Predicting immunogenicity of t cell epitopes

Abstract

The present invention relates to methods for predicting T cell epitopes. In particular, the present invention relates to methods for predicting whether modifications in peptides or polypeptides such as tumor-associated neoantigens are immunogenic or not. The methods of the invention are useful, in particular, for the provision of vaccines which are specific for a patient's tumor and thus, in the context of personalized cancer vaccines.

1 . A method for predicting immunogenic amino acid modifications, the method comprising the steps:
 a) ascertaining a score for binding of a modified peptide to one or more MHC molecules, and   b) ascertaining a score for binding of the non-modified peptide to one or more MHC molecules, and/or   c) ascertaining a score for binding of the modified peptide when present in a MHC-peptide complex to one or more T cell receptors.   
     
     
         2 . The method of  claim 1  wherein the modified peptide comprises a fragment of a modified protein, said fragment comprising the modification(s) present in the protein. 
     
     
         3 . The method of  claim 1  or  2  wherein the non-modified peptide has the germline amino acid at the position(s) corresponding to the position(s) of the modification(s) in the modified peptide. 
     
     
         4 . The method of any one of  claims 1  to  3  wherein the non-modified peptide and modified peptide are identical but for the modification(s). 
     
     
         5 . The method of any one of  claims 1  to  4  wherein the non-modified peptide and modified peptide are 8 to 15, preferably 8 to 12 amino acids in length. 
     
     
         6 . The method of any one of  claims 1  to  5  wherein the one or more MHC molecules comprise different MHC molecule types, in particular different MHC alleles. 
     
     
         7 . The method of any one of  claims 1  to  6  wherein the one or more MHC molecules are MHC class I molecules and/or MHC class II molecules. 
     
     
         8 . The method of any one of  claims 1  to  7  wherein the score for binding to one or more MHC molecules is ascertained by a process comprising a sequence comparison with a database of MHC-binding motifs. 
     
     
         9 . The method of any one of  claims 1  to  8  wherein step a) comprises ascertaining whether said score satisfies a pre-determined threshold for binding to one or more MHC molecules. 
     
     
         10 . The method of any one of  claims 1  to  9  wherein step b) comprises ascertaining whether said score satisfies a pre-determined threshold for binding to one or more MHC molecules. 
     
     
         11 . The method of any one of  claims 1  to  10  wherein the threshold applied in step a) is different to the threshold applied in step b). 
     
     
         12 . The method of any one of  claims 1  to  11  wherein the pre-determined threshold for binding to one or more MHC molecules reflects a probability for binding to one or more MHC molecules. 
     
     
         13 . The method of any one of  claims 1  to  12  wherein step c) comprises ascertaining a score for the chemical and physical similarities between the non-modified and modified amino acids. 
     
     
         14 . The method of any one of  claims 1  to  13  wherein step c) comprises ascertaining whether said score satisfies a pre-determined threshold for the chemical and physical similarities between amino acids. 
     
     
         15 . The method of any one of  claims 1  to  14  wherein the score for the chemical and physical similarities is ascertained on the basis of the probability of amino acids being interchanged in nature. 
     
     
         16 . The method of any one of  claims 1  to  15  wherein the more frequently amino acids are interchanged in nature the more similar the amino acids are considered. 
     
     
         17 . The method of any one of  claims 1  to  16  wherein the chemical and physical similarities are determined using evolutionary based log-odds matrices. 
     
     
         18 . The method of any one of  claims 1  to  17  wherein, if the non-modified peptide has a score for binding to one or more MHC molecules satisfying a threshold indicating binding to one or more MHC molecules and the modified peptide has a score for binding to one or more MHC molecules satisfying a threshold indicating binding to one or more MHC molecules, the modification or modified peptide is predicted as immunogenic if the non-modified and modified amino acids have a score for the chemical and physical similarities satisfying a threshold indicating chemical and physical dissimilarity. 
     
     
         19 . The method of any one of  claims 1  to  18  wherein if the non-modified peptide binds to one or more MHC molecules or has a probability for binding to one or more MHC molecules and the modified peptide binds to one or more MHC molecules or has a probability for binding to one or more MHC molecules, the modification or modified peptide is predicted as immunogenic if the non-modified and modified amino acids are chemically and physically dissimilar or have a probability of being chemically and physically dissimilar. 
     
