Nucleic acids encoding GTPase activating proteins

Abstract

The invention provides GTPase activating proteins, their encoding cDNAs, and antibodies that specifically bind the proteins. The invention also provides for the use of these compositions in the diagnosis, prognosis, treatment and evaluation of progression and treatment of signaling, immune, and cell proliferative disorders, particularly colon cancer.

What is claimed is:  
     
         1 . A purified protein comprising a polypeptide having the amino acid sequence of SEQ ID NO:30 or SEQ ID NO:31.  
     
     
         2 . A biologically active portion of the protein of  claim 1  wherein the portion is selected from residue L 8  to residue S 169 , from residue P 210  to residue A 235 , and from residue L 310  to residue L 350  of SEQ ID NO:30 or SEQ ID NO:31.  
     
     
         3 . An antigenic epitope of the protein of  claim 1  wherein the epitope extends from residue G 27  to residue P 45  of SEQ ID NO:30 or SEQ ID NO:31.  
     
     
         4 . A variant having at least 65% homology to the protein having the amino acid sequence of SEQ ID NO:30 or SEQ ID NO:31.  
     
     
         5 . A composition comprising the protein of  claim 1  and a labeling moiety.  
     
     
         6 . A composition comprising the protein of  claim 1  and a pharmaceutical carrier.  
     
     
         7 . A substrate upon which the protein of  claim 1  is immobilized.  
     
     
         8 . An array element comprising the protein of  claim 1 .  
     
     
         9 . A method for detecting expression of a protein in a sample, the method comprising: 
 a) performing an assay to determine the amount of the protein of  claim 1  in a sample; and    b) comparing the amount of protein to standards, thereby detecting expression of the protein having the amino acid sequence of SEQ ID NO:30 or SEQ ID NO:31 in the sample.    
     
     
         10 . The method of  claim 9  wherein the assay is selected from antibody or protein arrays, enzyme-linked immunosorbent assays, fluorescence-activated cell sorting, spatial immobilization such as 2D-PAGE and scintillation counting, high performance liquid chromatography, or mass spectrophotometry, radioimmunoassays and western analysis.  
     
     
         11 . The method of  claim 9  wherein the sample is from colon.  
     
     
         12 . The method of  claim 9  wherein the protein is differentially expressed when compared with at least one standard and is diagnostic of cancer.  
     
     
         13 . A method for using a protein to screen a plurality of molecules and compounds to identify at least one ligand, the method comprising: 
 a) combining the protein of  claim 1  with a plurality of molecules and compounds under conditions to allow specific binding; and    b) detecting specific binding, thereby identifying a ligand that specifically binds the protein.    
     
     
         14 . The method of  claim 13  wherein the molecules and compounds are selected from agonists, antibodies, small drug molecules, multispecific molecules, peptides, and proteins.  
     
     
         15 . A method for using a protein to identify an antibody that specifically binds the protein comprising: 
 a) contacting a plurality of antibodies with the protein of  claim 1  under conditions to allow specific binding, and    b) detecting specific binding between an antibody and the protein, thereby identifying an antibody that specifically binds the protein having the amino acid sequence of SEQ ID NO:30 or SEQ ID NO:31.    
     
     
         16 . The method of  claim 15 , wherein the plurality of antibodies are selected from a polyclonal antibody, a monoclonal antibody, a chimeric antibody, a recombinant antibody, a humanized antibody, a single chain antibody, a Fab fragment, an F(ab′) 2  fragment, an Fv fragment; and an antibody-peptide fusion protein.  
     
     
         17 . A method of using a protein to prepare and purify a polyclonal antibody comprising: 
 a) immunizing a animal with a protein of  claim 1  under conditions to elicit an antibody response;    b) isolating animal antibodies;    c) attaching the protein to a substrate;    d) contacting the substrate with isolated antibodies under conditions to allow specific binding to the protein; and    e) dissociating the antibodies from the protein, thereby obtaining purified polyclonal antibodies.    
     
     
         18 . A method of using a protein to prepare a monoclonal antibody comprising: 
 a) immunizing a animal with a protein of  claim 1  under conditions to elicit an antibody response;    b) isolating antibody-producing cells from the animal;    c) fusing the antibody-producing cells with immortalized cells in culture to form monoclonal antibody producing hybridoma cells;    d) culturing the hybridoma cells; and    e) isolating from culture monoclonal antibody that specifically binds the protein having the amino acid sequence of SEQ ID NO:30 or SEQ ID NO:31.    
     
     
         19 . A method for using a protein to diagnose a cancer comprising: 
 a) performing an assay to quantify the expression of the protein of  claim 1  in a sample; and    b) comparing the expression of the protein to standards, thereby diagnosing cancer.    
     
     
         20 . The method of  claim 19  wherein the sample is from colon.  
     
     
         21 . A method for testing a molecule or compound for effectiveness as an antagonist comprising: 
 a) exposing a sample comprising the protein of  claim 1  to the molecule or compound; and    b) detecting antagonist activity in the sample.    
     
