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 . The method of  claim 1 , wherein the optimized recombinant polynucleotide is incorporated into a genetic vaccine vector.  
     
     
         3 . The method of  claim 1 , wherein the optimized recombinant polynucleotide, or a polypeptide encoded by the optimized recombinant polynucleotide, is administered in conjunction with a genetic vaccine vector.  
     
     
         4 . The method of  claim 1 , wherein the library of recombinant polynucleotides is created by a process selected from the group consisting of DNA shuffling, error-prone PCR, oligonucleotide-directed mutagenesis, uracil-mediated mutagenesis, and repair-deficient host mutagenesis.  
     
     
         5 . The method of  claim 1 , wherein the polynucleotide that has a modulatory effect on an immune response is obtained by: 
 (1) recombining at least first and second forms of a nucleic acid that is, or encodes a molecule that is, involved in modulating an immune response, wherein the first and second forms differ from each other in two or more nucleotides, to produce a library of recombinant polynucleotides; and    (2) screening the library to identify at least one optimized recombinant polynucleotide that exhibits, either by itself or through the encoded molecule, an enhanced ability to modulate an immune response than a form of the nucleic acid from which the library was created.    
     
     
         6 . The method of  claim 5 , wherein the method further comprises the steps of: 
 (3) recombining at least one optimized recombinant polynucleotide with a further form of the nucleic acid, which is the same or different from the first and second forms, to produce a further library of recombinant polynucleotides;    (4) screening the further library to identify at least one further optimized recombinant polynucleotide that exhibits an enhanced ability to modulate an immune response than a form of the nucleic acid from which the library was created; and    (5) repeating (3) and (4), as necessary, until the further optimized recombinant polynucleotide exhibits an further enhanced ability to modulate an immune response than a form of the nucleic acid from which the library was created.    
     
     
         7 . The method of  claim 1 , wherein the optimized recombinant polynucleotide encodes a peptide or polypeptide that can interact with a cellular receptor involved in mediating an immune response, wherein the peptide or polypeptide acts as an agonist or antagonist of the receptor.  
     
     
         8 . The method of  claim 7 , wherein the cellular receptor is a macrophage scavenger receptor.  
     
     
         9 . The method of  claim 7 , wherein the cellular receptor is selected from the group consisting of a cytokine receptor and a chemokine receptor.  
     
     
         10 . The method of  claim 9 , wherein the chemokine receptor is CCR6.  
     
     
         11 . The method of  claim 7 , wherein the peptide or polypeptide mimics the activity of a natural ligand for the receptor but does not induce immune reactivity to the natural ligand.  
     
     
         12 . The method of  claim 7 , wherein the library is screened 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 cells that display the receptor; and    identifying cells that exhibit a modulation of an immune response mediated by the receptor.    
     
     
         13 . The method of  claim 12 , wherein the replicable genetic package is selected from the group consisting of a bacteriophage, a cell, a spore, and a virus.  
     
     
         14 . The method of  claim 13 , wherein the replicable genetic package is an M13 bacteriophage and the protein is encoded by geneIII or geneVII.  
     
     
         15 . The method of  claim 7 , which method further comprises introducing the optimized recombinant polynucleotide into a genetic vaccine vector and administering the vector to a mammal, wherein the peptide or polypeptide is expressed and acts as an agonist or antagonist of the receptor.  
     
     
         16 . The method of  claim 7 , which method further comprises producing the peptide or polypeptide encoded by the optimized recombinant polynucleotide and introducing the peptide or polypeptide into a mammal in conjunction with a genetic vaccine vector.  
     
     
         17 . The method of  claim 7 , wherein the optimized recombinant polynucleotide is inserted into an antigen-encoding nucleotide sequence of a genetic vaccine vector.  
     
     
         18 . The method of  claim 17 , wherein the optimized recombinant polypeptide is introduced into a nucleotide sequence that encodes an M-loop of an HBsAg polypeptide.  
     
     
         19 - 40 . (canceled)  
     
     
         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 . The method of  claim 41 , wherein the screening involves: 
 introducing the library of recombinant polynucleotides into a genetic vaccine vector that encodes an antigen to form a library of vectors;    introducing the library of vectors into mammalian cells; and    identifying mammalian cells that exhibit increased or decreased immunogenicity to the antigen.    
     
     
         43 - 46 . (canceled)