CIITA-interacting proteins and methods of use therefor

Abstract

Isolated nucleic acid molecules encoding a novel protein, CIP104, that interacts with CIITA, an MHC class II transcriptional activator, are disclosed. The invention further provides antisense nucleic acid molecules, recombinant expression vectors containing a nucleic acid molecule of the invention, host cells into which the expression vectors have been introduced and non-human transgenic animals carrying a CIP104 transgene. The invention further provides isolated CIP104 proteins and peptides, CIP104 fusion proteins and anti-CIP104 antibodies. Methods of using the CIP104 compositions of the invention are also disclosed, including methods for detecting CIP104 activity (e.g, CIP104 protein or mRNA) in a biological sample, methods of modulating CIP104 activity in a cell, and methods for identifying agents that modulate an interaction between CIP104 and CIITA.

We claim:  
     
         1 . An isolated nucleic acid molecule comprising a nucleotide sequence encoding CIP104.  
     
     
         2 . The isolated nucleic acid molecule of  claim 1 , which comprises a nucleotide sequence encoding a protein, wherein the protein: (i) comprises an amino acid sequence at least 60% homologous to the amino acid sequence of SEQ ID NO: 2 and (ii) interacts with CIITA or enhances transcription from an MHC class II promoter.  
     
     
         3 . The isolated nucleic acid molecule of  claim 2 , wherein the protein comprises an amino acid sequence at least 70% homologous to the amino acid sequence of SEQ ID NO:2  
     
     
         4 . The isolated nucleic acid molecule of  claim 2 , wherein the protein comprises an amino acid sequence at least 80% homologous to the amino acid sequence of SEQ ID NO: 2.  
     
     
         5 . The isolated nucleic acid molecule of  claim 2 , wherein the protein comprises an amino acid sequence at least 90% homologous to the amino acid sequence of SEQ ID NO: 2.  
     
     
         6 . The isolated nucleic acid molecule of  claim 1 , which comprises a nucleotide sequence at least 60% homologous to the nucleotide sequence of SEQ ID NO: 1, wherein the nucleic acid molecule encodes a protein that interacts with CIITA or enhances transcription from an MHC class II promoter.  
     
     
         7 . The isolated nucleic acid molecule of  claim 6 , which comprises a nucleotide sequence at least 70% homologous to the nucleotide sequence of SEQ ID NO: 1.  
     
     
         8 . The isolated nucleic acid molecule of  claim 6 , which comprises a nucleotide sequence at least 80% homologous to the nucleotide sequence of SEQ ID NO: 1.  
     
     
         9 . The isolated nucleic acid molecule of  claim 6 , which comprises a nucleotide sequence at least 90% homologous to the nucleotide sequence of SEQ ID NO: 1.  
     
     
         10 . An isolated nucleic acid molecule at least 15 nucleotides in length which hybridizes under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1.  
     
     
         11 . The isolated nucleic acid molecule of  claim 10 , which comprises a naturally-occurring inucleotide sequence.  
     
     
         12 . The isolated nucleic acid molecule of  claim 10 , which encodes human CIP104.  
     
     
         13 . The isolated nucleic acid molecule of  claim 10 , which encodes mouse CIP104.  
     
     
         14 . An isolated nucleic acid molecule comprising the coding region of the nucleotide sequence of SEQ ID NO: 1.  
     
     
         15 . The isolated nucleic acid molecule of  claim 14 , comprising the nucleotide sequence of SEQ ID NO: 1.  
     
     
         16 . An isolated nucleic acid molecule encoding the amino acid sequence of SEQ ID NO: 2.  
     
     
         17 . A vector comprising the nucleic acid molecule of  claim 1 .  
     
     
         18 . The vector of  claim 17 , which is an expression vector.  
     
     
         19 . A host cell containing the vector of  claim 18 .  
     
