable of both specifically binding SAMs and/or neuropilin 1, as well as detection by an imaging device, can be administered to a patient with diabetes mellitus, and an image can be created by an imaging device. The resulting image can be used to determine the total β-cell mass in the pancreas. From this total cell mass the extent of the disease, if any, can be determined. Images generated at successive time points using the described method can be compared and progression of disease can be monitored. Additionally, the described method can be used to monitor the efficacy of treatments administered for the purpose of increasing, maintaining, or reversing loss of total β-cell mass. 
         [0178]    Further, in another aspect of the present invention, it has been determined that SAMs are important in terms of insulin release. Thus, another aspect of the present invention includes targeting these particular molecules for drug therapies useful in the treatment of diabetes mellitus. 
         [0179]    Pancreatic Cancer 
         [0180]    In pancreatic cancer, as in most cancers, it is thought that metastatic spread is the critical threshold in the process of cancer progression that leads to significant decline in patient survival. Although surgical modalities are the preferred intervention, the potential for occult metastatic spread of the disease often requires the administration of systemic therapies. Some of the patients who receive systemic treatment do so unnecessarily as surgical resection of the primary and local metastatic lesions is curative. Conversely, some patients may not receive any systemic therapy when in fact they harbor occult metastatic or micrometastatic lesions. 
         [0181]    Islet cell caricomas are derived from pancreatic islet β-cells and often express many of the same cell surface proteins as the β-cells from which they arise. The present invention provides a key diagnostic method for the detection of occult metastatic lesions and for the early detection of pancreatic cancers. 
         [0182]    The current invention provides a method for locating local and distal metastatic lesions arising from a primary pancreatic cancer expressing SAMs and/or neuropilin 1. The method includes administering to a mammal an agent capable of both specifically binding SAMs and/or neuropilin 1 and detection by an imaging device. The resulting image generated by the method can be analyzed and potentially metastatic lesions expressing SAMs and/or neuropilin 1 can be identified. Additionally, the imaging could be repeated over a period of time to determine the rate of growth of the primary or metastatic lesion, or to assess the efficacy of an intervening modality, including but not limited to surgery, radiation, chemotherapy, pharmaceutical therapy, or otherwise. 
         [0183]    Transplantation 
         [0184]    Transplantation of pancreatic islet cells is emerging as a new therapy for the treatment of diabetes. The transplantation of pancreatic islet cells allows many patients to become insulin independent; however, some of these patients will later revert back to a insulin dependence. The potential causes of these reversions are not known but the loss of transplanted islet cell mass is believed to be a major factor. The lack of an effective method for imaging these islet cell masses in vivo has hindered research into the causes and potential treatments for these reversions to insulin dependence. 
         [0185]    The current invention provides a method for determining the total transplanted β-cell mass. Subsequent to transplantation an agent can be administered that binds selectively to SAMs and/or neuropilin 1, and images taken. The resulting image generated by the method can be analyzed and the total β-cell mass can be assessed. Images generated both pre- and post-transplantation can be compared to determine the increase in total β-cell mass, post implantation. Continued follow up images can be used to assess the stability of transplanted cells. 
         [0186]    Conjugated Agents 
         [0187]    One non-limiting aspect of the current invention includes administering to a mammal in need thereof a first agent that is conjugated to a second agent, wherein the first agent is capable of specifically binding to SAMs and/or neuropilin 1, and the second agent is a reporter agent capable of detection by an external imaging device. For the purposes of imaging the second agent may be selected from the group comprising radioistopes, fluorescent tags, paramagnetic ions, enzymes. Several radioisotopes could be used including, but not limited to, iodine 131, yttrium 90, Iodide 124, Zirconium 89, Technicium-99, and Indium 111. Methods of conjugating radioisotopes and paramagnetic ions are well known in the art. Additionally, methods of imaging radioistopes and paramagnetic ions are also well known in the art. Alternatively, the first and second agents could be administered separately, such that the first agent is allowed to bind to SAMs and/or neuropilin 1, and the second agent is then administered and allowed to bind to the first agent. 
         [0188]    Multiple Agents with Binding Capacities 
         [0189]    It is further recognized that several layers of agents are possible. For example, in one non-limiting aspect of the present invention, a first agent capable of binding SAMs and/or neuropilin 1 is administered to a mammal followed by second agent capable of binding the first agent which is conjugated to a third agent. In this scenario the third agent consists of a radioisotope, fluorescent tag, paramagnetic ion, or enzyme capable of detection by an imaging device. 
