Methods for identifying functionally related genes and drug targets

Abstract

The identification and evaluation of mRNA and protein targets associated with mRNP complexes and implicated in the expression of proteins involved in common physiological pathways is described. Effective targets are useful for treating a disease, condition or disorder associated with the physiological pathway.

1 . A method for assessing the metabolic state of a cell, the method comprising the steps of: 
 a) isolating at least one RNP complex comprising at least one RNA binding protein and at least one RNA; and,    b) determining the level of expression of the at least one RNA, wherein the level of expression of the at least one RNA is indicative of the metabolic state of the cell.    
     
     
         2 . The method of  claim 1 , wherein the cell is infected with a pathogen.  
     
     
         3 . The method of  claim 1 , wherein the cell is treated with a compound.  
     
     
         4 . The method of  claim 3 , wherein the compound inhibits binding between the at least one RNA binding protein and the at least one RNA.  
     
     
         5 . The method of  claim 1 , further comprising the step of altering the expression of the at least one RNA binding protein or the at least one RNA.  
     
     
         6 . The method of  claim 5 , wherein said altering step comprises contacting the cell sample with a molecule selected from the group consisting of a protein, a nucleic acid, an antibody, an antibody fragment, a peptide nucleic acid, and a peptide.  
     
     
         7 . The method of  claim 5 , wherein said altering step comprises a genetic alteration.  
     
     
         8 . The method of  claim 5 , wherein said altering step comprises contacting the cell sample with a nucleic acid comprising an antisense nucleic acid, a ribozyme, an RNAi, a decoy nucleic acid, or a competitor nucleic acid.  
     
     
         9 . The method of  claim 1 , wherein the at least one RNP complex is isolated by a ligand binding onto a support.  
     
     
         10 . The method of  claim 1 , wherein the at least one RNP complex is isolated by immunoprecipitation.  
     
     
         11 - 49 . (canceled)  
     
     
         50 . A method for assessing the presence or absence of a cell type in a population of cells, the method comprising the steps of: 
 a) isolating at least one RNP complex from a population of cells, wherein the at least one component is specific for a cell type; and    b) detecting the expression of the at least one component, wherein the expression of the at least one component is indicative that the cell type is present in the population of cells.    
     
     
         51 . The method of  claim 50 , wherein the population of cells comprises a tumor, a tissue, a cultured cell, a body fluid, an organ, a cell extract, and/or a cell lysate.  
     
     
         52 . The method of  claim 50 , wherein said detecting step comprises detecting the expression of a gene product selected from the group consisting of an RNA, an RNP complex-associated protein, an RNA binding protein, an RNA encoding the RNA binding protein, and an RNA encoding the RNP complex-associated protein.  
     
     
         53 . (canceled)  
     
     
         54 . The method of  claim 2 , wherein the cell is treated with a compound.  
     
     
         55 . The method of  claim 54 , wherein the compound inhibits binding between the at least one RNA binding protein and the at least one RNP complex-associated protein, or between the at least one RNA and the at least one RNP complex-associated protein.  
     
     
         56 . The method of  claim 1 , wherein the RNP complex further comprises at least one RNP complex-associated protein.  
     
     
         57 . The method of  claim 56 , wherein the cell is infected with a pathogen.  
     
     
         58 . The method of  claim 57 , wherein the pathogen inhibits binding between the at least one RNA binding protein and the at least one RNP complex-associated protein, or between the at least one RNA and the at least one RNP complex-associated protein.  
     
     
         59 . The method of  claim 56 , wherein the cell is treated with a compound.  
     
     
         60 . The method of  claim 59 , wherein the compound inhibits binding between the at least one RNA binding protein and the at least one RNP complex-associated protein, or between the at least one RNA and the at least one RNP complex-associated protein.  
     
     
         61 . The method of  claim 56 , further comprising the step of altering the expression of the at least one RNP complex-associated protein.  
     
     
         62 . The method of  claim 61 , wherein said altering step comprises contacting the cell sample with a molecule selected from the group consisting of a protein, a nucleic acid, an antibody, an antibody fragment, a peptide nucleic acid, and a peptide.  
     
     
         63 . The method of  claim 61 , wherein said altering step comprises a genetic alteration.  
     
     
         64 . The method of  claim 61 , wherein said altering step comprises contacting the cell sample with a nucleic acid comprising an antisense nucleic acid, a ribozyme, an RNAi, a decoy nucleic acid, or a competitor nucleic acid.  
     
     
         65 . The method of  claim 1 , wherein the RNA is an mRNA.  
     
     
         66 . The method of  claim 1 , wherein the RNA is a mature mRNA.  
     
     
         67 . The method of  claim 1 , wherein the RNP is an mRNP.  
     
     
         68 . The method of  claim 50 , wherein the component is selected from the group consisting of an RNA, an RNP complex-associated protein, an RNA binding protein, an RNA encoding the RNA binding protein, and an RNA encoding the RNP complex-associated protein.  
     
     
         69 . The method of  claim 68 , wherein the RNA is an mRNA.  
     
     
         70 . The method of  claim 68 , wherein the RNA is a mature mRNA.  
     
     
         71 . The method of  claim 68 , wherein the RNP is an mRNP.  
     
     
         72 . The method of  claim 1 , wherein the at least one RNP complex is isolated by the steps of: 
 (a) obtaining a cDNA encoding an RBP of interest;    (b) ligating the cDNA to a tagging DNA that encodes a peptide epitope when expressed in a cell;    (c) expressing the epitope tagged RBP in a cell to produce a lysate comprising an RBP-peptide epitope fusion;    (d) contacting the lysate with an antibody that binds the peptide epitope;    (e) contacting the lysate with a ligand attached to a solid support that binds to the antibody;    (f) separating the RBP-peptide epitope fusion from the solid support; and    (g) isolating at least one RNA, at least one RBP, or at least one RNP-associated protein.    
     
     
         73 . The method of  claim 1 , wherein the at least one RNP complex is isolated by the steps of: 
 (a) obtaining a cDNA encoding an RBP of interest;    (b) ligating the cDNA to a tagging DNA that encodes a biotin acceptor domain when expressed in a cell;    (c) expressing the biotin acceptor domain tagged RBP in a cell to produce a lysate that contains a biotinylated RBP-biotin acceptor domain fusion;    (d) contacting the lysate with solid support immobilized ligand that binds biotin;    (e) separating the biotinylated RBP-biotin acceptor domain fusion from the solid support; and    (f) isolating at least one RNA, at least one RBP, or at least one RNP-associated protein.