Multiepitope vaccine cassettes
Disclosed herein are compositions that include antigen-encoding nucleic acid sequences having multiple iterations of KRAS neoepitope-encoding sequences and/or lacking immunodominant epitopes. Also disclosed are nucleotides, cells, and methods associated with the compositions including their use as vaccines.
1. A method for treating a subject with cancer, the method comprising administering to the subject an immunotherapy comprising an antigen-based vaccine to the subject, wherein the antigen-based vaccine comprises an antigen expression system, comprising:
the antigen expression system,
wherein the antigen expression system comprises one or more vectors,
the one or more vectors comprising:
(a) a vector backbone, wherein the backbone comprises:
(i) at least one promoter nucleotide sequence, and
(ii) at least one polyadenylation (poly(A)) sequence; and
(b) a cassette, wherein the cassette comprises an antigen-encoding nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 65.
2. The method of claim 1 , wherein the vector backbone comprises either:
a chimpanzee adenovirus vector, or
a self-amplifying RNA (samRNA) vector.
3. The method of claim 2 , wherein the samRNA vector comprises the sequence of SEQ ID NO:6.
4. The method of claim 3 , wherein the cassette is inserted at position 7544 of the sequence of SEQ ID NO:6.
5. The method of claim 2 , wherein the chimpanzee adenovirus vector is a ChAdV68 vector comprising:
the sequence of SEQ ID NO:1;
the sequence of SEQ ID NO:1, except that the sequence is fully deleted or functionally deleted in at least one gene selected from the group consisting of the chimpanzee adenovirus E1A, E1B, E2A, E2B, E3, E4, L1, L2, L3, L4, and L5 genes of the sequence of SEQ ID NO:1;
a gene or regulatory sequence obtained from the sequence of SEQ ID NO:1;
a partially deleted E4 gene comprising a deleted or partially-deleted E4orf2 region and a deleted or partially-deleted E4orf3 region;
at least nucleotides 2 to 36,518 of the sequence of SEQ ID NO:1 and further comprising: (1) an E1 deletion of at least nucleotides 577 to 3403 of the sequence of SEQ ID NO:1, (2) an E3 deletion of at least nucleotides 27,125 to 31,825 of the sequence of SEQ ID NO:1, and (3) a partial deletion of at least nucleotides 34,916 to 35,642 of the sequence of SEQ ID NO:1;
the sequence of SEQ ID NO:68;
one or more deletions between base pair number 577 and 3403 or between base pair 456 and 3014; or
one or more deletions between base pair number 3957 and 10346, base pair number 21787 and 23370, and base pair number 33486 and 36193 of the sequence of SEQ ID NO:1.
6. The method of claim 2 , wherein the chimpanzee adenovirus vector is a ChAdV68 vector comprising a partially deleted E4 gene with reference to the adenovirus genome, wherein the partially deleted E4 gene comprises a partially-deleted E4orf2 region, a deleted E4orf3 region, and a partially-deleted E4orf4 region.
7. The method of claim 5 , wherein the cassette is inserted in the ChAdV68 vector at any one of the deleted E1 regions, any one of the deleted E3 regions, or any one of the deleted ChAdV68 regions that allows incorporation of the cassette.
8. The method of claim 1 , wherein the method further comprises administering to the subject a second antigen expression system.
9. An antigen-encoding cassette, or a polypeptide encoded by the cassette, wherein the antigen-encoding cassette comprises an antigen-encoding nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 65.
10. The method of claim 2 , wherein the chimpanzee adenovirus vector is a ChAdV68 vector comprising at least nucleotides 2 to 36,518 of the sequence of SEQ ID NO:1 and further comprising: (1) an E1 deletion of nucleotides 577 to 3403 of the sequence of SEQ ID NO:1, (2) an E3 deletion of nucleotides 27,125 to 31,825 of the sequence of SEQ ID NO: 1, and (3) a partial E4 deletion of nucleotides 34,916 to 35,642 of the sequence of SEQ ID NO:1; wherein the antigen cassette is inserted within the E1 deletion.
