Developing a Novel Platform for Neoantigen Identification

Abstract

Tumor infiltrating CD8+ cytotoxic T lymphocytes (CTLs) recognize tumor-derived peptide antigens, or neoantigens, presented on MHC Class I molecules to elicit an anti-tumor immune response. Neoantigens originate from the accumulation of tumor-specific somatic mutations in DNA sequences, such as point and frameshift mutations. These mutations generate modified peptides that can be found uniquely on the surface of a tumor cell, making them crucial target molecules in cancer immunotherapies for limiting off-target toxicity effects. The ability to identify neoantigens remains a great challenge in the field. This thesis is focused on the development of a platform for neoantigen discovery and isolation employing a novel magnetic bead based system to enrich for cells expressing peptide MHC Class I complexes. Using a B16 F10 mouse melanoma cell line as a model system we present a unique approach for peptide presentation and peptide elution for mass spectrometry (MS) and high performance liquid chromatography (HPLC). Utilizing this approach for detection of abundant peptides in an in vitro setting could then be translated to isolate neoantigens of low abundance in a clinical tumor model. This protein purification based method provides an alternative to current methods, such as high-throughput sequencing for neoantigen predictions, which may not be reliable. Improving upon methods to discover neoantigens is necessary for developing targeted, personalized treatment therapies that can boost anti-tumor immune responses.