Predicting t cell epitopes useful for vaccination

Abstract

The present invention relates to methods for predicting T cell epitopes useful for vaccination. In particular, the present invention relates to methods for predicting whether modifications in peptides or polypeptides such as tumor-associated neoantigens are immunogenic and, in particular, useful for vaccination, or for predicting which of such modifications are most immunogenic and, in particular, most useful for vaccination. The methods of the invention may be used, 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 .- 29 . (canceled) 
     
     
         30 . A method for predicting immunogenicity of an amino acid modification, the method comprising steps of:
 a) ascertaining a score for binding of a modified peptide comprising a fragment of a modified protein to one or more MHC class II molecules (“its MHC class II binding score”);   b) ascertaining a score for expression or abundance (its “abundance score”) of the modified protein; and   c) predicting immunogenicity of the amino acid modification based on the score for binding of the modified peptide to the one or more MHC class II molecules and the score for expression or abundance of the modified protein.   
     
     
         31 . The method of  claim 31 , wherein predicting immunogenicity of an amino acid modification comprises predicting whether a peptide comprising an amino acid modification will be immunogenic. 
     
     
         32 . A method for selecting and/or ranking immunogenic amino acid modifications, the method comprising steps of:
 a) ascertaining a score for binding of a modified peptide comprising a fragment of a modified protein to one or more MHC class II molecules (“its MHC class II binding score”);   b) ascertaining a score for expression or abundance (its “abundance score”) of the modified protein;   c) performing steps a) and b) for two or more different immunogenic amino acid modifications; and   d) selecting and/or ranking the two or more different immunogenic amino acid modifications by comparing the MHC class II binding scores of the corresponding modified peptide and the abundance scores for the corresponding modified protein.   
     
     
         33 . The method of  claim 32 , wherein selecting and/or ranking the two or more different immunogenic amino acid modifications comprises a selection and/or ranking of peptides comprising the two or more different immunogenic amino acid modifications for their immunogenicity. 
     
     
         34 . The method of  claim 32 , wherein comparing the MHC class II binding scores and the abundance scores comprises ranking the two or more different amino acid modifications by their MHC class II binding scores and removing amino acid modifications for which the corresponding modified protein has an expression or abundance of less than a given threshold. 
     
     
         35 . The method of  claim 30 , wherein the modified protein comprises a tumor-associated neoantigen of a patient. 
     
     
         36 . The method of  claim 35 , wherein the tumor-associated neoantigen is a peptide or protein comprising a tumor-specific amino acid modification. 
     
     
         37 . The method of  claim 30 , wherein the MHC class II binding score reflects a probability for binding of the modified peptide to the one or more MHC class II molecules. 
     
     
         38 . The method  claim 30 , wherein the abundance score is based on a score for level of expression of a protein to which the one or more amino acid modifications are associated and a score for variant allele frequency for the modified protein. 
     
     
         39 . The method of  claim 38 , wherein the abundance score is determined by multiplying the score for level of expression of the protein to which the one or more amino acid modifications are associated with the score for variant allele frequency of the modified protein. 
     
     
         40 . The method of  claim 38 , wherein the score for variant allele frequency is determined from a sum of detected sequence reads covering mutation site(s) corresponding to the amino acid modification(s) and carrying the amino acid modification(s) divided by a sum of all detected sequence reads covering the mutation site(s). 
     
     
         41 . The method of  claim 38 , wherein the score for variant allele frequency is determined from a sum of mutated nucleotides detected at the mutation site(s) corresponding to the one or more amino acid modifications divided by a sum of all nucleotides detected at the mutation site(s). 
     
     
         42 . The method of  claim 30 , wherein two or more different amino acid modifications are present in the same and/or in different modified proteins. 
     
     
         43 . The method of  claim 30 , further comprising performing step a) on two or more different modified peptides, said two or more different modified peptides comprising the same amino acid modification(s). 
     
     
         44 . The method of  claim 43 , wherein the two or more different modified peptides comprising the same amino acid modification(s) comprise different fragments of a modified protein, said different fragments comprising the same amino acid modification(s) present in the modified protein. 
     
     
         45 . The method of  claim 44 , wherein the two or more different modified peptides comprising the same amino acid modification(s) comprise different potential MHC class II binding fragments of a modified protein, said fragments comprising the same amino acid modification(s) present in the modified protein. 
     
