In silico identification of universal HLA stimulating b and T-cell restricted mage epitopes for vaccine development

Abstract

Melanoma antigens (MAGE) are imrnunogcns expressed ill malignancies but silenced III somatic tissues except testis. They are grouped into ten subfamilies and at least one subfamily is expressed ill a cancer type. In vaccinology, their tumor specific expression eliminates autoimmunity, antitumor effects arrests tumorigenesis and epitopes promiscuity matches human leukocyte antigen polymorphism. MAGE based vaccines in clinical trials are limited to subfamilies and target single tumors. Many epitopes have been reported but an analysis or universal epitopes that cut across all subfamilies has never been investigated. This in silico study was focused on finding conserved epitopes within the subfamilies, A conserved motif analysis of all proteornes was done using ClustalO, Jalview and Cyto scape tools. There was a notable absence of strong conservation explained as a consequence of weak functional constraints during gene evolution. An analysis of the antigens' extracellular topology was achieved using TMI IMM server and all antigens except MAGE 11I were found to be extracellular. 13 and T cell cpitopes within the extracellular conserved motifs were then identified via a pipeline ofpredietive servers (BCPreds, IEOB, ProPred 1 and Il, MHCPred and T-epitope designer) and tested for antigenicity using VaxiJen server. For results, 20 antigenic 13 cell epitopes (18-20 mer) and> lOT cell epitopes (8-15 mer) binding to human leukocyt.e antigen alleles; HLA-A*020 I, -A*0204, - 13*2705, -ORB I *0 101, and -DRB 1*040 I, are given. 8-mer T cell epitopes were found to be the most conserved and are thus considered universal epitopes. However, other epitopes (9-15 Iller) are only conserved wit.hin subfamilies hence strings of epitopes were formed to get universal polytopes. These findings will inform the design of a multivalent universal MAGE vaccine that targets more than nineteen tumors. This pipeline confirms six reported epitopes (from in vitro studies) thus showing the efficacy or using in silica tools in epitope prediction.