         [0190]    Imaging Devices 
         [0191]    In any of various methods described herein utilizing imaging devices, any suitable imaging device may be used. Devices currently known in the art include, but are not limited to, devices for nuclear magnetic resonance, magnetic resonance imaging, computer tomography, and positron emission tomography. Other methods for imaging include the use of radioisotopes, paramagnetic ions, labeled antibodies, labeled antibody fragments, labeled polypeptides, labeled nucleic acids, labeled probes, fluorescent imaging methods, and the like. As noted herein, the imaging device or method may detect a first agent bound directly to SAMs and/or neuropilin 1, or may detect a second or third agent bound to the first as described herein. In some instances, more than three agents may be used and layered as described herein. 
         [0192]    Methods for Treating Pancreatic Disease 
         [0193]    The current invention provides a method for treating disease comprising administering to a mammal in need thereof an agent that selectively binds SAMs and/or neuropilin 1. In accordance with a further aspect of the invention the agent is selected from a group consisting of an antibody, antibody fragment, variable region of an antibody, protein, polypeptide, nucleic acids, probes, oligonucleotides, and ribozymes. 
         [0194]    Conjugated First Agents 
         [0195]    One non-limiting aspect of the current invention comprises administering to a mammal in need thereof a first agent that is conjugated to a second agent, wherein the first agent is capable of specifically binding to SAMs and/or neuropilin 1. Because anti-SAMs and/or anti-neuropilin 1 antibodies selectively bind cells expressing the SAMs and/or neuropilin 1 (e.g., cells from patients suffering from pancreatic disease), they can be used in methods to target and/or destroy such SAM or neuropilin 1 expressing cells. Thus, the second agent may be, for example, selected from the group consisting of a cytotoxic agent, radioisotope, toxin, agent capable of inducing cellular senescence, an enzyme, or any other agent capable of providing a desired effect when bound to the first agent. For example, to treat synaptic adhesion molecule associated pancreatic disease, anti-synaptic adhesion molecule antibodies can be labeled with a cytotoxic agent (e.g., ricin), or a radioisotope and administered to an animal having the pancreatic disease (e.g., by intratumoral injection). Further, to treat neuropilin 1 associated pancreatic disease, anti-neuropilin 1 antibodies can be labeled with a cytotoxic agent or radioisotope, as described above, and administered to an animal having the pancreatic disease. 
         [0196]    The current invention is also well adapted to treatments known in the art as Antibody-directed Enzyme Prodrug Therapy. In this aspect the second conjugated agent consists of an enzyme capable of converting a third agent, a pro-drug, into an biologically active product. The third agent may be selected from a group of agents that, when modified by the enzymatic action of the second agent, generate a product with cytotoxic or cytostatic properties. 
         [0197]    Method for Preventing Autoimmune Diabetes and/or Other Autoimmune Diseases 
         [0198]    Antibodies, polypeptides, or other agents that bind to, block, or otherwise interfere with SAMs and/or neuropilin 1 may be used to treat patients with autoimmune diabetes, or may be used prophylactically to prevent individuals at risk for autoimmune diabetes from contracting the disorder. Such agents may function in a number of ways by preventing immune attack on insulin-producing islet β-cells. Any suitable agent may be used as described above, including antibodies, antibody fragments, variable regions of antibodies, proteins, polypeptides, nucleic acids, probes, oligonucleotides, protein-methylation compounds, and ribozymes. Any of various SAMs that serves as part of the “immunological synapse” may be targeted in this manner, including SynCam and Thy-1. In addition, neuropilin 1 may be targeted in this aspect of the present invention. 
         [0199]    Other Agents 
         [0200]    For the purposes of treatment, in many aspects of the present invention, antibodies may be used. Antibodies have properties that make them especially adapted to the current invention. Specifically, they have the ability to recognize almost limitless epitopes, including linear and conformational epitopes comprised of proteins, carbohydrates, glycoproteins, lipoproteins, and/or lipids. 
         [0201]    In the case of administration of the antibody to a human, the antibodies may comprise fully humanized antibodies. Antibodies derived from non-human sources generally cannot be administered to humans because the primary, secondary, and tertiary structures of the antibodies, particularly the crystallizable fragments, are subject to interspecies variations. In most instances the human immune system recognizes these variations as foreign. Methods for the production of antibodies are known in the art. Such antibodies include but are not limited to polyclonal, monoclonal, chimeric, single chain, Fab fragments and a Fab expression library. Additionally, the use of peptide mimetrics to target a specific protein is known in the art. 
         [0202]    In other aspects, the present invention utilizes proteins capable of binding SAMs and/or neuropilin 1. In one non-limiting aspect of the current invention the proteins capable of binding SAMs and/or neuropilin 1 are purified native ligands of SAMs and/or neuropilin 1. Native ligands of SAMs include, but are not limited to, neuroligin 2, neurexin 1, neurexin 2, SynCam, Thy-1, and neuronal pentraxin. Variants of these native ligands such as fragments, analogs and derivatives of native ligands are also within the scope of the present invention. Such variants include, e.g., a polypeptide encoded by a naturally occurring allelic variant of a native ligand, a polypeptide encoded by an alternative splice form of a native ligand, a polypeptide encoded by a homolog of a native ligand, and polypeptides encoded by a non-naturally occurring variant of a native ligand. 
