Here, we will argue that the requirement for a stable MHC interaction is one of those “other” factors. It is generally recognized that Torin 1 order the requirement for binding

and presentation by MHC-I molecules is by far the most selective event of antigen processing and presentation [[6, 22-24]]. When searching for CD8+ T-cell epitopes, an affinity better than 500 nM (termed a good binder) is commonly used as a threshold to select candidate immunogenic peptides [[25]]. Sette and colleagues recently estimated that “the vast majority of epitopes (85%) bound their restricting MHC-I with an affinity of 500 nM or better, and most (75%) bound with an affinity of 100 nM or better” [[6]]. Unfortunately, this criterion leads to the inclusion of many nonimmunogenic peptides (i.e. false positives). Others and

we have observed that only some 10–20% of pathogen-derived peptides, which bind to MHC-I with an experimentally verified affinity of 500 nM, or better, are subsequently found to be immunogenic [[6, 25, 26]]. Testing the immunogenicity of all predicted immunogenic epitopes is currently a very slow, costly process, and any computational T-cell epitope discovery process would benefit from a better and more quantitative understanding of antigen processing and presentation. It has been suggested that the stability of pMHC complex correlates with immunogenicity (both for MHC-I [[1, 27-32]], and for MHC-II buy Nivolumab [[2, 33]]); and it has even been suggested that stability correlates better with immunogenicity than affinity of peptide interaction

with MHC-I [[34-37]] and MHC-II [[38]]. Common BCKDHB to all these reports is that the experimental data are limited to a few epitopes. Here, we have examined the stability of 739 peptides that bind to HLA-A*02:01 with an affinity of about 1000 nM or better. We found that the rate of dissociation at 37°C varied from a half-life of over 40 h to one of less than 0.1 h. To neutralize the effect of affinity, affinity-balanced pairs of known versus “not-known-to-be” immunogens restricted to different HLA alleles (A*01:01, A*02:01, B*07:02, and B*35:01) were extracted and analyzed biochemically. We found a highly significant difference in the stability of immunogens compared to “not-known-to-be” immunogens for three of the four HLA class I molecules examined. In parallel studies of the immunogenicity of HIV-derived epitopes restricted to B*57:02, B*57:03, B*58:01, B*07:02, B*42:01, and B*42:02, we have found that stability is a better discriminator of immunogenicity than affinity is (Kløverpris et al., manuscripts in preparation). Thus, the proposition that stability is a better indicator of immunogenicity can be extended to a wide range of HLA class I molecules. We were, however, concerned that the underlying data set was not representative of an unbiased epitope discovery process, since many reported CTL epitopes have been discovered using simple rule-based predictions of high-affinity binding to MHC-I.