Individualized vaccines for cancer
The present invention relates to the provision of vaccines which are specific for a patient's tumor and are potentially useful for immunotherapy of the primary tumor as well as tumor metastases. In one aspect, the present invention relates to a method for providing an individualized cancer vaccine comprising the steps: (a) identifying cancer specific somatic mutations in a tumor specimen of a cancer patient to provide a cancer mutation signature of the patient; and (b) providing a vaccine featuring the cancer mutation signature obtained in step (a). In a further aspect, the present invention relates to vaccines which are obtainable by said method.
1. A method for producing an individualized cancer vaccine, the method comprising steps of:
(a) obtaining nucleic acid sequence information from a sample comprising tumor cells from a patient;
(b) obtaining nucleic acid sequence information from a sample comprising non-tumor cells from the same patient;
(c) comparing the tumor cell sequence information with the non-tumor-cell sequence information so that somatic mutations present in the tumor cell sequence information are identified;
(d) classifying as immunogenic neo-epitopes at least two of the identified somatic mutations, wherein each immunogenic neo-epitope is characterized in that it:
(i) occurs in a transcript;
(ii) occurs in a protein-coding region;
(iii) introduces a change in amino acid sequence;
(iv) is predicted to exhibit MHC binding; and
(e) producing a nucleic acid vaccine comprising RNA encoding a recombinant polyepitopic polypeptide, wherein said polypeptide comprises two or more immunogenic neo-epitopes identified in steps (a)-(d) and the neo-epitopes are fused together by peptide bonds or linkers.
2. The method according to claim 1 , wherein the step of obtaining nucleic acid sequence information from the sample comprising tumor cells from the patient comprises single cell sequencing of one or more tumor cells from the patient.
3. The method according to claim 2 , wherein the tumor cells are circulating tumor cells.
4. The method according to claim 1 , wherein the step of obtaining nucleic acid sequence information from the sample comprising tumor cells from the patient involves using next generation sequencing (NGS).
5. The method according to claim 1 , wherein the nucleic acid sequence information of (i) and/or (ii) comprises nucleic acid sequence information from replicates of the sample from the patient.
6. The method according to claim 1 , wherein the recombinant polyepitopic polypeptide encoded by the RNA comprises up to 30 neo-epitopes.
7. The method according to claim 1 , wherein the recombinant polyepitopic polypeptide encoded by the RNA further comprises one or more epitopes that are expressed by that patient's tumor, which epitopes do not contain the tumor-specific somatic mutation(s) of the neo-epitopes.
8. The method according to claim 1 , wherein RNA encoding a vaccine sequence of each neo-epitope is or comprises a RNA sequence encoding (i) the respective somatic mutation(s) and (ii) its epitope flanking regions as present in a respective naturally occurring protein.
9. The method according to claim 8 , wherein the vaccine sequence of each neo-epitope encoded by the RNA is about 30 amino acids long.
10. The method according to claim 1 , wherein the neo-epitopes encoded by the RNA are arranged in a head-to-tail configuration.
11. The method according to claim 1 , wherein the RNA encoding the recombinant polyepitopic polypeptide comprises a linker sequence between each of the encoded neo-epitopes.
12. The method according to claim 1 , wherein the vaccine is a prophylactic or therapeutic vaccine.
13. The method according to claim 1 , wherein the nucleic acid sequence information of (i) and/or (ii) is or comprises genomic sequence information.
14. The method according to claim 1 , wherein the nucleic acid sequence information of (i) and/or (ii) is or comprises exome sequence information.
15. The method according to claim 1 , wherein the nucleic acid sequence information of (i) and/or (ii) is or comprises transcriptome sequence information.
16. The method according to claim 7 , wherein the one or more epitopes, in combination with the neo-epitopes, are arranged in a head-to-tail configuration.
17. The method according to claim 8 , wherein the RNA encoding each neo-epitope is arranged relative to each other in a head-to-tail configuration.
18. The method according to claim 7 , wherein the RNA further encoding the one or more epitopes comprises a linker sequence between each of the encoded epitopes.
19. The method according to claim 8 , wherein the RNA encoding vaccine sequences of the neo-epitopes comprises a linker sequence between each of the encoded vaccine sequences.
20. The method according to claim 1 , wherein the recombinant polyepitopic polypeptide encoded by the RNA comprises 5 or more neo-epitopes.
21. The method according to claim 1 , wherein the recombinant polyepitopic polypeptide encoded by the RNA comprises 10 or more neo-epitopes.
22. The method according to claim 1 , wherein the recombinant polyepitopic polypeptide encoded by the RNA comprises 20 or more neo-epitopes.
23. The method according to claim 1 , wherein one or more of the neo-epitopes comprises at least one primary basal mutation.
24. The method of claim 8 , wherein the vaccine sequence of each neo-epitope encoded by the RNA comprises 20 or more amino acids.
25. The method of claim 11 , wherein the linker sequence encodes a peptide linker characterized in that at least 60% of amino acids of the peptide linker are glycine and serine residues.