         [0203]    Isolated peptidyl portions of native ligands can be obtained by screening peptides recombinantly produced from the corresponding fragment of the nucleic acid encoding such peptides. In addition, fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry. For example, synaptic adhesion molecule or neuropilin 1 proteins of the present invention may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or preferably divided into overlapping fragments of a desired length. The fragments can be produced (recombinantly or by chemical synthesis) and tested to identify those peptidyl fragments which can bind synaptic adhesion molecule or neuropilin 1 proteins. 
         [0204]    Variants of synaptic adhesion molecule or neuropilin 1 ligands can be generated through various techniques known in the art. For example, ligand variants can be made by mutagenesis, such as by introducing discrete point mutation(s), or by truncation. Mutation can give rise to a ligand variant having substantially the same, or merely a subset of the functional activity of a ligand. Other variants of ligands that can be generated include those that are resistant to proteolytic cleavage, for example, due to mutations that alter protease target sequences. Whether a change in the amino acid sequence of a peptide results in ligand variant having one or more functional activities of a native ligands can be readily determined by testing the variant for a native synaptic adhesion molecule or neuropilin 1 protein&#39;s functional activity. 
         [0205]    Combinatorial mutagenesis has a potential to generate very large libraries of mutant proteins. To screen a large number of protein mutants, techniques that allow one to avoid the very high proportion of non-functional proteins in a random library and simply enhance the frequency of functional proteins (thus decreasing the complexity required to achieve a useful sampling of sequence space) can be used. For example, recursive ensemble mutagenesis (REM), an algorithm that enhances the frequency of functional mutants in a library when an appropriate selection or screening method is employed, might be used. Arkin and Yourvan (1992) Proc. Natl. Acad. Sci. USA 89:7811-7815; Yourvan et al. (1992) Parallel Problem Solving from Nature, Maenner and Manderick, eds., Elsevier Publishing Co., Amsterdam, pp. 401-410; Delgrave et al. (1993) Protein Engineering 6(3): 327-331. 
         [0206]    The invention also provides for reduction of ligands, antibodies to SAMs and/or neuropilin 1, or other proteins capable of specifically binding SAMs and/or neuropilin 1 to generate mimetics, e.g. peptide or non-peptide agents, that are able to bind SAMs or neuropilin 1. 
         [0207]    For example, non-hydrolyzable peptide analogs of such residues can be generated using benzodiazepine (see, e.g., Freidinger et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings (Garvey et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), keto-methylene pseudopepitides (Ewenson et al. (1986) J. Med. Chem. 29:295; and Ewenson et al. in Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium) Pierce Chemical Co. Rockland, Ill., 1985), beta-turn dipeptide cores (Nagai et al. (1985) Tetrahedron Lett 26:647; and Sato et al. (1986) J. Chem. Soc. Perkin. Trans. 1: 1231), and beta-aminoalcohols (Gordon et al. (1985) Biochem. Biophys. Res. Commun. 126:419; and Dann et al. (1986) Biochem. Biophys. Res. Commun. 134:71). Ligands may also be chemically modified to create ligand derivatives by forming covalent or aggregate conjugates with other chemical moieties, such as glycosyl groups, lipids, phosphate, acetyl groups and the like. Covalent derivatives of ligands can be prepared by linking the chemical moieties to functional groups on amino acid side chains of the protein or at the N-terminus or at the C-terminus of the polypeptide. 
         [0208]    Identification and Separation 
         [0209]    The current invention provides a method for identifying and separating mammalian cells expressing SAMs and/or neuropilin 1 from cells not expressing SAMs or neuropilin 1 comprising combining cells with an agent capable of binding SAMs and separating the cells capable of binding the agent from cells incapable of binding the agent. The synaptic adhesion molecule may include neuroligin 1, neuroligin 2, neuroligin 3, neuroligin 4X, neuroligin 4Y, neurexin 1α, neurexin 2α, neurexin 3α, neurexin 1β, neurexin 2β, neurexin 3β, SynCam, Thy-1, and neuronal pentraxin. Further, neuropilin 1 may be utilized. In accordance with a further aspect of the invention the agent is selected from a group consisting of an antibody, antibody fragment, variable region of an antibody, protein, polypeptide, nucleic acids, probes, oligonucleotides, and ribozymes. 
         [0210]    In one non-limiting aspect of the present invention, the cells to be separated are obtained from a tissue. Methods for isolating cells from a tissue explant are well known by those skilled in the art. 
