RT Journal Article SR Electronic T1 Deciphering the tumor-specific immunopeptidome in vivo with genetically engineered mouse models JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.06.30.450516 DO 10.1101/2021.06.30.450516 A1 Alex M. Jaeger A1 Lauren E. Stopfer A1 Emma A. Sanders A1 Demi A. Sandel A1 William A. Freed-Pastor A1 William M. Rideout III A1 Santiago Naranjo A1 Tim Fessenden A1 Peter S. Winter A1 Ryan E. Kohn A1 Jason Schenkel A1 Sean-Luc Shanahan A1 Alex K. Shalek A1 Stefani Spranger A1 Forest M. White A1 Tyler Jacks YR 2021 UL http://biorxiv.org/content/early/2021/07/01/2021.06.30.450516.abstract AB Effective immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex Class I (MHC-I). Recent developments in proteomics have improved the identification of peptides that are naturally presented by MHC-I, collectively known as the “immunopeptidome”. Current approaches to profile tumor immunopeptidomes have been limited to in vitro investigation, which fails to capture the in vivo repertoire of MHC-I peptides, or bulk tumor lysates, which are obscured by the lack of tumor-specific MHC-I isolation. To overcome these limitations, we report here the engineering of a Cre recombinase-inducible affinity tag into the endogenous mouse MHC-I gene and targeting of this allele to the KrasLSL-G12D/+; p53fl/fl (KP) mouse model (KP; KbStrep). This novel approach has allowed us to isolate tumor-specific MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) in vivo. With this powerful analytical tool, we were able to profile the evolution of the LUAD immunopeptidome through tumor progression and show that in vivo MHC-I presentation is shaped by post-translational mechanisms. We also uncovered novel, putative LUAD tumor associated antigens (TAAs). Many peptides that were recurrently presented in vivo exhibited very low expression of the cognate mRNA, provoking reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance. Beyond cancer, the KbStrep allele is compatible with a broad range of Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease, and autoimmunity.Competing Interest StatementT.J. is a member of the Board of Directors of Amgen and Thermo Fisher Scientific, and a co-Founder of Dragonfly Therapeutics and T2 Biosystems. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics. T.J. is also President of Break Through Cancer. His laboratory currently receives funding from Johnson & Johnson and The Lustgarten Foundation, and funds from the Lustgarten Foundation supported the research described in this manuscript. None of these affiliations influenced the work conducted or analysis of data presented in this manuscript.