Compositions and methods of identifying tumor specific neoantigens

Abstract

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.

We claim: 
     
         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.