Hi-TIDe : Immunopeptidomics

Our main goal is to identify clinically relevant cancer specific Human Leukocyte Antigen (HLA) ligands that will guide the development of personalized cancer immunotherapy using mass-spectrometry (MS), currently the only methodology to unbiasedly identify HLA binding peptides that are presented in vivo to cytotoxic T cells.

Proteogenomics and MS-based immunopeptidomics approaches to identify HLA ligands derived from tumor-associated proteins, mutated neoantigens, non-canonical ORFs and post translationally modified peptides.

• We developed a high-throughput and in depth MS-based immunopeptidomics pipeline that now enables robust and reproducible sample preparation and measurement of HLA/MHC class I and class II peptides. We are currently applying this methodology to identify tumor-associated ligands extracted from cell lines and tumor tissues from humans and mouse models. 
• We have initiated fundamental discovery work to elucidate how tumor cells present antigens and what are the bases of tumor immunogenicity.
• We are investigating the differences between tumor types in terms of antigen presentation and how drugs modulate the immunopeptidome.
• In collaboration with the Vital-IT group (SIB), we have established a continuous bio-informatics pipeline enabling direct identification of neoantigens by combining genomic information derived from exome-seq analysis with measured immunopeptidomics data.
• In collaboration with Gfeller Lab, we are improving the performance of HLA class I and class II binding prediction tools by training them with our measured immunopeptidomics data.
• We apply proteogenomics approaches to identify personalized neo-antigens from patient tumor samples. These tumor-specific antigens will be further developed into personalized cancer vaccines or to enrich tumor-reactive and antigen-specific T cells for adoptive T cell-based therapies.