Polycyclic aromatic hydrocarbon induced molecules

Abstract

The invention provides novel nucleic acid molecules and encoded proteins associated with response to polycyclic aromatic hydrocarbon exposure. The invention also provides expression vectors, host cells, and antibodies. The invention also provides methods for screening or purifying ligands and diagnosing, treating or preventing disorders associated with polycyclic aromatic hydrocarbon exposure.

What is claimed is:  
     
         1 . A substantially purified nucleic acid molecule expressed in response to polycyclic aromatic hydrocarbon exposure comprising: 
 (a) a nucleic acid molecule encoding a protein selected from SEQ ID NOs: 7, 8 and 14;    (b) a nucleic acid molecule selected from the group consisting of SEQ ID NOs: 1-5 and 9-13; or    (c) a nucleic acid molecule which is the complement of the nucleic acid molecule of (a) or    (b) wherein each and every nucleotide of the complement is complementary to each and every nucleotide of the nucleic acid molecule of (a) or (b).    
     
     
         2 . A substantially purified nucleic acid molecule expressed in response to polycyclic aromatic hydrocarbon exposure comprising: 
 (a) a nucleic acid molecule encoding a protein of SEQ ID NO: 6; or    (b) a nucleic acid molecule which is the complement of the nucleic acid molecule of (a) wherein each and every nucleotide of the complement is complementary to each and every nucleotide of the nucleic acid molecule of (a).    
     
     
         3 . A method of using a nucleic acid molecule to screen a library of molecules or compounds to identify at least one ligand which specifically binds the nucleic acid molecule, the method comprising: 
 (a) combining the nucleic acid molecule of  claim 1  with a library of molecules or compounds under conditions to allow specific binding; and    (b) detecting specific binding, thereby identifying a ligand which specifically binds the nucleic acid molecule.    
     
     
         4 . A method of using a nucleic acid molecule to screen a library of molecules or compounds to identify at least one ligand which specifically binds the nucleic acid molecule, the method comprising: 
 (a) combining the nucleic acid molecule of  claim 2  with a library of molecules or compounds under conditions to allow specific binding; and    (b) detecting specific binding, thereby identifying a ligand which specifically binds the nucleic acid molecule.    
     
     
         5 . The method of  claim 3  wherein the library is selected from DNA molecules, RNA molecules, peptide nucleic acids, mimetics, and proteins.  
     
     
         6 . The method of  claim 4  wherein the library is selected from DNA molecules, RNA molecules, peptide nucleic acids, mimetics, and proteins.  
     
     
         7 . A ligand identified by the method of  claim 3  which modulates the activity of the nucleic acid molecule.  
     
     
         8 . A ligand identified by the method of  claim 5  which modulates the activity of the nucleic acid molecule.  
     
     
         9 . A method of using a nucleic acid molecule to purify a ligand which specifically binds the nucleic acid molecule, the method comprising: 
 (a) combining the nucleic acid molecule of  claim 1  with a sample under conditions to allow specific binding;    (b) detecting specific binding between the nucleic acid molecule and a ligand;    (c) recovering the bound nucleic acid molecule; and    (d) separating the nucleic acid molecule from the ligand, thereby obtaining purified ligand.    
     
     
         10 . A method of using a nucleic acid molecule to purify a ligand which specifically binds the nucleic acid molecule, the method comprising: 
 (a) combining the nucleic acid molecule of  claim 2  with a sample under conditions to allow specific binding;    (b) detecting specific binding between the nucleic acid molecule and a ligand;    (c) recovering the bound nucleic acid molecule; and    (d) separating the nucleic acid molecule from the ligand, thereby obtaining purified ligand.    
     
     
         11 . A method for diagnosing a disorder or condition associated with the altered expression of a gene expressed in response to polycyclic aromatic hydrocarbon exposure in a plurality of biological samples, the method comprising the steps of: 
 (a) hybridizing a nucleic acid molecule of  claim 1  to a sample under conditions effective to form one or more hybridization complexes;    (b) detecting the hybridization complexes; and    (c) comparing the levels of the hybridization complexes with the level of hybridization complexes in a control sample, wherein the altered level of hybridization complexes compared with the level of hybridization complexes of a control sample indicates the presence of the disorder or condition.    
     
     
         12 . A method for diagnosing a disorder or condition associated with the altered expression of a gene expressed in response to polycyclic aromatic hydrocarbon exposure in a plurality of biological samples, the method comprising the steps of: 
 (a) hybridizing a nucleic acid molecule of  claim 2  to a sample under conditions effective to form one or more hybridization complexes;    (b) detecting the hybridization complexes; and    (c) comparing the levels of the hybridization complexes with the level of hybridization complexes in a control sample, wherein the altered level of hybridization complexes compared with the level of hybridization complexes of a control sample indicates the presence of the disorder or condition.    
     
     
         13 . A method for detecting or diagnosing effect of a compound on expression level of at least one nucleic acid molecule in a subject, the method comprising: 
 (a) treating the subject with the compound;    (b) obtaining a sample containing nucleic acid molecules from the subject;    (c) contacting the sample with at least one nucleic acid molecule of  claim 1  under conditions for the formation of hybridization complexes; and    (d) detecting at least one hybridization complex, wherein the presence, absence, or change in amount of hybridization complex when compared with hybridization complex formed with a sample from an untreated subject indicates the effect of the compound.    
     