     
         20 . The method of  claim 18  or  19  wherein the modification is not in an anchor position for binding to one or more MHC molecules. 
     
     
         21 . The method of any one of  claims 1  to  17  wherein, if the non-modified peptide has a score for binding to one or more MHC molecules satisfying a threshold indicating no binding to one or more MHC molecules and the modified peptide has a score for binding to one or more MHC molecules satisfying a threshold indicating binding to one or more MHC molecules, the modification or modified peptide is predicted as immunogenic. 
     
     
         22 . The method of any one of  claims 1  to  17  and  21  wherein, if the non-modified peptide does not bind to one or more MHC molecules or has a probability for not binding to one or more MHC molecules and the modified peptide binds to one or more MHC molecules or has a probability for binding to one or more MHC molecules, the modification or modified peptide is predicted as immunogenic. 
     
     
         23 . The method of  claim 21  or  22  wherein the modification is in an anchor position for binding to one or more MHC molecules. 
     
     
         24 . The method of any one of  claims 1  to  23  which comprises performing step a) on two or more different modified peptides, said two or more different modified peptides comprising the same modification(s). 
     
     
         25 . The method of  claim 24  wherein the two or more different modified peptides comprising the same modification(s) comprise different fragments of a modified protein, said different fragments comprising the same modification(s) present in the protein. 
     
     
         26 . The method of  claim 24  or  25  wherein the two or more different modified peptides comprising the same modification(s) comprise all potential MHC binding fragments of a modified protein, said fragments comprising the same modification(s) present in the protein. 
     
     
         27 . The method of any one of  claims 24  to  26  further comprising selecting (the) modified peptide(s) from the two or more different modified peptides comprising the same modification(s) having a probability or having the highest probability for binding to one or more MHC molecules. 
     
     
         28 . The method of any one of  claims 24  to  27  wherein the two or more different modified peptides comprising the same modification(s) differ in length and/or position of the modification(s). 
     
     
         29 . The method of any one of  claims 1  to  28  which comprises performing step a) and optionally one or both of steps b) and c) on two or more different modified peptides. 
     
     
         30 . The method of  claim 29  wherein said two or more different modified peptides comprise the same modification(s) and/or comprise different modifications. 
     
     
         31 . The method of  claim 30  wherein the different modifications are present in the same and/or in different proteins. 
     
     
         32 . The method of any one of  claims 24  to  31  which comprises comparing the scores of two or more of said different modified peptides. 
     
     
         33 . The method of  claim 32  wherein a score for binding of the modified peptide to one or more MHC molecules is weighted higher than a score for binding of the modified peptide when present in a MHC-peptide complex to one or more T cell receptors, preferably a score for the chemical and physical similarities between the non-modified and modified amino acids and a score for binding of the modified peptide when present in a MHC-peptide complex to one or more T cell receptors, preferably a score for the chemical and physical similarities between the non-modified and modified amino acids is weighted higher than a score for binding of the non-modified peptide to one or more MHC molecules. 
     
     
         34 . The method of any one of  claims 1  to  33  further comprising identifying non-synonymous mutations in one or more protein-coding regions. 
     
     
         35 . The method of any one of  claims 1  to  34  wherein modifications are identified by partially or completely sequencing the genome or transcriptome of one or more cells such as one or more cancer cells and optionally one or more non-cancerous cells and identifying mutations in one or more protein-coding regions. 
     
     
         36 . The method of  claim 34  or  35  wherein said mutations are somatic mutations. 
     
     
         37 . The method of  claim 34  to  36  wherein said mutations are cancer mutations. 
     
     
         38 . The method of any one of  claims 1  to  37  which is used in the manufacture of a vaccine. 
     
     
         39 . The method of  claim 38  wherein the vaccine is derived from (a) modification(s) or (a) modified peptide(s) predicted as immunogenic by said method. 
     
     
         40 . A method for providing a vaccine comprising the step:
 identifying (a) modification(s) or (a) modified peptide(s) predicted as immunogenic by the method of any one of  claims 1  to  37 .   
     
     
         41 . The method of  claim 40  further comprising the step:
 providing a vaccine comprising a peptide or polypeptide comprising the modification(s) or modified peptide(s) predicted as immunogenic, or a nucleic acid encoding the peptide or polypeptide. 
 
     
     
         42 . A vaccine produced according to the method of any one of  claims 38  to  41 .