Deciphering the immunopeptidome in vivo reveals novel tumor antigens

Immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex class I (MHC-I) 1 , 2 , 3 , 4 , 5 . Current approaches to profile MHC-I associated peptides, collectively known as the “immunopeptidome”, are limited to in vitro investigation or bulk tumor lysates, limiting our understanding of cancer-specific patterns of antigen presentation in vivo 6 . To overcome these limitations, we engineered an inducible affinity tag into the mouse MHC-I gene ( H2-K1 ) and targeted this allele to the Kras LSL-G12D/+ ; p53 fl/fl (KP) mouse model (KP/K b Strep) 7 . This approach allowed us to precisely isolate MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) in vivo . In addition, we profiled the LUAD immunopeptidome from the alveolar type 2 cell-of-origin through late-stage disease. Differential peptide presentation in LUAD was not predictable by mRNA expression or translation efficiency and is likely driven by post-translational mechanisms. Vaccination with peptides presented by LUAD in vivo provoked CD8 + T cell responses in naïve and tumor-bearing mice. Many peptides unique to LUAD, including immunogenic peptides, exhibited minimal expression of the cognate mRNA, provoking reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance 8 . Beyond cancer, the K b Strep allele is compatible with other Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease, and autoimmunity.