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 identifying a neoantigen comprising:
 a. identifying a tumor specific mutation in an expressed gene of a subject having cancer,   b. wherein when said mutation identified in step (a) is a point mutation:
 i. identifying a mutant peptide having the mutation identified in step (a), wherein said mutant peptide binds to a class I HLA protein with a greater affinity than a wild-type peptide; and has an IC50 less than 500 nm; 
   c. wherein when said mutation identified in step (a) is a splice-site, frameshift, read-through or gene-fusion mutation:
 i. identifying a mutant polypeptide encoded by the mutation identified in step (a), wherein said mutant polypeptide binds to a class I HLA protein. 
   
     
     
         2 . The method of  claim 1 , wherein the mutant peptide is about 8-10 amino acids in length. 
     
     
         3 . The method of  claim 1 , wherein the mutant peptide is greater than 10 amino acids in length. 
     
     
         4 . The method of  claim 3 , wherein the mutant peptide is greater than 15 amino acids in length. 
     
     
         5 . The method of  claim 4 , wherein the mutant peptides is greater than 20 amino acids in length. 
     
     
         6 . The method of  claim 5 , wherein the mutant peptides is greater than 30 amino acids in length. 
     
     
         7 . The method of  claim 1 , wherein the mutant peptides is about 8 to 50 amino acids in length. 
     
     
         8 . The method of  claim 1 , wherein the mutant peptides is about 24-40 amino acids in length. 
     
     
         9 . The method of  claim 1 , wherein tumor specific mutations are identified by nucleic acid sequencing. 
     
     
         10 . The method of  claim 1 , further comprising selecting a peptide identified in step (b) or the polypeptide of step (c) that activates anti-tumor CD8 T cells. 
     
     
         11 . A method of inducing a tumor specific immune response in a subject comprising administering one or more peptides or polypeptides identified according to  claim 1  and an adjuvant. 
     
     
         12 . The method of  claim 11 , wherein the adjuvant is a TLR-based adjuvant. 
     
     
         13 . The method of  claim 11 , wherein the peptide or polypeptide is emulsified with a mineral-oil based adjuvant. 
     
     
         14 . The method of  claim 11 , wherein the peptide or polypeptide and a TLR-based adjuvant are emulsified with a mineral-oil based adjuvant. 
     
     
         15 . The method of  claim 11 , further comprising administering an anti-immunosuppressive agent. 
     
     
         16 . The method of  claim 15 , wherein the anti-immunosuppressive agent is an anti-CTLA-4 antibody, an anti-PD 1 antibody, an anti-PD-L1 antibody, an anti-CD25 antibody or an inhibitor of IDO. 
     
     
         17 . A method of inducing a tumor specific immune response in a subject comprising administering to the subject autologous dendritic cells or antigen presenting cells that have been pulsed with one or more of the peptides or polypeptides identified according to  claim 1 . 
     
     
         18 . The method of  claim 17 , further comprising administering an adjuvant. 
     
     
         19 . The method of  claim 18 , wherein the adjuvant is a TLR-based adjuvant. 
     
     
         20 . The method of  claim 17 , further comprising administering an anti-immunosuppressive agent. 
     
     
         21 . The method of  claim 20 , wherein said anti-immunosuppressive agent is an anti-CTLA-4 antibody, an anti-PD 1 antibody, an anti-PD-L1 antibody, an anti-CD25 antibody or an inhibitor of IDO. 
     
     
         22 . A method of vaccinating or treating a subject for cancer comprising:
 a. identifying a plurality of tumor specific mutations in an expressed gene of the subject wherein when said mutation identified is a:
 i. point mutation further identifying a mutant peptide having the point mutation; and/or 
 ii. splice-site, frameshift, read-through or gene-fusion mutation further identifying a mutant polypeptide encoded by the mutation; 
   b. selecting one or more mutant peptides or polypeptides identified in step (a) that binds to a class I HLA protein;   c. selecting the one or more mutant peptides or polypeptides identified in step (b) that is capable of activating anti-tumor CD8 T-cells; and   d. administering to the subject the one or more peptides or polypeptides, autologous dendritic cells or antigen presenting cells pulsed with the one or more peptides or polypeptides selected in step (c).   
     
     
         23 . The method of  claim 22 , further comprising administering the subject an adjuvant. 
     
     
         24 . The method of  claim 23 , wherein the adjuvant is a TLR-based adjuvant. 
     
     
         25 . The method of  claim 22 , further comprising administering an anti-immunosuppressive agent. 
     
     
         26 . The method of  claim 25 , wherein said anti-immunosuppressive agent is an anti-CTLA-4 antibody, an anti-PD 1 antibody, an anti-PD-L1 antibody, an anti-CD25 antibody or an inhibitor of IDO. 
     
     
         27 . The method of  claim 22 , wherein the mutant peptide is about 8-10 amino acids in length. 
     
     
         28 . The method of  claim 22 , wherein the mutant peptides is about 8 to 50 amino acids in length. 
     
     
         29 . The method of  claim 22 , wherein the mutant peptide is about 24-40 amino acids in length. 
     
     
         30 . The method of  claim 22 , wherein said subject is has received a hematopoictic stem cell transplant. 
     
