Expression vectors encoding epitopes of target-associated antigens and methods for their design

An isolated nucleic acid molecule comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of tumor-associated antigen NY-ESO (SEQ ID NO:

• 11), wherein the first sequence comprises less than 60% of the length of the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC Class I receptor peptide binding cleft, wherein the first sequence comprises an epitope cluster chosen from the group consisting of amino acids 79-104, 86-171, 108-140, and 108-174 of NY-ESO, and wherein said first sequence encodes a fragment of NY-ESO, and wherein said encoded fragment consists essentially of amino acids 79-174 of NY-ESO.

An isolated nucleic acid molecule comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of tumor-associated antigen NY-ESO (SEQ ID NO:

• 11), wherein the first sequence comprises less than 90% of the length of the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC Class I receptor peptide binding cleft, wherein the first sequence comprises an epitope cluster chosen from the group consisting of amino acids 86-171, 108-140, and 108-174 of NY-ESO.

An isolated nucleic acid molecule comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of tumor-associated antigen NY-ESO (SEQ ID NO:

• 11), wherein the first sequence comprises less than 60% of the length of the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC Class I receptor peptide binding cleft, wherein the first sequence comprises an epitope cluster chosen from the group consisting of amino acids 79-104, 86-171, 108-140, and 108-174 of NY-ESO, wherein said first sequence further comprises amino acids 148-167 of NY-ESO.

An isolated nucleic acid molecule comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of a tumor-associated antigen, wherein the antigen is NY-ESO (SEQ ID NO:

• 11), wherein the first sequence comprises less than 30% of the length of the antigen, or greater than 55% and less than 60% of the length of the antigen, wherein the reading frame does not encode the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC Class I receptor peptide binding cleft, wherein at least one cluster is at least 11% of the length of the antigen, wherein said encoded fragment comprises an amino acid sequence beginning at one of amino acids selected from the group consisting of 77, 79, 86, and 108 of NY-ESO, and ending at one of the amino acids selected from the group consisting of 104, 140, 167, 171, 174, and 180 of NY-ESO.

An isolated nucleic acid molecule comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of a tumor-associated antigen, wherein the antigen is NY-ESO (SEQ ID NO:

• 11), wherein the first sequence comprises less than 30% of the length of the antigen, or greater than 55% and less than 60% of the length of the antigen, wherein the reading frame does not encode the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC Class I receptor peptide binding cleft, wherein at least one cluster is at least 11% of the length of the antigen, wherein said encoded fragment consists essentially of amino acids 79-174 of NY-ESO.

The nucleic acid molecule of 23, wherein said first sequence encodes exactly amino acids 77-180 of NY-ESO.

An isolated nucleic acid molecule comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of tumor-associated antigen NY-ESO (SEQ ID NO:

• 11), wherein the first sequence comprises less than 60% of the length of the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC Class I receptor peptide binding cleft, wherein the first sequence comprises an epitope cluster chosen from the group consisting of amino acids 86-171, 108-140, and 108-174 of NY-ESO.

The nucleic acid molecule of 25, wherein said first sequence encodes a fragment of NY-ESO.

The nucleic acid molecule of 1, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 25% of the length of NY-ESO.

The nucleic acid molecule of 1, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 10% of the length of NY-ESO.

An isolated nucleic acid molecule comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of tumor-associated antigen NY-ESO (SEQ ID NO:

• 11), wherein the first sequence comprises less than 60% of the length of the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC Class I receptor peptide binding cleft, wherein the first sequence comprises an epitope cluster chosen from the group consisting of amino acids 79-104, 108-140, and 108-174 of NY-ESO, wherein said first sequence further comprises amino acids 144-171 of NY-ESO.