         [0211]    Separation and Transplantation 
         [0212]    Transplantation of islet β-cells from the pancreas is emerging as a potential therapy for the treatment of diabetes mellitus. The transplantation procedure consists of harvesting pancreatic tissue from a donor. The β-cells are then identified and separated from the remaining population of cells. The resulting population of islet β-cells are either transplanted directly into the recipient or are expanded in vitro and then transplanted. Transplantation occurs by injection into the portal vein with the resulting formation of islet masses in the hepatic tissue. 
         [0213]    The current technique provides a method for separating β-cells from a mixture of cells comprising adding an agent capable of binding SAMs and/or neuropilin 1 to a mixture of cells and separating the cells capable of binding the agent from those incapable of binding the agent based on the ability of cells to bind the agent. The resulting population of islet β-cells could be used for transplantation into a recipient in need thereof. Additionally, the current invention could be used to separate a population of synaptic adhesion molecule expressing stem cells from a sample of stem cells. 
         [0214]    Pancreatic Cells 
         [0215]    One non-limiting aspect of the current invention comprises combining pancreatic tissue or cells obtained therefrom with an agent capable of binding SAMs and/or neuropilin 1 and separating the cells binding the agent from the cells not binding the agent. Separating pancreatic cells expressing SAMs and/or neuropilin 1 could be useful for numerous purposes. For example, isolated pancreatic cancer cells expressing SAMs and/or neuropilin 1 could be used in the preparation of a cancer vaccine. It is appreciated that separation could be obtained by a variety of methods. 
         [0216]    Affinity for Agent 
         [0217]    In one aspect of the invention cells are mixed with an agent that is capable of binding SAMs and/or neuropilin 1 whether it is immobilized on a solid surface or free in solution. The cells that bind the immobilized agent are then separated from the non-binding cells based on the affinity of SAM and/or neuropilin 1 expressing cells for the immobilized agent. The solid phase used in this invention may be any surface commonly used in such methods. For example, the solid phase may be particulate; it may be the surface of beads, e.g., glass or polystyrene beads, or it may be the solid wall surface of any of a variety of containers, e.g., centrifuge tubes, columns, microtiter plate wells, filters, membranes and tubing, among other containers. 
         [0218]    In one aspect of the present invention, the agent is immobilized on magnetic or magnetizable particles, such as paramagnetic particles. A sample of cells is added to the particles and separation occurs based on the affinity of the cells expressing SAMs and/or neuropilin 1 to the agent bound to paramagnetic particles. The application of an external magnetic field aids the separation of the paramagnetic particles with the bound cells from the unbound cells. The sample is then washed with a buffer solution and the cells which remain bound to the immobilized agent are retained. 
         [0219]    FACS Analysis 
         [0220]    In one aspect of the present invention the method of separation is fluorescence-activated cell sorting (FACS). In this embodiment the cell sample would be treated with an agent, preferably an antibody that is conjugated to fluorescent tag. The population would be then be placed into a FACS analyzer and the cells binding the antibody would be separated from the non-binding cells based on intensity of emitted fluorescent radiation. 
         [0221]    It is appreciated that several insubstantial substitutions could be made to this embodiment, as this method of cell sorting is readily known in the art. For example, the use of an unconjugated primary antibody capable of binding SAMs and/or neuropilin 1 followed by the addition of a conjugated secondary antibody, derived from a distinct species of animal, would be readily known to one skilled in the art. Additionally, any number of fluorescent tags with varying excitation and emission wavelengths could be used and would be readily known to one skilled in the art. 
         [0222]    Identification 
         [0223]    The current invention provides a method for identifying mammalian cells expressing SAMs and/or neuropilin 1 comprising combining a sample of cells with an agent capable of binding SAMs and/or neuropilin 1 and identifying the cells, directly or indirectly, that are capable of binding the agent. The synaptic adhesion molecule may be selected from the group consisting of neuroligin 1, neuroligin 2, neuroligin 3, neuroligin 4X, neuroligin 4Y, neurexin 1α, neurexin 2α, neurexin 3α, neurexin 1β, neurexin 2β, neurexin 3β, SynCam, Thy-1, and neuronal pentraxin. Further, neuropilin 1 may be used. In accordance with a further aspect of the invention the agent is selected from a group consisting of an antibody, antibody fragment, variable region of an antibody, protein, polypeptide, nucleic acids, probes, oligonucleotides, and ribozymes. 
         [0224]    In one non-limiting aspect of the current invention the first agent is conjugated to a second agent which is capable of generating a signal either directly or indirectly, the signal being perceptible either visually or with the aid of an imaging device. The second agent may be selected from the group consisting of a fluorescent tag, radioisotope, enzyme, or paramagnetic ion. 
