Neoantigen immunotherapies

A method for treating cancer in a subject comprising designing a group of ten or more tumor-specific T-cell stimulating peptides, or nucleic acids encoding T cell stimulating peptides, which have a desired predicted binding affinity for the MHC alleles of the subject, comprising the following steps:

• obtaining a biopsy of the subject's tumor;
• obtaining sequences for proteins in said biopsy;
• identifying proteins from the biopsy containing mutated amino acids and the peptide comprising each of said mutated amino acids;
• determining T cell exposed motifs which comprise mutated amino acids in each of the proteins;
• determining the predicted binding affinity to the subject's MHC alleles of peptides which comprises each of said T cell exposed motifs which comprise mutated amino acids and identifying MHC allele-T cell exposed motif combinations which bind with an affinity greater than the mean for the protein from which the peptide is derived;
• generating an array of alternative peptides not present in the tumor from the identified MHC allele-T cell exposed motif combinations which bind with an affinity greater than the mean for the protein from which the peptide is derived, wherein each peptide in the array comprises the amino acids of one of said T cell exposed motifs which comprise mutated amino acids, and in which one or more of the amino acids not within the T cell exposed motif are substituted to change the predicted MHC binding affinity;
• selecting a group of ten or more selected peptides from said array of alternative peptides, wherein the group of selected peptides comprises peptides collectively predicted to bind to at least 4 different MHC alleles carried by the subject and further wherein the desired predicted binding affinity of each of the ten selected peptides is from 100 to 500 nM;
• synthesizing said group of ten or more selected peptides, or nucleic acids encoding the selected peptides;
• and
• treating cancer in the subject by a process selected from the group consisting of 1) administering the peptides or nucleic acids to the patient to stimulate a tumor specific T cell response, 2) contacting an antigen presenting cell in vitro with said group of one or more selected peptides, or the nucleic acids that encode them and administering said antigen presenting cells to a subject, and 3) stimulating T cells in vitro with said group of one or more selected peptides, or the nucleic acids that encode them, to provide stimulated T cells and administering said stimulated T cells to a subject.