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.

What is claimed: 
     
         1 . A method comprising
 (a) identifying a plurality of nucleic acid sequences from nucleic acid sequences from cancer cells of a subject that are unique to the cancer cells and that do not include nucleic acid sequences from non-cancer cells of the subject, wherein the identified plurality of nucleic acid sequences encode two or more different peptide sequences, wherein each of the two or more different peptide sequences are expressed by the cancer cells and comprise a cancer specific mutation;   (b) predicting which epitopes of the two or more different peptide sequences form a complex with an expressed protein encoded by an HLA allele of the subject by an HLA peptide binding analysis; and   (c) selecting at least two epitopes predicted in (b) based on the HLA peptide binding analysis.   
     
     
         2 . The method of  claim 1 , further comprising
 (a) producing at least two cancer neoantigen peptides comprising the at least two epitopes selected in (c), wherein producing the at least two cancer neoantigen peptides comprises expressing or synthesizing the at least two cancer neoantigen peptides; or   (b) producing one or more polynucleotides encoding the at least two cancer neoantigen peptides.   
     
     
         3 . The method of  claim 2 , further comprising formulating a pharmaceutical composition comprising the at least two cancer neoantigen peptides or one or more polynucleotides encoding the at least two cancer neoantigen peptides. 
     
     
         4 . The method of  claim 3 , wherein formulating comprises formulating the pharmaceutical composition with an adjuvant. 
     
     
         5 . The method of  claim 3 , wherein each of the at least two cancer neoantigen peptides is present in the pharmaceutical composition at an amount of from 50 μg to 1.5 mg. 
     
     
         6 . The method of  claim 3 , wherein each peptide of the pharmaceutical composition or each peptide encoded by the one or more polynucleotides is a peptide of the at least two cancer neoantigen peptides selected in (c). 
     
     
         7 . The method of  claim 3 , further comprising administering the pharmaceutical composition to the subject. 
     
     
         8 . The method of  claim 1 , wherein
 (i) each of the epitopes predicted to form a complex with an expressed protein encoded by a class I HLA allele of the subject in (b) has a length of from 8 to 12 amino acids, and   (ii) each of the epitopes predicted to form a complex with an expressed protein encoded by a class II HLA allele of the subject in (b) has a length of from 15-24 amino acids.   
     
     
         9 . The method of  claim 2 , wherein each of the at least two cancer neoantigen peptides has a length of from 8 to 50 naturally occurring amino acids. 
     
     
         10 . The method of  claim 9 , wherein each of the at least two cancer neoantigen peptides is greater than 15 amino acids in length. 
     
     
         11 . The method of  claim 10 , wherein selecting comprises selecting at least two of the epitopes predicted in (b) that bind to an expressed protein encoded by an HLA allele of the subject with a stronger affinity than corresponding wild-type epitopes. 
     
     
         12 . The method of  claim 1 , wherein
 (i) a first epitope of the at least two epitopes selected in (c) binds to an expressed protein encoded by a first HLA allele of the subject; and   (ii) the first or a second epitope of the at least two epitopes selected in (c) binds to an expressed protein encoded by a second HLA allele of the subject that is different than the first HLA allele.   
     
     
         13 . The method of  claim 1 , wherein identifying a plurality of nucleic acid sequences comprises comparing the nucleic acid sequences from cancer cells of a subject to the nucleic acid sequences from non-cancer cells of the subject. 
     
     
         14 . The method of  claim 1 , wherein predicting comprises predicting binding affinities of the epitopes to the expressed protein encoded by an HLA allele of the subject. 
     
     
         15 . The method of  claim 1 , wherein each epitope of the at least two epitopes selected in (c) comprises a point mutation and is predicted to bind to the protein encoded by an HLA allele of the subject with an IC 50  less than 500 nM. 
     
     
         16 . The method of  claim 1 , wherein the HLA peptide binding analysis comprises using a program implemented on computer system. 
     
     
         17 . The method of  claim 1 , wherein the at least two epitopes selected in (c) comprises at most 20 epitopes. 
     
     
         18 . The method of  claim 1 , wherein the cancer cells of the subject are cancer cells of a solid cancer, a leukemia or a lymphoma. 
     
     
         19 . The method of  claim 1 , wherein the at least two epitopes selected in (c) comprises at least 4 epitopes. 
     
     
         20 . The method of  claim 1 , wherein identifying comprises identifying the plurality of nucleic acid sequences from nucleic acid sequences from cancer cells of a subject and nucleic acid sequences from non-cancer cells of the subject by whole genome nucleic acid sequencing or whole exome nucleic acid sequencing.