         [0225]    Pharmaceutical Preparations and Methods of Administration 
         [0226]    In addition to administration of the antibodies described above, other identified agents treat, inhibit, control and/or prevent, or at least partially arrest or partially prevent, pancreatic disease and can be administered to a subject at therapeutically effective doses for the inhibition, prevention, prophylaxis or therapy for damage caused by pancreatic disease. The agents of the present invention comprise a therapeutically effective dosage of an antibody, antibody fragment, variable region of an antibodies, proteins, polypeptides, nucleic acids, probes, oligonucleotides, ribozymes, and any combination thereof, and other compounds that bind SAMs and/or neuropilin 1, a term which includes therapeutically, inhibitory, preventive and prophylactically effective doses of the agents of the present invention and is more particularly defined below. Without being bound to any particular theory, applicants surmise that these pharmaceutical agents prevent damage caused by pancreatic diseases when administered to a subject suffering from a related condition by modulating β-cell adhesion, spreading, and migration. The subject is an animal, including, but not limited to, mammals, reptiles and avians, horses, cows, dogs, cats, sheep, pigs, and chickens, and specifically, humans. 
         [0227]    Therapeutically Effective Dosage 
         [0228]    Toxicity and therapeutic efficacy of such agents can be determined by standard pharmaceutical procedures in cell cultures or experimental animals for determining the LD 50  (the dose lethal to 50% of the population) and the ED 50 , (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index that can be expressed as the ratio LD 50 /ED 50 . Agents that exhibit large therapeutic indices are preferred. While agents exhibiting toxic side effects may be used, care should be taken to design a delivery system that targets such agents to the site affected by the disease or disorder in order to minimize potential damage to unaffected cells and reduce side effects. 
         [0229]    The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosages for use in humans and other mammals. The dosage of such agents lies preferably within a range of circulating plasma or other bodily fluid concentrations that include the ED 50  with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any agents of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dosage may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 50  (the concentration of the test agent that achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful dosages in humans and other mammals. Agent levels in plasma may be measured, for example, by high performance liquid chromatography. 
         [0230]    The amount of an agent that may be combined with pharmaceutically acceptable carriers to produce a single dosage form will vary depending upon the host treated and the particular mode of administration. It will be appreciated by those skilled in the art that the unit content of a agent contained in an individual dose of each dosage form need not in itself constitute a therapeutically effective amount, as the necessary therapeutically effective amount could be reached by administration of a number of individual doses. The selection of dosage depends upon the dosage form utilized, the condition being treated, and the particular purpose to be achieved according to the determination of those skilled in the art. 
         [0231]    The dosage regime for treating a disease or condition with the agents and/or agent combinations of this invention is selected in accordance with a variety of factors, including the type, age, weight, sex, diet and medical condition of the patient, the route of administration, pharmacological considerations such as activity, efficacy, pharmacokinetic and toxicology profiles of the particular agent employed, whether an agent delivery system is utilized and whether the agent is administered as a pro-drug or part of a drug combination. Thus, the dosage regime actually employed may vary widely from subject to subject. 
         [0232]    Formulations and Use 
         [0233]    The agents of the present invention may be formulated by known methods for administration to a subject using several routes which include, but are not limited to, parenteral, oral, topical, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and ophthalmic routes. The individual agents may also be administered in combination with one or more additional agents of the present invention and/or together with other biologically active or biologically inert agents (“agent combinations”). Such biologically active or inert agents may be in fluid or mechanical communication with the agent(s) or attached to the agent(s) by ionic, covalent, Van der Waals, hydrophobic, hydrophilic or other physical forces. It is preferred that administration is localized in a subject, but administration may also be systemic. 
         [0234]    The agents or agent combinations may be formulated by any conventional manner using one or more pharmaceutically acceptable carriers and/or excipients. Thus, the agents and their pharmaceutically acceptable salts and solvates may be specifically formulated for administration, e.g., by inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral or rectal administration. The agent or agent combinations may take the form of charged, neutral and/or other pharmaceutically acceptable salt forms. Examples of pharmaceutically acceptable carriers include, but are not limited to, those described in Remington&#39;s Pharmaceutical Sciences (A. R. Gennaro, Ed.), 20th edition, Williams &amp; Wilkins PA, USA (2000). 
         [0235]    The agents may also take the form of solutions, suspensions, emulsions, tablets, pills, capsules, powders, controlled- or sustained-release formulations and the like. Such agents will contain a therapeutically effective amount of the agent, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration. 
         [0236]    Parenteral Administration 
         [0237]    The agent or agent combination may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form in ampoules or in multi-dose containers with an optional preservative added. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass, plastic or the like. The agent may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. 
