Malignant cell MHC-II immunopeptidomes reveal the evolution of tumor-host interactions

Adaptive immunity to cancer requires effective antigen presentation on Major Histocompatibility Complexes1. While recent advances in identifying cancer-specific MHC-I antigens have ushered in a new era of antigenspecific immunotherapies2-4, studies on MHC-II are less developed due to the lack of robust tools that enable isolation of MHC-II from cell types of interest in physiologically relevant models. We engineered an Cre-inducible endogenous affinity-tagged mouse MHC-II beta chain allele (H2-Ab1, “AbStrep”), the application of which to models of cancer, infectious disease, and autoimmunity has great potential for basic immunology discovery. We applied this tool to lung adenocarcinoma (LUAD), enabling precise and specific purification of MHC-II peptides from malignant LUAD cells or healthy AT2 cells in vivo. We found that numerous peptides were derived from the tumor microenvironment (TME) and systemic circulation. Leveraging these insights, we introduced synthetic antigens systemically, which were scavenged and presented by malignant cells in the TME. Moreover, LUAD cells presented a highly complex landscape of post-translationally modified MHC-II peptides, revealing additional MHC-II peptide binding modes and reflecting intracellular oncogenic signaling5. During LUAD progression, both tumor-host interactions and post-translational modifications dynamically remodel the MHC-II immunopeptidome. These observations suggest the presence of an ever-evolving landscape of MHC-II targets for CD4+ T cells during tumor progression that influences the success or failure of immunotherapy.