mRNA Multipeptide-HLA Class II Immunotherapy for Melanoma

Human Leukocyte Antigen (HLA) Class II (HLA-II) molecules bind peptides of phagocytosed non-self proteins and present them on the cell surface to circulating CD4+ T lymphocytes. A successful binding of the presented peptide with the T cell receptor (TCR) activates the CD4+ T cell, leading to the production of antibodies against the peptide (and the protein of its origin) by the B cell and augmentation of the cytotoxic and memory functions of CD8+ T cells. The first and essential step in this process is the successful formation of a stable peptide-HLA-II complex (pHLA-II), which is achieved when the peptide binds with high affinity to the HLA-II molecule. Such highly antigenic non-self peptides occur in melanoma-associated proteins and could be used as antitumor agents when bound to a matching HLA-II molecule. The objective of this study was to identify such peptides from 15 melanoma-associated proteins. We determined in silico the predicted binding affinity (IC₅₀) of all pHLA-II pairs between 192 common HLA-II molecules and all possible linear 15-amino acid (15-mer) peptides (epitopes) of 15 known melanoma-associated antigens (N = 3466 epitopes) for a total of 192 × 3466 = 665,472 determinations. From this set, we identified epitopes with strong antigenicity (predicted best binding affinity [PBBA] IC₅₀ < 50 nM). Of a total of 665,472 pHLA-II tested, 5941 (0.89%) showed strong PBBA, stemming from 117 HLA-II alleles and 679 distinct epitopes. This set of 5941 pHLA-II pairs with predicted high antigenicity possesses the requisite information for devising multipeptide vaccines with those epitopes alone or in combination with the corresponding HLA-II molecules. The results obtained have a major implication for cancer therapy, namely that the administration of subsets of the 679 high antigenicity epitopes above, alone or in combination with their associated HLA-II molecules, would be successful in engaging CD4+ T helper lymphocytes to augment the cytotoxic action and memory of CD8+ T lymphocytes and induce the production of antitumor antibodies by B cells. This therapy would be effective in other solid tumors (in addition to melanoma) and would be enhanced by concomitant immunotherapy with immune checkpoint inhibitors.