         [0238]    For example, a parenteral preparation may be a sterile injectable solution or suspension in a nontoxic parenterally acceptable diluent or solvent (e.g., as a solution in 1,3-butanediol). Among the acceptable vehicles and solvents that may be employed are water, Ringer&#39;s solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil may be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid may be used in the parenteral preparation. 
         [0239]    Alternatively, the agent may be in powder form for constitution with a suitable vehicle, such as sterile pyrogen-free water, before use. For example, a agent suitable for parenteral administration may comprise a sterile isotonic saline solution containing between 0.1 percent and 90 percent weight per volume of the agent or agent combination. By way of example, a solution may contain from about 5 percent to about 20 percent, more preferably from about 5 percent to about 17 percent, more preferably from about 8 to about 14 percent, and still more preferably about 10 percent of the agent. The solution or powder preparation may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Other methods of parenteral delivery of agents will be known to the skilled artisan and are within the scope of the invention. 
         [0240]    Oral Administration 
         [0241]    For oral administration, the agent or agent combination may take the form of tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents, fillers, lubricants and disintegrants: 
         [0242]    A. Binding Agents 
         [0243]    Binding agents include, but are not limited to, corn starch, potato starch, or other starches, gelatin, natural and synthetic gums such as acacia, sodium alginate, alginic acid, other alginates, powdered tragacanth, guar gum, cellulose and its derivatives (e.g., ethyl cellulose, cellulose acetate, carboxymethyl cellulose calcium, sodium carboxymethyl cellulose), polyvinyl pyrrolidone, methyl cellulose, pre-gelatinized starch, hydroxypropyl methyl cellulose, (e.g., Nos. 2208, 2906, 2910), microcrystalline cellulose, and mixtures thereof. Suitable forms of microcrystalline cellulose include, for example, the materials sold as AVICEL-PH-101, AVICEL-PH-103 and AVICEL-PH-105 (available from FMC Corporation, American Viscose Division, Avicel Sales, Marcus Hook, Pa., USA). An exemplary suitable binder is a mixture of microcrystalline cellulose and sodium carboxymethyl cellulose sold as AVICEL RC-581 by FMC Corporation. 
         [0244]    B. Fillers 
         [0245]    Fillers include, but are not limited to, talc, calcium carbonate (e.g., granules or powder), lactose, microcrystalline cellulose, powdered cellulose, dextrates, kaolin, mannitol, silicic acid, sorbitol, starch, pre-gelatinized starch, and mixtures thereof. 
         [0246]    C. Lubricants 
         [0247]    Lubricants include, but are not limited to, calcium stearate, magnesium stearate, mineral oil, light mineral oil, glycerin, sorbitol, mannitol, polyethylene glycol, other glycols, stearic acid, sodium lauryl sulfate, talc, hydrogenated vegetable oil (e.g., peanut oil, cottonseed oil, sunflower oil, sesame oil, olive oil, corn oil, and soybean oil), zinc stearate, ethyl oleate, ethyl laurate, agar, and mixtures thereof. Additional lubricants include, for example, a syloid silica gel (AEROSIL 200, manufactured by W.R. Grace Co. of Baltimore, Md., USA), a coagulated aerosol of synthetic silica (marketed by Deaussa Co. of Plano, Tex., USA), CAB-O-SIL (a pyrogenic silicon dioxide product sold by Cabot Co. of Boston, Mass., USA), and mixtures thereof. 
         [0248]    D. Disintegrants 
         [0249]    Disintegrants include, but are not limited to, agar-agar, alginic acid, calcium carbonate, microcrystalline cellulose, croscarmellose sodium, crospovidone, polacrilin potassium, sodium starch glycolate, potato or tapioca starch, other starches, pre-gelatinized starch, other starches, clays, other algins, other celluloses, gums, and mixtures thereof. 
         [0250]    The tablets or capsules may optionally be coated by methods well known in the art. If binders and/or fillers are used with the agents of the invention, they are typically formulated as about 50 to about 99 weight percent of the agent. Preferably, about 0.5 to about 15 weight percent of disintegrant, preferably about 1 to about 5 weight percent of disintegrant, may be used in the agent. A lubricant may optionally be added, typically in an amount of less than about 1 weight percent of the agent. Techniques and pharmaceutically acceptable additives for making solid oral dosage forms are described in Marshall, Solid Oral Dosage Forms, Modern Pharmaceutics (Banker and Rhodes, Eds.), 7:359-427 (1979). Other less typical formulations are known in the art. 