     
         46 . The method of  claim 43 , further comprising selecting the modified peptide(s) from the two or more different modified peptides comprising the same amino acid modification(s) having a probability or having the highest probability for binding to one or more MHC class II molecules. 
     
     
         47 . The method of  claim 43 , wherein the two or more different modified peptides comprising the same amino acid modification(s) differ in length and/or position of the amino acid modification(s). 
     
     
         48 . The method of  claim 43 , wherein a highest score for binding to one or more MHC class II molecules of the two or more different modified peptides comprising the same amino acid modification(s) is assigned to the amino acid modification(s). 
     
     
         49 . The method of  claim 38 , further comprising a step of determining a score for level of expression (an “RNA expression score”) of the RNA encoding the protein to which the one or more amino acid modifications are associated, wherein is determined by measuring the level of expression of RNA encoding the protein. 
     
     
         50 . The method of  claim 38 , further comprising a step of determining a score for variant allele frequency (a “variant allele frequency score”) for the modified protein, wherein the score is determined by measuring the level of expression of RNA encoding the modified protein. 
     
     
         51 . The method of  claim 30 , wherein the modified peptide comprises a fragment of the modified protein, said fragment comprising the amino acid modification(s) present in the modified protein. 
     
     
         52 . The method of  claim 30 , further comprising identifying non-synonymous mutations in one or more protein-coding regions of a transcript corresponding to the modified protein. 
     
     
         53 . The method  claim 30 , wherein amino acid modifications are identified by partially or completely sequencing the genome, exome, or transcriptome of one or more cells. 
     
     
         54 . The method of  claim 30 , wherein mutation(s) corresponding to the amino acid modification(s) are somatic mutation(s). 
     
     
         55 . The method of  claim 54 , wherein said mutation(s) are cancer mutation(s). 
     
     
         56 . The method of  claim 30 , further comprising a step of manufacturing a vaccine that delivers one or more peptides or polypeptides comprising the one or more amino acid modifications predicted as being immunogenic or more immunogenic, and/or one or more modified peptides predicted as being immunogenic or more immunogenic. 
     
     
         57 . The method of  claim 56 , wherein the vaccine is a nucleic acid vaccine comprising a nucleic acid encoding the one or more peptides or polypeptides comprising the one or more amino acid modifications predicted as being immunogenic or more immunogenic, and/or one or more modified peptides predicted as being immunogenic or more immunogenic. 
     
     
         58 . The method of  claim 56 , wherein the vaccine is a peptide or polypeptide vaccine comprising one or more peptides or polypeptides comprising the one or more amino acid modifications predicted as being immunogenic or more immunogenic, and/or one or more modified peptides predicted as being immunogenic or more immunogenic. 
     
     
         59 . The method of  claim 58 , wherein the step of manufacturing comprises in vitro transcription to generate an RNA encoding the one or more peptides or polypeptides comprising the one or more amino acid modifications predicted as being immunogenic or more immunogenic, and/or one or more modified peptides predicted as being immunogenic or more immunogenic. 
     
     
         60 . A method for manufacturing a vaccine, the method comprising steps of:
 a) detecting a mutation corresponding to a non-synonymous amino acid modification by partial or complete sequencing of the genome, exome, or transcriptome of one or more cells from a subject;   b) predicting one or more immunogenic amino acid modifications or one or more immunogenic modified peptides by the method of  claim 30 ; and   c) manufacturing a vaccine comprising one or more peptides or polypeptides comprising the one or more immunogenic amino acid modifications predicted as being immunogenic or more immunogenic or comprising the one or more immunogenic modified peptides predicted as being immunogenic or more immunogenic, or a nucleic acid encoding the one or more peptides or polypeptides.   
     
     
         61 . The method of  claim 60 , wherein the one or more peptides or polypeptides comprises one or more neo-epitopes or T-cell epitopes. 
     
     
         62 . The method of  claim 60 , wherein the one or more neo-epitopes or T-cell epitopes each comprises one or more tumor-specific amino acid modifications. 
     
     
         63 . The method of  claim 60 , wherein the one or more peptides or polypeptides further comprises one or more epitopes that do not comprise tumor-specific amino acid modifications. 
     
