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1427 Evaluating MHC-II antigen presentation in vivo to identify targets for immunotherapy
  1. Andrew Weeden1,
  2. Anika Ali1,
  3. Victoria Izumi1,
  4. Bin Fang1,
  5. Emma Sanders2,
  6. William Rideout2,
  7. John Koomen1,
  8. Paul Stewart1,
  9. Tyler Jacks2 and
  10. Alex M Jaeger1
  1. 1H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
  2. 2Koch Institute at MIT, Cambridge, MA, USA
  • Journal for ImmunoTherapy of Cancer (JITC) preprint. The copyright holder for this preprint are the authors/funders, who have granted JITC permission to display the preprint. All rights reserved. No reuse allowed without permission.


Background Central to the success of immunotherapy is antigen presentation on Major Histocompatibility Class I and II (MHC-I and MHC-II).1 While much effort has been paid to characterize MHC-I antigens recognized by CD8+ T cells, our understanding of MHC-II antigens, which are recognized by CD4+ T cells, is far less developed. The importance of MHC-II antigen presentation is particularly evident in lung adenocarcinoma (LUAD), where the alveolar type 2 (AT2) cell-of-origin is one of the only non-hematopoetic cell lineages known to present high levels of MHC-II.2 These observations prompt the need to understand the contribution of direct MHC-II presentation in LUAD.3 4 While advances in mass spectrometry have enabled direct interrogation of peptides presented by MHC-I and MHC-II, collectively known as the ‘immunopeptidome’, the field lacks tools to evaluate antigen presentation in vivo.5–7 Here we present a novel mouse model to interrogate the MHC-II immunopeptidome in vivo in LUAD and set the stage for future investigations of MHC-II antigen presentation beyond lung cancer.

Methods GEMMs, including the KrasLox-stop-Lox-G12D; p53fl/fl (KP), model faithfully recapitulate histopathological features of human LUAD and represent an excellent tool to understand MHC-II in the LUAD microenvironment.8 To profile MHC-II ligands in LUAD, we engineered a Cre-recombinase inducible affinity tagged MHC-II (H2-AbStrep) and incorporated this allele to the KP model (KP/AbStrep), enabling precise isolation of MHC-II peptides from malignant cells in the heterogeneous microenvironment. We thoroughly validated this novel model at the genetic, transcriptomic, and proteomic levels and isolated MHC-II peptides from LUAD tumors at various stages of tumor progression and with multiple targeted and immune therapies.

Results We demonstrate that LUAD cells present a diverse array of MHC-II peptides in vivo and found that source proteins that are processed and presented on MHC-II are highly divergent from those identified on LUAD MHC-I.8 Peptides derived from secreted proteins are abundant on LUAD MHC-II complexes, including those that are lowly expressed in LUAD cells but highly expressed by other cells in the tumor microenvironment. Finally, we found that the repertoire of MHC-II peptides is highly dynamic with respect to tumor progression and treatment context.

Conclusions These results have profound implications for our understanding of the immunobiology of lung cancer in distinct tumor microenvironments. Moreover, application of the AbStrep system to other disease and tissue contexts will pave the way forward for a deeper understanding of the MHC-II immunopeptidome in vivo to be exploited for next generation immunotherapies.


  1. Jhunjhunwala S, Hammer C, Delamarre L. Antigen presentation in cancer: insights into tumour immunogenicity and immune evasion. Nature Reviews Cancer, 2021:1--15.–021-00339-z

  2. Naranjo S, et al. Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform. Genes Dev 2022;36:936–949.

  3. Oliveira G, et al. Landscape of helper and regulatory antitumour CD4(+) T cells in melanoma. Nature 2022;605:532–538.–022-04682–5

  4. Alspach E, et al. MHC-II neoantigens shape tumour immunity and response to immunotherapy. Nature 2019;574:696--701.–019-1671–8

  5. Sarkizova S, et al. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nature Biotechnology 2019;38:199--209.–019-0322–9

  6. Abelin JG, et al. Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity 2017;46:315--326.

  7. Ouspenskaia T, et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature Biotechnology 2022;40:209--217.–021-01021–3

  8. Jaeger AM, et al. Deciphering the immunopeptidome in vivo reveals new tumour antigens. Nature 2022;607:149--155.–022-04839–2

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