     
         22 . A method for testing a molecule or compound for effectiveness as an agonist comprising: 
 a) exposing a sample comprising the protein of  claim 1  to the molecule or compound; and    b) detecting agonist activity in the sample.    
     
     
         23 . An isolated antibody that specifically binds a protein having the amino acid sequence of SEQ ID NO:30.  
     
     
         24 . A polyclonal antibody produced by the method of  claim 17 .  
     
     
         25 . A monoclonal antibody produced by the method of  claim 18 .  
     
     
         26 . A method for using an antibody to detect expression of a protein in a sample, the method comprising: 
 a) combining the antibody of  claim 23  with a sample under conditions which allow the formation of antibody:protein complexes; and    b) detecting complex formation, wherein complex formation indicates expression of the protein in the sample.    
     
     
         27 . The method of  claim 26  wherein the sample is from colon.  
     
     
         28 . The method of  claim 26  wherein complex formation is compared with standards and is diagnostic of cancer.  
     
     
         29 . A method for using an antibody to immunopurify a protein comprising: 
 a) attaching the antibody of  claim 23  to a substrate;    b) exposing the antibody to a sample containing protein under conditions to allow antibody:protein complexes to form;    c) dissociating the protein from the complex; and d) collecting the purified protein.    
     
     
         30 . A composition comprising an antibody of  claim 23  and a labeling moiety.  
     
     
         31 . A kit comprising the composition of  claim 30 .  
     
     
         32 . An array element comprising the antibody of  claim 23 .  
     
     
         33 . A substrate upon which the antibody of  claim 23  is immobilized.  
     
     
         34 . A composition comprising an antibody of  claim 23  and a pharmaceutical agent.  
     
     
         35 . The composition of  claim 34  wherein the composition is lyophilized.  
     
     
         36 . A method for using a composition to assess efficacy of a molecule or compound, the method comprising: 
 a) treating a sample containing protein with a molecule or compound;    b) contacting the protein in the sample with the composition of  claim 30  under conditions for complex formation;    c) determining the amount of complex formation; and    d) comparing the amount of complex formation in the treated sample with the amount of complex formation in an untreated sample, wherein a difference in complex formation indicates efficacy of the molecule or compound.    
     
     
         37 . A method for using a composition to assess toxicity of a molecule or compound, the method comprising: 
 a) treating a sample containing protein with a molecule or compound;    b) contacting the protein in the sample with the composition of  claim 30  under conditions for complex formation;    c) determining the amount of complex formation; and    d) comparing the amount of complex formation in the treated sample with the amount of complex formation in an untreated sample, wherein a difference in complex formation indicates toxicity of the molecule or compound.    
     
     
         38 . A method for treating a cancer comprising administering to a subject in need of therapeutic intervention the antibody of  claim 23 .  
     
     
         39 . A method for treating a cancer comprising administering to a subject in need of therapeutic intervention the antibody of  claim 25 .  
     
     
         40 . A method for treating a cancer comprising administering to a subject in need of therapeutic intervention the composition of  claim 34 .  
     
     
         41 . A method for delivering a therapeutic agent to a cell comprising: 
 a) attaching the therapeutic agent to a multispecific molecule identified by the method of  claim 13;  and    b) administering the multi specific molecule to a subject in need of therapeutic intervention, wherein the multispecific molecule specifically binds the protein having the amino acid sequence of SEQ ID NO:30 thereby delivering the therapeutic agent to the cell.    
     
     
         42 . The method of  claim 40 , wherein the cell is an epithelial cell of the colon.  
     
     
         43 . An agonist that specifically binds the protein of  claim 1 .  
     
     
         44 . A composition comprising an agonist of  claim 43  and a pharmaceutical carrier.  
     
     
         45 . An antagonist that specifically binds the protein of  claim 1 .  
     
     
         46 . A composition comprising the antagonist of  claim 44  and a pharmaceutical carrier.  
     
     
         47 . A pharmaceutical agent that specifically binds the protein of  claim 1 .  
     
     
         48 . A composition comprising the pharmaceutical agent of  claim 47  and a pharmaceutical carrier.  
     
     
         49 . A small drug molecule that specifically binds the protein of  claim 1 .  
     
     
         50 . A composition comprising the small drug molecule of  claim 49  and a pharmaceutical carrier.  
     
     
         51 . An antisense molecule of 18 to 30 nucleotides in length that specifically binds a portion of a polynucleotide having a nucleic acid sequence of SEQ ID NO:30 wherein the antisense molecule inhibits expression of the protein encoded by the polynucleotide.  
     
     
         52 . The antisense molecule of  claim 51  wherein the antisense molecule comprises at least one modified internucleoside linkage.  
     
     
         53 . The antisense molecule of  claim 52  wherein the modified internucleoside linkage is a phosphorothioate linkage.  
     
     
         54 . The antisense molecule of  claim 51  wherein the antisense molecule contains at least one nucleotide analog.  
     
     
         55 . The antisense molecule of  claim 54  wherein the nucleotide analog is a 5-methylcytosine.