     
         31 . The method of  claim 22 , wherein the subject is a human, dog, cat, or horse. 
     
     
         32 . The method of  claim 22 , wherein the cancer is breast cancer, ovarian cancer, prostate cancer, lung cancer, kidney cancer, gastric cancer, colon cancer, testicular cancer, head and neck cancer, pancreatic cancer, brain cancer, melanoma lymphoma or leukemia. 
     
     
         33 . The method of  claim 32 , wherein the lymphoma is a B cell lymphoma. 
     
     
         34 . The method of  claim 32 , wherein the leukemia is acute myelogenous leukemia, chronic myelogenous leukemia, chronic lymphocytic leukemia, or T cell lymphocytic leukemia. 
     
     
         35 . A pharmaceutical composition comprising the peptide identified according  claim 1  and a pharmaceutically acceptable carrier. 
     
     
         36 . A composition comprising at least two distinct:
 a. SF3B1 peptides wherein each peptide is equal to or less than 50 amino acids in length and contains
 i. a leucine at amino acid position 625; 
 ii. a histidine at amino acid position 626; 
 iii. a glutamic acid at amino acid position 700; 
 iv. an aspartic acid at amino acid position 742; or 
 v. an arginine at amino acid position 903, when numbered in accordance with wild-type SF3B1; 
   b. MYD88 peptides wherein each peptide is equal to or less than 50 amino acids in length and contains
 i. a threonine at amino acid position 232; 
 ii. a leucine at amino acid position 258; or 
 iii. a proline at amino acid position 265, when numbered in accordance with wild-type MYD88; 
   c. TP53 peptides wherein each peptide is equal to or less than 50 amino acids in length and contains
 i. an arginine at amino acid position 111; 
 ii. an arginine at amino acid position 215; 
 iii. a serine at amino acid position 238; 
 iv. a glutamine at amino acid position 248; 
 v. a phenylalanine at amino acid position 255; 
 vi. a cysteine at amino acid position 273 or 
 vii. an asparagine at amino acid position 281, when numbered in accordance with wild-type TP53; 
   d. ATM peptides wherein each peptide is equal to or less than 50 amino acids in length and contains
 i. a phenylalanine at amino acid position 1252; 
 ii. an arginine at amino acid position 2038; 
 iii. a histidine at amino acid position 2522; or 
 iv. a cysteine at amino acid position 2954, when numbered in accordance with wild-type ATM; 
   e. abl peptides wherein each peptide is equal to or less than 50 amino acids in length and contains
 i. a valine at amino acid position 244; 
 ii. a valine at amino acid position 248; 
 iii. a glutamic acid at amino acid position 250; 
 iv. an alanine at amino acid position 250; 
 v. a histidine at amino acid position 252; 
 vi. an arginine at amino acid position 252; 
 vii. a phenylalanine at amino acid position 253; 
 viii. a histidine at amino acid position 253; 
 ix. a lysine at amino acid position 255; 
 x. a valine at amino acid position 255; 
 xi. a glycine at amino acid position 276; 
 xii. an isoleucine at amino acid position 315; 
 xiii. an asparagine at amino acid position 315; 
 xiv. a leucine at amino acid position 317; 
 xv. a threonine at amino acid position 343; 
 xvi. a threonine at amino acid position 351; 
 xvii. a glycine at amino acid position 355; 
 xviii. a valine at amino acid position 359; 
 xix. an alanine at amino acid position 359; 
 xx. an isoleucine at amino acid position 379; 
 xxi. a leucine at amino acid position 382; 
 xxii. a methionine at amino acid position 387; 
 xxiii. a proline at amino acid position 396; 
 xxiv. an arginine at amino acid position 396; 
 xxv. a tyrosine at amino acid position 417; or 
 xxvi. a serine at amino acid position 486, when numbered in accordance with wild-type abl; 
   f. FBXW7 peptides wherein each peptide is equal to or less than 50 amino acids in length and contains:
 i. a leucine at amino acid position 280; 
 ii. a histidine at amino acid position 465; 
 iii. a cysteine at amino acid position 505; or 
 iv. a glutamic acid at amino acid position 597, when numbered in accordance with wild-type FBXW7; 
   g. MAPK1 peptides wherein each peptide is equal to or less than 50 amino acids in length and contains
 i. an asparagine at amino acid position 162; 
 ii. a glycine at amino acid position 291; or 
 iii. a phenylalanine at amino acid position 316, when numbered in accordance with wild-type MAPK1; or 
   h. GNB1 peptides wherein each peptide is equal to or less than 50 amino acids in length and contains a threonine at amino acid position 180, when numbered in accordance with wild-type GNB1.   
     
     
         37 . The composition of  claim 36 , further comprising an adjuvant. 
     
     
         38 . A method of treating a subject with an imatinib resistant tumor comprising administering to a HLA-A3 positive subject a composition a Bcr-abl peptide equal to or less than 50 amino acid in length that contains a lysine at position 255 when numbered in accordance with wild-type bcr-abl. 
     
     
         39 . A method of treating a subject with an imatinib resistant tumor comprising administering to said subject one or more peptides containing a bcr-abl mutation wherein said peptide is equal to or less than 50 amino acid and binds to a class I HLA protein with an IC50 less than 500 nm.