         [0251]    Liquid preparations for oral administration may take the form of solutions, syrups or suspensions. Alternatively, the liquid preparations may be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and/or preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations may also contain buffer salts, flavoring, coloring, perfuming and sweetening agents as appropriate. Preparations for oral administration may also be formulated to achieve controlled release of the agent. Oral formulations preferably contain 10% to 95% agent. In addition, the agents of the present invention may be formulated for buccal administration in the form of tablets or lozenges formulated in a conventional manner. Other methods of oral delivery of agents will be known to the skilled artisan and are within the scope of the invention. 
         [0252]    Controlled-Release Administration 
         [0253]    Controlled-release (or sustained-release) preparations may be formulated to extend the activity of the agent or agent combination and reduce dosage frequency. Controlled-release preparations can also be used to effect the time of onset of action or other characteristics, such as blood levels of the agent, and consequently affect the occurrence of side effects. 
         [0254]    Controlled-release preparations may be designed to initially release an amount of a agent that produces the desired therapeutic effect, and gradually and continually release other amounts of the agent to maintain the level of therapeutic effect over an extended period of time. In order to maintain a near-constant level of an agent in the body, the agent could be released from the dosage form at a rate that will replace the amount of agent being metabolized and/or excreted from the body. The controlled-release of an agent may be stimulated by various inducers, e.g., change in pH, change in temperature, enzymes, water, or other physiological conditions or molecules. 
         [0255]    Controlled-release systems may include, for example, an infusion pump which may be used to administer the agent in a manner similar to that used for delivering insulin or chemotherapy to specific organs or tumors. Typically, using such a system, the agent is administered in combination with a biodegradable, biocompatible polymeric implant that releases the agent over a controlled period of time at a selected site. Examples of polymeric materials include polyanhydrides, polyorthoesters, polyglycolic acid, polylactic acid, polyethylene vinyl acetate, and copolymers and blends thereof. In addition, a controlled release system can be placed in proximity of a therapeutic target, thus requiring only a fraction of a systemic dosage. 
         [0256]    The agents of the invention may be administered by other controlled-release means or delivery devices that are well known to those of ordinary skill in the art. These include, for example, hydropropylmethyl cellulose, other polymer matrices, gels, permeable membranes, osmotic systems, multilayer coatings, microparticles, liposomes, microspheres, or the like, or a combination of any of the above to provide the desired release profile in varying proportions. Other methods of controlled-release delivery of agents will be known to the skilled artisan and are within the scope of the invention. 
         [0257]    Inhalation Administration 
         [0258]    The agent or agent combination may also be administered directly to the lung by inhalation. For administration by inhalation, a agent may be conveniently delivered to the lung by a number of different devices. For example, a Metered Dose Inhaler (“MDI”) which utilizes canisters that contain a suitable low boiling point propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas may be used to deliver an agent directly to the lung. MDI devices are available from a number of suppliers such as 3M Corporation, Aventis, Boehringer Ingleheim, Forest Laboratories, Glaxo-Wellcome, Schering Plough and Vectura. 
         [0259]    Alternatively, a Dry Powder Inhaler (DPI) device may be used to administer an agent to the lung. DPI devices typically use a mechanism such as a burst of gas to create a cloud of dry powder inside a container, which may then be inhaled by the patient. DPI devices are also well known in the art and may be purchased from a number of vendors which include, for example, Fisons, Glaxo-Wellcome, Inhale Therapeutic Systems, ML Laboratories, Qdose and Vectura. A popular variation is the multiple dose DPI (“MDDPI”) system, which allows for the delivery of more than one therapeutic dose. MDDPI devices are available from companies such as AstraZeneca, GlaxoWellcome, IVAX, Schering Plough, SkyePharma and Vectura. For example, capsules and cartridges of gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch for these systems. 
         [0260]    Another type of device that may be used to deliver an agent to the lung is a liquid spray device supplied, for example, by Aradigm Corporation. Liquid spray systems use extremely small nozzle holes to aerosolize liquid agent formulations that may then be directly inhaled into the lung. For example, a nebulizer device may be used to deliver a agent to the lung. Nebulizers create aerosols from liquid agent formulations by using, for example, ultrasonic energy to form fine particles that may be readily inhaled. Examples of nebulizers include devices supplied by Sheffield/Systemic Pulmonary Delivery Ltd., Aventis and Batelle Pulmonary Therapeutics. 
         [0261]    In another example, an electrohydrodynamic (“EHD”) aerosol device may be used to deliver an agent to the lung. EHD aerosol devices use electrical energy to aerosolize liquid agent solutions or suspensions. The electrochemical properties of the agent formulation are important parameters to optimize when delivering this agent to the lung with an EHD aerosol device. Such optimization is routinely performed by one of skill in the art. Other methods of intra-pulmonary delivery of agents will be known to the skilled artisan and are within the scope of the invention. 
