Molecular approaches to identify cancer T cell antigens and improve immunogenicity

Abstract

Recent advances in our understanding of immunotherapeutic strategies against cancer and the development of improved analysis tools and computing power have led to a highly anticipated progression of the cancer-vaccine field. The possibilities of personalized approaches to vaccinate patients against tumor-specific antigens by the prediction of MHC-binding peptides are already in clinical studies. Currently, the field is lacking behind in antigen identification tools and optimal delivery of vaccines. The studies in this thesis are divided in two major parts which address these topics. The first part reports a novel approach for the identification of relevant MHC class I and II binding epitopes. With the combined use of exome sequencing and mass-spectrometric analysis, relevant neoantigens were characterized from MHC class I and II in murine and human models. Meanwhile, significant genomic differences were observed in the MC38 murine colorectal cancer model of different sources. The second part shows the development of a molecular approach for the tracking of ligands and peptides to improve our understanding of vaccine delivery. Therefore, bioorthogonal ‘click’ chemistry was applied for in situ ligation of fluorophores to antigen, thus providing a quantification method of processed antigens. Subsequent optimizations were explored into bioorthogonal reactions independent of copper.