11. The method of claim 2 , wherein the samRNA vector is a Venezuelan equine encephalitis virus vector.
12. The method of claim 8 , wherein the second antigen expression system is different from the antigen expression system of claim 1 .
13. The method of claim 6 , wherein the partially-deleted E4orf2 region, the deleted E4orf3 region, and the partially-deleted E4orf4 region is a deletion of nucleotides 34,916 to 35,642 of the sequence of SEQ ID NO:1.
14. An antigen-based vaccine comprising:
an antigen expression system,
wherein the antigen expression system comprises one or more vectors,
the one or more vectors comprising:
(a) a vector backbone, wherein the backbone comprises:
(i) at least one promoter nucleotide sequence, and
(ii) at least one polyadenylation (poly(A)) sequence; and
(b) a cassette, wherein the cassette comprises an antigen-encoding nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 65.
15. The composition of claim 14 , wherein the vector backbone comprises either:
a chimpanzee adenovirus vector, or
a self-amplifying RNA (samRNA) vector.
16. The composition of claim 15 , wherein the samRNA vector is a Venezuelan equine encephalitis virus vector.
17. The composition of claim 15 , wherein the samRNA vector comprises the sequence of SEQ ID NO:6.
18. The composition of claim 17 , wherein the cassette is inserted at position 7544 of the sequence of SEQ ID NO:6.
19. The composition of claim 14 , wherein the chimpanzee adenovirus vector is a ChAdV68 vector comprising:
the sequence of SEQ ID NO:1;
the sequence of SEQ ID NO:1, except that the sequence is fully deleted or functionally deleted in at least one gene selected from the group consisting of the chimpanzee adenovirus E1A, E1B, E2A, E2B, E3, E4, L1, L2, L3, L4, and L5 genes of the sequence of SEQ ID NO:1;
a gene or regulatory sequence obtained from the sequence of SEQ ID NO:1;
a partially deleted E4 gene comprising a deleted or partially-deleted E4orf2 region and a deleted or partially-deleted E4orf3 region;
at least nucleotides 2 to 36,518 of the sequence of SEQ ID NO:1 and further comprising: (1) an E1 deletion of at least nucleotides 577 to 3403 of the sequence of SEQ ID NO:1, (2) an E3 deletion of at least nucleotides 27,125 to 31,825 of the sequence of SEQ ID NO:1, and (3) a partial deletion of at least nucleotides 34,916 to 35,642 of the sequence of SEQ ID NO:1;
the sequence of SEQ ID NO:68;
one or more deletions between base pair number 577 and 3403 or between base pair 456 and 3014; or
one or more deletions between base pair number 3957 and 10346, base pair number 21787 and 23370, and base pair number 33486 and 36193 of the sequence of SEQ ID NO:1.
20. The composition of claim 19 , wherein the cassette is inserted in the ChAdV68 vector at any one of the deleted E1 regions, any one of the deleted E3 regions, or any one of the deleted ChAdV68 regions that allows incorporation of the cassette.
21. The composition of claim 15 , wherein the chimpanzee adenovirus vector is a ChAdV68 vector comprising a partially deleted E4 gene with reference to the adenovirus genome, wherein the partially deleted E4 gene comprises a partially-deleted E4orf2 region, a deleted E4orf3 region, and a partially-deleted E4orf4 region.
22. The composition of claim 21 , wherein the partially-deleted E4orf2 region, the deleted E4orf3 region, and the partially-deleted E4orf4 region is a deletion of nucleotides 34,916 to 35,642 of the sequence of SEQ ID NO:1.
23. The composition of claim 15 , wherein the chimpanzee adenovirus vector is a ChAdV68 vector comprising at least nucleotides 2 to 36,518 of the sequence of SEQ ID NO:1 and further comprising: (1) an E1 deletion of nucleotides 577 to 3403 of the sequence of SEQ ID NO:1, (2) an E3 deletion of nucleotides 27,125 to 31,825 of the sequence of SEQ ID NO:1, and (3) a partial E4 deletion of nucleotides 34,916 to 35,642 of the sequence of SEQ ID NO:1; wherein the antigen cassette is inserted within the E1 deletion.