Deciphering the immunopeptidome in vivo reveals new tumour antigens

Abstract

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 Kras LSL-G12D/+ ; p53 fl/fl (KP) mouse model (KP; K b Strep). 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 K b Strep 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.

Identification of distinct tumor cell patterns with single-cell RNA sequencing integrating primary lung adenocarcinoma and brain metastasis tumor

“…Cell adhesion molecules were enriched in the intermediate stage. Antigen processing and presentation, which is required for the immunosurveillance of cancer cells ( 34 - 37 ) and the modulation of antigen expression and human leukocyte antigen type I (HLA-I) surface levels, were enriched in all 3 stages ( Figure S2C ). Alterations in the antigen processing and presentation could be protective for tumor cells via immune evasion ( 34 ).…”

Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform

“…We transduced transformed KP organoids with a lentivirus containing the fluorescent reporter mScarlet fused to SIINFEKL, a MHC class I-restricted peptide antigen derived from chicken ovalbumin (OVA 257–264 ), to generate KP-mScarlet-SIINFEKL (KP-SIIN) organoids. mScarlet can then be used as a proxy for sustained antigen expression in organoids and tumors ( Freed-Pastor et al 2021 ; Jaeger et al 2022 ). KP-SIIN organoids were transplanted into bleomycin-pretreated, immunocompetent syngeneic recipients.…”

Direct Presentation of Tumor‐Associated Antigens to Induce Adaptive Immunity by Personalized Dendritic Cell‐Mimicking Nanovaccines

“…[15] However, identifying actionable TAAs is one of the biggest challenges in developing DCs-based vaccines. To date, several strategies have been developed to identify TAAs for immune induction, such as mass spectrometry analysis and RNA-or Ribo-seqbased approaches, [16][17][18][19] but most of them are time-consuming and costly. Notably, tumor cells are highly heterogeneous, [20,21] making it extremely challenging to construct targeted antigens expressed in all subpopulations.…”