         [0262]    Liquid agent formulations suitable for use with nebulizers and liquid spray devices and EHD aerosol devices will typically include the agent with a pharmaceutically acceptable carrier. In one exemplary embodiment, the pharmaceutically acceptable carrier is a liquid such as alcohol, water, polyethylene glycol or a perfluorocarbon. Optionally, another material may be added to alter the aerosol properties of the solution or suspension of the agent. For example, this material may be a liquid such as an alcohol, glycol, polyglycol or a fatty acid. Other methods of formulating liquid agent solutions or suspensions suitable for use in aerosol devices are known to those of skill in the art. 
         [0263]    Depot Administration 
         [0264]    The agent or agent combination may also be formulated as a depot preparation. Such long-acting formulations may be administered by implantation (e.g., subcutaneously or intramuscularly) or by intramuscular injection. Accordingly, the agents may be formulated with suitable polymeric or hydrophobic materials such as an emulsion in an acceptable oil or ion exchange resins, or as sparingly soluble derivatives such as a sparingly soluble salt. Other methods of depot delivery of agent s will be known to the skilled artisan and are within the scope of the invention. 
         [0265]    Topical Administration 
         [0266]    For topical application, the agent or agent combination may be combined with a carrier so that an effective dosage is delivered, based on the desired activity ranging from an effective dosage, for example, of 1.0 μM to 1.0 mM. In one embodiment, a topical agent is applied to the skin. The carrier may be in the form of, for example, and not by way of limitation, an ointment, cream, gel, paste, foam, aerosol, suppository, pad or gelled stick. 
         [0267]    A topical formulation may also consist of a therapeutically effective amount of the agent in an opthalmologically acceptable excipient such as buffered saline, mineral oil, vegetable oils such as corn or arachis oil, petroleum jelly, Miglyol 182, alcohol solutions, or liposomes or liposome-like products. Any of these agents may also include preservatives, antioxidants, antibiotics, immunosuppressants, and other biologically or pharmaceutically effective agents which do not exert a detrimental effect on the agent. Other methods of topical delivery of agents will be known to the skilled artisan and are within the scope of the invention. 
       Suppository Administration 
       [0268]    The agent or agent combination may also be formulated in rectal formulations such as suppositories or retention enemas containing conventional suppository bases such as cocoa butter or other glycerides and binders and carriers such as triglycerides, microcrystalline cellulose, gum tragacanth or gelatin. Suppositories may contain the agent in the range of 0.5% to 10% by weight. Other methods of suppository delivery of agents will be known to the skilled artisan and are within the scope of the invention. 
         [0269]    Other Systems of Administration 
         [0270]    Various other delivery systems are known in the art and can be used to administer the agents of the invention. Moreover, these and other delivery systems may be combined and/or modified to optimize the administration of the agents of the present invention. Exemplary formulations using the agents of the present invention are described below (the agents of the present invention are indicated as the active ingredient, but those of skill in the art will recognize that pro-drugs and agent combinations are also meant to be encompassed by this term). 
         [0271]    Biological Methods 
         [0272]    Methods involving conventional molecular biology techniques are generally known in the art and are described in detail in methodology treatises such as M OLECULAR  C LONING : A L ABORATORY  M ANUAL,  2nd ed., vol. 1-3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; and C URRENT  P ROTOCOLS IN  M OLECULAR  B IOLOGY , ed. Ausubel et al., Greene Publishing and Wiley-Interscience, New York, 1992 (with periodic updates). Various techniques using polymerase chain reaction (PCR) are described, e.g., in Innis et al., PCR P ROTOCOLS : A G UIDE TO  M ETHODS AND  A PPLICATIONS , Academic Press: San Diego, 1990. PCR-primer pairs can be derived from known sequences by known techniques such as using computer programs intended for that purpose. Immunological methods (e.g., preparation of antigen-specific antibodies, immunoprecipitation, and immunoblotting) are described, e.g., in Current Protocols in Immunology, ed. Coligan et al., John Wiley &amp; Sons, New York, 1991; and Methods of Immunological Analysis, ed. Masseyeff et al., John Wiley &amp; Sons, New York, 1992. Each reference is incorporated herein by reference in its entirety. 
       OTHER EMBODIMENTS 
       [0273]    The detailed description set forth above is provided to aid those skilled in the art in practicing the present invention. The invention described and claimed herein, however, is not to be limited in scope by the specific embodiments herein disclosed because these embodiments are intended as illustration of several aspects of the invention. Any equivalent embodiments are intended to be within the scope of the present invention. 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 which do not depart from the spirit or scope of the present inventive discovery. Such modifications are also intended to fall within the scope of the appended claims. 
       REFERENCES CITED 
       [0274]    All publications, patents, patent applications, and other references cited in this application are incorporated herein by reference in their entirety for all purpose to the same extent as if each individual publication, patent, patent application, or other reference was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.