COMPOSITIONS AND METHODS OF IDENTIFYING TUMOR SPECIFIC NEOANTIGENS
The present invention related to immunotherapeutic peptides and their use in immunotherapy, in particular the immunotherapy of cancer. Specifically, the invention provides a method of identifying tumor specific neoantigens that alone or in combination with other tumor-associated peptides serve as active pharmaceutical ingredients of vaccine compositions which stimulate anti-tumor responses.
1 . A method of inducing a tumor specific immune response in a subject in need thereof comprising administering to the subject:
(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides; or
(b) one or more polynucleotide encoding the 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides;
wherein the subject has a tumor and said subject-specific peptides are specific to the subject's tumor,
wherein each of said subject-specific peptides has a different tumor neo-epitope that is an epitope specific to the tumor of the subject,
wherein each neo-epitope binds to a HLA protein of the subject with an IC50 less than 500 nM; and
wherein each neo-epitope represents a tumor-specific non-silent mutation selected from the group comprising
(i) non-synonymous mutations leading to different amino acids in the protein;
(ii) read-through mutations in which a stop codon is modified or deleted, leading to translation of a longer protein with a novel tumor-specific sequence at the C-terminus;
(iii) splice site mutations that lead to the inclusion of an intron in the mature mRNA and thus a unique tumor-specific protein sequence;
(iv) chromosomal rearrangements that give rise to a chimeric protein with tumor-specific sequences at the junction of two proteins (i.e., gene fusion);
(v) frameshift mutations or deletions that lead to a new open reading frame with a novel tumor-specific protein sequence.
2 . The method of claim 1 wherein the tumor specific response comprises the induction of anti-tumor cytotoxic T cells.
3 . The method of claim 1 wherein at least one subject-specific peptide is about 8 to 50 amino acids in length.
4 . The method of claim 1 wherein at least one subject-specific peptide is greater than 15 amino acids in length.
5 . The method of claim 1 wherein at least one subject-specific peptide is about 20 to 40 amino acids in length.
6 . The method of claim 1 wherein at least one subject-specific peptide binds to the HLA protein of the subject with an 1050 less than 250 nM.
7 . The method of claim 1 wherein at least one subject-specific peptide binds to the HLA protein of the subject with an 1050 less than 100 nM.
8 . The method of claim 1 wherein at least one subject-specific peptide binds to the HLA protein of the subject with an 1050 less than 50 nM.
9 . The method of claim 1 comprising administering 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides.
10 . The method of claim 9 further comprising administering a peptide epitope that is capable of inducing a T helper cell response.
11 . The method of claim 10 wherein at least one subject specific peptide is linked to the peptide epitope that is capable of inducing a T helper cell response.
12 . The method of claim 1 comprising administering one or more polynucleotide encoding the 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides.
13 . The method of claim 12 further comprising administering a polynucleotide encoding an epitope that is capable of inducing a T helper cell response.
14 . The method of claim 12 , wherein the one or more polynucleotide encoding the 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides comprises a minigene.
15 . The method of claim 14 , wherein the minigene encodes at least one peptide epitope that is capable of inducing a T helper cell response.
16 . The method of claim 12 , wherein the one or more polynucleotide encoding the 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides comprises a viral vector.
17 . The method of claim 1 wherein the tumor is a solid tumor.
18 . The method of claim 1 wherein the tumor is a hematological tumor.
19 . The method of claim 1 wherein the tumor a breast tumor, an ovarian tumor, a prostate tumor, a lung tumor, a kidney tumor, a gastric tumor, a colon tumor, a testicular tumor, a head and neck tumor, a pancreatic tumor, a brain tumor, a melanoma, a lymphoma or a leukemia.
20 . The method of claim 1 further comprising administering an adjuvant.
21 . The method of claim 1 further comprising administering a carrier.
22 . The method of claim 1 further comprising administering one or more additional cancer therapeutic agent.
23 . The method of claim 22 wherein the additional cancer therapeutic agent comprises a chemotherapeutic agent, radiation, or immunotherapy.
24 . The method of claim 1 further comprising administering an anti-immunosuppressive/immunostimulatory agent.
25 . The method of claim 24 wherein the anti-immunosuppressive/immunostimulatory agent provides a CTLA4, a PD-1, or a PD-L1 blockade.
26 . The method of claim 24 wherein the anti-immunosuppressive/immunostimulatory agent comprises an anti-CTLA4 antibody, an anti-PD 1 antibody, or an anti-PD-L1 antibody.
27 . The method of claim 1 , wherein the tumor is surgically removed and the subject specific peptide or one or more polynucleotide is administered at the time of the surgery.
28 . The method of claim 28 , wherein the subject specific peptide or one or more polynucleotide is administered at the site of surgical excision.
29 . A method of vaccinating a subject in need thereof against a tumor comprising: administering to the subject:
(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides; or
(b) one or more polynucleotide encoding the 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides; or
wherein the subject has a tumor and said subject-specific peptides are specific to the subject's tumor,
wherein each of said subject-specific peptides has a different tumor neo-epitope that is an epitope specific to the tumor of the subject,
wherein each neo-epitope binds to a HLA protein of the subject with an IC50 less than 500 nM; and
wherein each neo-epitope represents a tumor-specific non-silent mutation selected from the group comprising
(i) non-synonymous mutations leading to different amino acids in the protein;
(ii) read-through mutations in which a stop codon is modified or deleted, leading to translation of a longer protein with a novel tumor-specific sequence at the C-terminus;
(iii) splice site mutations that lead to the inclusion of an intron in the mature mRNA and thus a unique tumor-specific protein sequence;
(iv) chromosomal rearrangements that give rise to a chimeric protein with tumor-specific sequences at the junction of two proteins (i.e., gene fusion);
(v) frameshift mutations or deletions that lead to a new open reading frame with a novel tumor-specific protein sequence.
30 . A method of treating cancer a subject in need thereof comprising: administering to the subject
(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides; or
(b) one or more polynucleotide encoding the 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 subject-specific peptides;
wherein the subject has a cancer and said subject-specific peptides are specific to the subject's cancer,
wherein each of said subject-specific peptides has a different cancer neo-epitope that is an epitope specific to the cancer of the subject,
wherein each neo-epitope binds to a HLA protein of the subject with an IC50 less than 500 nM; and
wherein each neo-epitope represents a cancer-specific non-silent mutation selected from the group comprising
(i) non-synonymous mutations leading to different amino acids in the protein;
(ii) read-through mutations in which a stop codon is modified or deleted, leading to translation of a longer protein with a novel cancer-specific sequence at the C-terminus;
(iii) splice site mutations that lead to the inclusion of an intron in the mature mRNA and thus a unique cancer-specific protein sequence;
(iv) chromosomal rearrangements that give rise to a chimeric protein with cancer-specific sequences at the junction of two proteins (i.e., gene fusion);
(v) frameshift mutations or deletions that lead to a new open reading frame with a novel cancer-specific protein sequence.