     
         64 . The method of  claim 62 , wherein the one or more neo-epitopes or T-cell epitopes are separated by linkers. 
     
     
         65 . The method of  claim 60 , wherein the vaccine provides WIC class II-presented epitopes that are capable of eliciting a CD4 +  helper T cell response against cells expressing antigens from which the WIC class II-presented epitopes are derived. 
     
     
         66 . The method of  claim 60 , wherein the vaccine provides WIC class I-presented epitopes that are capable of eliciting a CD8 +  T cell response against cells expressing antigens from which the WIC class I-presented epitopes are derived. 
     
     
         67 . The method of  claim 60 , wherein the nucleic acid is ribonucleic acid (RNA). 
     
     
         68 . The method of  claim 67 , wherein the RNA has been modified to increase stability or expression. 
     
     
         69 . A vaccine comprising:
 a peptide or polypeptide comprising one or more amino acid modification(s) predicted as being immunogenic or more immunogenic by the method of  claim 30 , or a nucleic acid encoding said peptide or polypeptide.   
     
     
         70 . The vaccine of  claim 69 , wherein the vaccine is specific for a subject's tumor. 
     
     
         71 . The vaccine of  claim 69 , wherein the peptide or polypeptide comprises one or more neo-epitopes or T-cell epitopes. 
     
     
         72 . The vaccine of  claim 71 , wherein the one or more neo-epitopes or T-cell epitopes each comprise one or more tumor-specific amino acid modifications. 
     
     
         73 . The vaccine of  claim 69 , wherein the peptide or polypeptide further comprises one or more epitopes that do not comprise tumor-specific amino acid modifications. 
     
     
         74 . The vaccine of  claim 71 , wherein the one or more neo-epitopes or T-cell epitopes are separated by linkers. 
     
     
         75 . The vaccine of  claim 69 , wherein the vaccine provides MHC class II-presented epitopes that are capable of eliciting a CD4 +  helper T cell response against cells expressing antigens from which the MHC class II-presented epitopes are derived. 
     
     
         76 . The vaccine of  claim 69 , wherein the vaccine provides MHC class I-presented epitopes that are capable of eliciting a CD8 +  T cell response against cells expressing antigens from which the MHC class I-presented epitopes are derived. 
     
     
         77 . The vaccine of  claim 69 , wherein the nucleic acid is ribonucleic acid (RNA). 
     
     
         78 . The vaccine of  claim 77 , wherein the RNA has been modified to increase stability or expression. 
     
     
         79 . The vaccine of  claim 69 , wherein the vaccine further comprises a pharmaceutically acceptable carrier. 
     
     
         80 . The vaccine of  claim 69 , wherein the vaccine further comprises one or more adjuvants or stabilizers. 
     
     
         81 . A method for analyzing and selecting modified peptides for use in producing a vaccine, the method comprising:
 employing a computer-based analytical process comprising predicting, ranking, and/or selecting one or more immunogenic amino acid modifications in a protein by the method  claim 30 .   
     
     
         82 . The method of  claim 81 , wherein the protein comprises a tumor-associated neoantigen of a patient. 
     
     
         83 . A method of manufacturing a vaccine, the method comprising:
 a) performing the method of  claim 82 ; and   b) manufacturing a vaccine comprising a peptide or polypeptide comprising the one or more immunogenic amino acid modifications or modified peptides predicted as being immunogenic or more immunogenic, or a nucleic acid encoding the peptide or polypeptide.   
     
     
         84 . A method for manufacturing a vaccine, the method comprising steps of:
 a) detecting a mutation corresponding to a non-synonymous amino acid modification by partial or complete sequencing of the genome, exome, or transcriptome of one or more cells from a subject;   b) predicting one or more immunogenic amino acid modifications in a protein comprising a tumor-associated neoantigen by the method of  claim 30 ; and   c) manufacturing a vaccine comprising a peptide or polypeptide comprising the one or more immunogenic amino acid modifications or modified peptides predicted as being immunogenic or more immunogenic, or a nucleic acid encoding the peptide or polypeptide.   
     
     
         85 . The method of  claim 84 , wherein the vaccine comprises a synthetic mRNA vaccine encoding one or more neo-epitopes or T-cell epitopes.