Optimization of immunomodulatory properties of genetic vaccines

Abstract

This invention provides methods for obtaining molecules that can modulate an immune response, and immunomodulatory molecules obtained using the methods. The molecules find use, for example, in the tailoring of an immune response induced by a genetic vaccine for a desired purpose.

1 . A method for obtaining a polynucleotide that has a modulatory effect on an immune response, or encodes a polypeptide that has a modulatory effect on an immune response, that is induced by a genetic vaccine vector, the method comprising: 
 creating a library of recombinant polynucleotides; and    screening the library to identify an optimized recombinant polynucleotide that has, or encodes a polypeptide that has, a modulatory effect on an immune response induced by a genetic vaccine vector;    wherein the optimized recombinant polynucleotide or the polypeptide encoded by the recombinant polynucleotide exhibits an enhanced ability to modulate an immune response compared to a non-recombinant polynucleotide from which the library was created.    
     
     
         2 - 18 . (canceled)  
     
     
         19 . The method of  claim 1 , wherein the optimized recombinant polynucleotide comprises a nucleotide sequence rich in unmethylated CpG.  
     
     
         20 . The method of  claim 1 , wherein the optimized recombinant polynucleotide encodes a polypeptide that inhibits an allergic reaction.  
     
     
         21 . The method of  claim 20 , wherein the polypeptide is selected from the group consisting of interferon-α, interferon-γ, IL-10, IL-12, an antagonist of IL-4, an antagonist of IL-5, and an antagonist of IL-13.  
     
     
         22 . The method of  claim 1 , wherein the optimized recombinant polynucleotide encodes an antagonist of IL-10.  
     
     
         23 . The method of  claim 22 , wherein the antagonist of IL-10 is soluble or defective IL-10 receptor or IL-20/MDA-7.  
     
     
         24 . The method of  claim 1 , wherein the optimized recombinant polynucleotide encodes a costimulator.  
     
     
         25 . The method of  claim 24 , wherein the costimulator is B7-1 (CD80) or B7-2 (CD86) and the screening step involves selecting variants with altered activity through CD28 or CTLA-4.  
     
     
         26 . The method of  claim 24 , wherein the costimulator is CD1, CD40, CD154 (ligand for CD40) or CD150 (SLAM).  
     
     
         27 . The method of  claim 24 , wherein the costimulator is a cytokine.  
     
     
         28 . The method of  claim 27 , wherein the cytokine is selected from the group consisting of IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, GM-CSF, G-CSF, TNF-α, IFN-α, IFN-γ, and IL-20 (MDA-7).  
     
     
         29 . The method of  claim 28 , wherein the library of recombinant polynucleotides is screened by testing the ability of cytokines encoded by the recombinant polynucleotides to activate cells which contain a receptor for the cytokine.  
     
     
         30 . The method of  claim 29 ,wherein the cells contain a heterologous nucleic acid that encodes the receptor for the cytokine.  
     
     
         31 . The method of  claim 28 , wherein the cytokine is interleukin-12 and the screening is performed by: 
 growing mammalian cells which contain the genetic vaccine vector in a culture medium; and    detecting whether T cell proliferation or T cell differentiation is induced by contact with the culture medium.    
     
     
         32 . The method of  claim 28 , wherein the cytokine is interferon-α and the screening is performed by: 
 expressing the recombinant polynucleotides so that the encoded peptides or polypeptides are produced as fusions with a protein displayed on the surface of a replicable genetic package;    contacting the replicable genetic packages with a plurality of B cells; and    identifying phage library members that are capable of inhibiting proliferation of the B cells.    
     
     
         33 . The method of  claim 28 , wherein the immune response of interest is differentiation of T cells to T H 1 cells and the screening is performed by contacting a population of T cells with the cytokines encoded by the members of the library of recombinant polynucleotides and identifying library members that encode a cytokine that induces the T cells to produce IL-2 and interferon-γ.  
     
     
         34 . The method of  claim 27 , wherein the cytokine encoded by the optimized recombinant polynucleotide exhibits reduced immunogenicity compared to a cytokine encoded by a non-optimized polynucleotide, and the reduced immunogenicity is detected by introducing a cytokine encoded by the recombinant polynucleotide into a mammal and determining whether an immune response is induced against the cytokine.  
     
     
         35 . The method of  claim 24 , wherein the costimulator is B7-1 (CD80) or B7-2 (CD86) and the cell is tested for ability to costimulate an immune response.  
     
     
         36 . The method of  claim 1 , wherein the optimized recombinant polynucleotide encodes a cytokine antagonist.  
     
     
         37 . The method of  claim 36 , wherein the cytokine antagonist is selected from the group consisting of a soluble cytokine receptor and a transmembrane cytokine receptor having a defective signal sequence.  
     
     
         38 . The method of  claim 36 , wherein the cytokine antagonist is selected from the group consisting of ΔIL-10R and ΔIL-4R.  
     
     
         39 . The method of  claim 1 , wherein the optimized recombinant polynucleotide encodes a polypeptide capable of inducing a predominantly T H 1 immune response.  
     
     
         40 . The method of  claim 1 , wherein the optimized recombinant polynucleotide encodes a polypeptide capable of inducing a predominantly T H 2 immune response.  
     
     
         41 . A method for obtaining a polynucleotide that encodes an accessory molecule that improves the transport or presentation of antigens by a cell, the method comprising: 
 creating a library of recombinant polynucleotides by subjecting to recombination nucleic acids that encode all or part of the accessory molecule; and    screening the library to identify an optimized recombinant polynucleotide that encodes a recombinant accessory molecule that confers upon a cell an increased or decreased ability to transport or present an antigen on a surface of the cell compared to an, accessory molecule encoded by the non-recombinant nucleic acids.    
     
     
         42 . canceled  
     
     
         43 . The method of  claim 41 , wherein the accessory molecule comprises a proteasome or a TAP polypeptide.  
     
     
         44 . The method of  claim 41 , wherein the accessory molecule comprises a cytotoxic T-cell inducing sequence.  
     
     
         45 . The method of  claim 44 , wherein the cytotoxic T-cell inducing sequence is obtained from a hepatitis B surface antigen.  
     
     
         46 . The method of  claim 41 , wherein the accessory molecule comprises an immunogenic agonist sequence.