A Fast, Flexible and Low Cost Process for Neo-Epitope Based Immune Monitoring

Abstract

Abstract Advances in genomic technologies have paved the way to developing personalized cancer vaccines targeting neo-antigens. Patient-specific vaccines, targeting several neo-antigens in one go have already entered the clinic. Such personalized, multi-target approach poses a challenge for immune monitoring of vaccine-specific T-cell responses in a fast, flexible and cost-effective fashion. Most immune monitoring protocols use 9–15-mer synthetic peptides originating from the vaccine target antigen. In contrast to detection of shared antigen-specific T-cells, for which the same peptide batch can be used for several patients, immune monitoring of individual neo-antigen-specific T-cell responses requires small amounts of large numbers of peptides (e.g. 40 × 15-mer peptides for 10 neo-epitopes of 27 amino-acids), which can only be used for one single patient. Therefore, standard peptide synthesis approaches applying commercial peptide synthesizers not only lack required throughput and speed but also generate peptides at prohibitive costs. Here, we present data demonstrating the flexible application of our high-throughput, low cost FastTrack peptide synthesis approach in comparison with different specifications of standard peptides in ex-vivo ELISPOT to monitor neo-antigen specific immune responses in patients participating in the IVAC MUTANOME Phase I clinical trial (NCT02035956). Application of the new peptide synthesis method enables the assembly of up to 1200 peptides in less than 3 weeks at appr. 20% of standard synthesis costs.