Publication
Deciphering the immunopeptidome in vivo reveals new tumour antigens
Alex M. Jaeger, Lauren E. Stopfer, Ryuhjin Ahn, Emma A. Sanders, Demi A. Sandel, William A. Freed-Pastor, William M. Rideout III, Santiago Naranjo, Tim Fessenden, Kim B. Nguyen, Peter S. Winter, Ryan E. Kohn, Peter M. K. Westcott, Jason M. Schenkel, Sean-Luc Shanahan, Alex K. Shalek, Stefani Spranger,Forest M. White & Tyler Jacks
Immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex class I (MHC-I) molecules. Current approaches to profling of MHC-I-associated peptides, collectively known as the immunopeptidome, are limited to in vitro investigation or bulk tumour lysates, which limits our understanding of cancer-specifc patterns of antigen presentation in vivo6. To overcome these limitations, we engineered an inducible afnity tag into the mouse MHC-I gene (H2-K1) and targeted this allele to the KrasLSL-G12D/+Trp53f/f mouse model (KP/Kb Strep). This approach enabled us to precisely isolate MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma and from lung adenocarcinoma (LUAD) in vivo. In addition, we profled the LUAD immunopeptidome from the alveolar type 2 cell of origin up to late-stage disease. Diferential peptide presentation in LUAD was not predictable by mRNA expression or translation efciency and is probably driven by post-translational mechanisms. Vaccination with peptides presented by LUAD in vivo induced CD8+T cell responses in naive mice and tumour-bearing mice. Many peptides specifc to LUAD, including immunogenic peptides, exhibited minimal expression of the cognate mRNA, which prompts the reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance8. Beyond cancer, the Kb 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