Expression system for modulating an immune response
The present invention discloses methods and compositions for modulating the quality of an immune response to a target antigen in a mammal, which response results from the expression of a polynucleotide that encodes at least a portion of the target antigen, wherein the quality is modulated by replacing at least one codon of the polynucleotide with a synonymous codon that has a higher or lower preference of usage by the mammal to confer the immune response than the codon it replaces.
1. A method for constructing a nucleic acid construct, comprising: (1) providing a synthetic polynucleotide from which a polypeptide is producible to confer a stronger or enhanced immune response to a target antigen in a mammal than that conferred by a parent polynucleotide that encodes the same polypeptide under the same conditions, wherein the synthetic polynucleotide is constructed by replacing at least 5% of codons in the parent polynucleotide with synonymous codons, wherein individual codon replacements are carried out by: (a) selecting a first codon of the parent polynucleotide for replacement with a synonymous codon, wherein the synonymous codon is selected on the basis that it exhibits a preference for producing a greater cellular or humoral immune response than the first codon in a comparison of codon preferences for producing the cellular or humoral immune response; and (b) replacing the first codon with the synonymous codon to construct the synthetic polynucleotide; and (2) operably connecting to the synthetic polynucleotide a nucleic acid sequence that encodes a protein-destabilizing element that increases processing and presentation of the polypeptide through the class I major histocompatibility (MHC) pathway wherein the first and synonymous codons are selected from TABLE 3:
TABLE 3
First Codon
Synonymous Codon
Ala GCG
Ala GCT
Ala GCA
Ala GCT
Ala GCC
Ala GCT
Arg CGG
Arg CGA
Arg CGG
Arg CGT
Arg CGG
Arg AGA
Arg AGG
Arg CGA
Arg AGG
Arg CGT
Arg AGG
Arg AGA
Glu GAG
Glu GAA
Gly GGC
Gly GGA
Gly GGT
Gly GGA
Gly GGG
Gly GGA
Leu TTA
Leu CTA
Leu TTA
Leu CTT
Leu TTA
Leu TTG
Leu TTG
Leu CTA
Leu TTG
Leu CTT
Phe TTC
Phe TTT
Pro CCG
Pro CCT
Pro CCA
Pro CCT
Ser AGT
Ser TCG
Ser AGT
Ser TCT
Ser AGT
Ser TCA
Ser AGC
Ser TCG
Ser AGC
Ser TCT
Ser AGC
Ser TCA
Ser AGC
Ser TCC
Ser TCC
Ser TCG
Ser TCA
Ser TCG
Ser TCT
Ser TCG
Thr ACT
Thr ACG
Thr ACT
Thr ACA
Thr ACA
Thr ACG
Thr ACC
Thr ACG
Val GTA
Val GTT .
2. The method according to claim 1 , wherein the protein-destabilizing element is selected from the group consisting of a destabilizing amino acid at the amino-terminus of the polypeptide, a PEST sequence and an ubiquitin.
3. The method according to claim 1 , wherein the synthetic polynucleotide confers a greater cellular or humoral immune response than the parent polynucleotide under the same conditions and wherein the first and synonymous codons are selected from TABLE 3, and wherein the target antigen is a herpes simplex virus antigen.
4. The method according to claim 3 , wherein the herpes simplex virus antigen is a glycoprotein D.
5. The method according to claim 3 , wherein the herpes simplex virus antigen is gD2.
6. The method according to claim 1 , wherein the protein-destabilizing element is an ubiquitin.
7. The method according to claim 1 , wherein the synthetic polynucleotide confers a greater cellular or humoral immune response than the parent polynucleotide under the same conditions and wherein the first and synonymous codons are selected from TABLE 3, and wherein the target antigen is a herpes simplex virus antigen and the protein-destabilizing element is an ubiquitin.
8. The method according to claim 7 , wherein the herpes simplex virus antigen is a glycoprotein D.
9. The method according to claim 7 , wherein the herpes simplex virus antigen is gD2.
10. The method according to claim 3 , further comprising selecting a second codon of the parent polynucleotide for replacement with a synonymous codon, wherein the synonymous codon is selected on the basis that it exhibits a preference for producing a greater cellular or humoral immune response than the first codon in a comparison of codon preferences for producing the cellular or humoral immune response; and (b) replacing the second codon with the synonymous codon, wherein the first and synonymous codons are selected from TABLE 4:
TABLE 4
Second
Synonymous
Second
Synonymous
Second
Synonymous
Codon
Codon
Codon
Codon
Codon
Codon
Ala GCG
Ala GCT
Ile ATA
Ile ATC
Ser AGT
Ser TCG
Ala GCG
Ala GCC
Ile ATA
Ile ATT
Ser AGT
Ser TCT
Ala GCA
Ala GCT
Ile ATT
Ile ATC
Ser AGT
Ser TCA
Ala GCA
Ala GCC
Ser AGT
Ser TCC
Ala GCC
Ala GCT
Leu TTA
Leu CTG
Ser AGC
Se rTCG
Leu TTA
Leu CTC
Ser AGC
Ser TCT
Arg CGG
Arg CGA
Leu TTA
Leu CTA
Ser AGC
Ser TCA
Arg CGG
Arg CGC
Leu TTA
Leu CTT
Ser AGC
Ser TCC
Arg CGG
Arg CGT
Leu TTA
Leu TTG
Ser TCC
Ser TCG
Arg CGG
Arg AGA
Leu TTG
Leu CTG
Ser TCA
Ser TCG
Arg AGG
Arg CGA
Leu TTG
Leu CTC
Ser TCT
Ser TCG
Arg AGG
Arg CGC
Leu TTG
Leu CTA
Arg AGG
Arg CGT
Leu TTG
Leu CTT
Thr ACT
Thr ACG
Arg AGG
Arg AGA
Leu CTT
Leu CTG
Thr ACT
Thr ACC
Leu CTT
Leu CTC
Thr ACT
Thr ACA
Asn AAT
Asn AAC
Leu CTA
Leu CTG
Thr ACA
Thr ACG
Leu CTA
Leu CTC
Thr ACA
Thr ACC
Asp GAT
Asp GAC
Thr ACC
Thr ACG
Pheu TTC
Phe TTT
Cys TGT
Cys TGC
Tyr TAT
Tyr TAC
Pro CCG
Pro CCC
Glu GAG
Glu GAA
Pro CCG
Pro CCT
Val GTA
Val GTG
Pro CCA
Pro CCC
Val GTA
Val GTC
Gly GGC
Gly GGA
Pro CCA
Pro CCT
Val GTA
Val GTT
Gly GGT
Gly GGA
Pro CCT
Pro CCC
Val GTT
Val GTG
Gly GGG
Gly GGA
Val GTT
Val GTC .