     
         20 . A method for producing CIP104 protein comprising culturing the host cell of  claim 19  in a suitable medium until CIP104 protein is produced.  
     
     
         21 . The method of  claim 20 , further comprising isolating the CIP104 protein from the medium or the host cell.  
     
     
         22 . An isolated CIP104 protein.  
     
     
         23 . The isolated protein of  claim 22 , which (i) comprises an amino acid sequence at least 60% homologous to the amino acid sequence of SEQ ID NO: 2 and (ii) interacts with CIITA or enhances transcription from an MHC class II promoter.  
     
     
         24 . The isolated protein of  claim 23 , which is at least 70% homologous to the amino acid sequence of SEQ ID NO: 2.  
     
     
         25 . The isolated protein of  claim 23 , which is at least 80% homologous to the amino acid sequence of SEQ ID NO: 2.  
     
     
         26 . The isolated protein of  claim 23 , which is at least 90% homologous to the amino acid sequence of SEQ ID NO: 2.  
     
     
         27 . An isolated protein comprising the amino acid sequence of SEQ ID NO: 2.  
     
     
         28 . A fusion protein comprising a CIP104 polypeptide operatively linked to a non-CIP104 polypeptide.  
     
     
         29 . Antibodies that specifically bind CIP104 protein.  
     
     
         30 . The antibodies of  claim 29 , which are polyclonal antibodies.  
     
     
         31 . The antibodies of  claim 29 , which are monoclonal antibodies.  
     
     
         32 . The antibodies of  claim 29 , which are coupled to a detectable substance.  
     
     
         33 . A nonhuman transgenic animal that contains cells carrying a transgene encoding CIP104 protein.  
     
     
         34 . The nonhuman transgenic animal of  claim 33 , which contains cells having an altered endogenous CIP104 gene.  
     
     
         35 . A method for detecting the presence of CIP104 activity in a biological sample comprising contacting the biological sample with an agent capable of detecting an indicator of CIP104 activity such that the presence of CIP104 activity is detected in the biological sample.  
     
     
         36 . The method of  claim 35 , wherein the agent is a labeled nucleic acid probe capable of hybridizing to CIP104 mRNA.  
     
     
         37 . The method of  claim 35 , wherein the agent is a labeled antibody that specifically binds to CIP104 protein.  
     
     
         38 . A method for modulating CIP104 activity in a cell comprising contacting the cell with an agent that modulates CIP104 activity such that CIP104 activity in the cell is modulated.  
     
     
         39 . The method of  claim 38 , wherein the agent is an antibody that specifically binds to CIP104 protein.  
     
     
         40 . The method of  claim 38 , wherein the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of a CIP104 mRNA or a CIP104 gene.  
     
     
         41 . A method for identifying a compound that modulates the activity of a CIP104 protein, comprising 
 providing an indicator composition that comprises a CIP104 protein;    contacting the indicator composition with a test compound; and    determining the effect of the test compound on the activity of the CIP014 protein in the indicator composition to thereby identify a compound that modulates the activity of a CIP104 protein.    
     
     
         42 . The method of  claim 41 , wherein: 
 the indicator composition comprises a CIP104 protein and a CIITA protein;and    the effect of the test compound on the activity of the CIP104 protein is determined by determining the degree of interaction between the CIP104 protein and the CIITA protein the presence and absence of the test compound.    
     
     
         43 . The method of  claim 41 , wherein: 
 the indicator composition is a cell comprising a CIP104 protein, a CIITA protein and a reporter gene responsive to CIITA; and    the effect of the test compound on the activity of the CIP104 protein is determined by determining the level of expression of the reporter gene in the presence and absence of the test compound.    
     
     
         44 . The method of  claim 43 , wherein the reporter gene responsive to CIITA comprises a major histocompatibility complex (MHC) class II gene promoter.  
     
     
         45 . The method of  claim 41 , further comprising determining the effect of the test compound on an immune response to thereby identify a compound that modulates an immune response.