     
         14 . A method for detecting or diagnosing effect of a compound on expression level of at least one nucleic acid molecule in a subject, the method comprising: 
 (a) treating the subject with the compound;    (b) obtaining a sample containing nucleic acid molecules from the subject;    (c) contacting the sample with at least one nucleic acid molecule of  claim 2  under conditions for the formation of hybridization complexes; and    (d) detecting at least one hybridization complex, wherein the presence, absence, or change in amount of hybridization complex when compared with hybridization complex formed with a sample from an untreated subject indicates the effect of the compound.    
     
     
         15 . A substantially purified protein expressed in response to polycyclic aromatic hydrocarbon exposure, comprising 
 (a) a protein selected from SEQ ID NOs: 6-8 or a portion thereof; and    (b) an oligopeptide comprising at least 6 sequential amino acids of the protein of (a); and    (c) an immunogenic fragment of the protein of (a).    
     
     
         16 . A protein of  claim 15 , comprising the amino acid sequence of SEQ ID NO: 6.  
     
     
         17 . A protein of  claim 15 , comprising the amino acid sequence of SEQ ID NO: 7.  
     
     
         18 . A protein of  claim 15 , comprising the amino acid sequence of SEQ ID NO: 8.  
     
     
         19 . A composition comprising a protein of  claim 15  and a pharmaceutical carrier.  
     
     
         20 . A method for using a protein to screen a library of molecules or compounds to identify at least one ligand which specifically binds the protein, the method comprising: 
 (a) combining the protein of  claim 15  with the library of molecules or compounds under conditions to allow specific binding; and    (b) detecting specific binding between the protein and ligand, thereby identifying a ligand which specifically binds the protein.    
     
     
         21 . The method of  claim 20  wherein the library is selected from DNA molecules, RNA molecules, peptide nucleic acids, mimetics, proteins, agonists, antagonists, and antibodies.  
     
     
         22 . A ligand identified by the method of  claim 20  which modulates the activity of the protein.  
     
     
         23 . A method of using the protein to purify a ligand from a sample, the method comprising: 
 (a) combining the protein of  claim 15  with a sample under conditions to allow specific binding;    (b) detecting specific binding between the protein and a ligand;    (c) recovering the bound protein; and    (d) separating the protein from the ligand, thereby obtaining purified ligand.    
     
     
         24 . An antibody which specifically binds to the protein of  claim 15 .  
     
     
         25 . A diagnostic test for a condition or disease associated with the expression of a protein in a biological sample comprising the steps of: 
 (a) combining the biological sample with an antibody of  claim 24 , under conditions suitable for the antibody to bind the protein and form an antibody:protein complex; and    (b) detecting the complex, wherein the presence of the complex correlates with the presence of the protein in the biological sample.    
     
     
         26 . The antibody of  claim 24 , wherein the antibody is: 
 (a) a chimeric antibody;    (b) a single chain antibody;    (c) a Fab fragment;    (d) a F(ab′) 2  fragment; or    (e) a humanized antibody.    
     
     
         27 . A composition comprising an antibody of  claim 24  and an acceptable excipient.  
     
     
         28 . A method of diagnosing a condition or disease associated with the expression of a protein in a subject, comprising administering to said subject an effective amount of the composition of  claim 26 .  
     
     
         29 . A composition of  claim 26 , wherein the antibody is labeled.  
     
     
         30 . A method of diagnosing a condition or disease associated with the expression of a protein in a subject, comprising administering to said subject an effective amount of the composition of  claim 29 .  
     
     
         31 . A method of preparing a polyclonal antibody comprising: 
 (a) immunizing an animal with a protein of  claim 15  under conditions to elicit an antibody response;    (b) isolating antibodies from said animal; and    (c) screening the isolated antibodies with the protein thereby identifying a polyclonal antibody which binds specifically to a protein of SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8.    
     
     
         32 . An antibody produced by a method of  claim 31 .  
     
     
         33 . A composition comprising the antibody of  claim 32  and a suitable carrier.  
     
     
         34 . A method of making a monoclonal antibody comprising: 
 (a) immunizing an animal with a protein of  claim 15  under conditions to elicit an antibody response;    (b) isolating antibody producing cells from the animal;    (c) fusing the antibody producing cells with immortalized cells to form monoclonal antibody-producing hybridoma cells;    (d) culturing the hybridoma cells; and    (e) isolating from the culture monoclonal antibody which binds specifically to a protein of SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8.    
     
     
         35 . A monoclonal antibody produced by a method of  claim 34 .  
     
     
         36 . The antibody of  claim 24 , wherein the antibody is produced by screening a Fab expression library.  
     
     
         37 . The antibody of  claim 24 , wherein the antibody is produced by screening a recombinant immunoglobulin library.  
     
     
         38 . A method for detecting a protein in a sample comprising the steps of: 
 (a) incubating the antibody of  claim 24  with a sample under conditions to allow specific binding of the antibody and the protein; and    (b) detecting specific binding, wherein specific binding indicates the presence of a protein of SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8 in the sample.    
     
     
         39 . A method of purifying a protein from a sample, the method comprising: 
 (a) incubating the antibody of  claim 24  with a sample under conditions to allow specific binding of the antibody and the protein; and    (b) separating the antibody from the sample and obtaining purified protein of SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8.