Individualized vaccines for cancer
The present invention is in the field of tumor immunotherapy. In particular, the present invention provides individualized cancer vaccines specific for a patient's tumor based on a transcriptome analysis in a tumor specimen of the patient for RNA transcripts which are excessively upregulated in one or more cancer cells of said patient. These individualized cancer vaccines when administered to the patient induce an immune response against tumor-associated antigens expressed in a tumor of the patient by the RNA transcripts which are excessively upregulated in one or more cancer cells of said patient. Due to the excessive upregulation of the RNA transcripts, the individualized cancer vaccines are effective for vaccination of a subject and for breaking the self-tolerance against tumor-associated antigens which are self-proteins in said subject.
1 . A method for producing an individualized therapeutic cancer vaccine comprising the steps:
(a) identifying one or more RNA transcripts present in a tumor specimen of a human cancer patient, wherein each of the one or more RNA transcripts encodes an amino acid sequence and wherein each of the one or more RNA transcripts is present in the tumor specimen in a copy number that exceeds a pre-determined expression threshold; and
(b) providing a vaccine comprising a polypeptide, wherein the polypeptide comprises one or more epitopes encoded by the one or more identified RNA transcripts, or a nucleic acid encoding said polypeptide, wherein
the step of identifying one or more RNA transcripts comprises determining the copy number of RNA transcripts present in the tumor specimen of the human cancer patient and comparing the copy number of each of the RNA transcripts to a respective pre-determined expression threshold, wherein said pre-determined expression threshold is obtained by annotating reference samples to 10 or more non-tumor tissues, calculating the median RNA expression of all samples for each unique tissue and calculating expression threshold c as
c= 10* M+ 1,
where M equals the 95 th percentile of all tissue RNA medians.
2 . The method according to claim 1 , wherein the step of identifying one or more RNA transcripts comprises single cell sequencing of one or more cancer cells.
3 . The method according to claim 2 , wherein the cancer cells are circulating tumor cells.
4 . The method according to claim 1 , wherein the step of identifying one or more RNA transcripts involves using next generation sequencing (NGS).
5 . The method according to claim 1 , wherein the step of identifying one or more RNA transcripts comprises sequencing RNA of the tumor specimen and/or a DNA library obtained from the RNA of the tumor specimen.
6 . The method according to claim 1 , wherein the epitopes are flanked N-terminally and/or C-terminally by amino acid sequences comprising 3 or more, 5 or more, or 10 or more amino acids also flanking said epitopes in the naturally occurring protein so as to form a vaccine sequence, and wherein the vaccine sequence is about 30 amino acids long.
7 . The method according to claim 1 , wherein the vaccine comprises a fusion polypeptide comprising at least two epitopes and/or vaccine sequences comprising epitopes.
8 . The method according to claim 1 , wherein the vaccine comprises a fusion polypeptide comprising at least two epitopes and/or vaccine sequences comprising epitopes and wherein the epitopes and/or vaccine sequences are spaced by linkers.