Abstract IA01: Cryptic antigens: Novel targets in pancreas cancer

Abstract Immunotherapies have revolutionized the treatment of multiple cancer types; however, pancreatic cancer (PDAC) remains largely refractory to traditional immune checkpoint inhibition. Computational predictions are often used to nominate putative neoantigens; however, empirical detection using mass spectrometry-based immunopeptidomics provides direct evidence of peptide presentation by human leukocyte antigen class I (HLA-I) on tumor cells. Emerging evidence suggests that certain malignancies aberrantly translate genomic regions outside of annotated protein coding areas, leading to HLA-I presentation of cryptic peptides. Non-canonical HLA-I bound peptides (ncHLAp) arise from translation of these ostensibly noncoding genomic elements. We utilized patient-derived organoids (PDOs) to enrich the malignant compartment from low neoplastic cellularity tumor specimens. We then employed a personalized proteogenomic platform coupled with high-depth immunopeptidomics and empirically identified 90, 000 unique PDAC HLA-I-bound peptides (HLAp). We detected HLAp arising from somatic mutations in a subset of PDAC patients. Moreover, we directly identified over 1, 700 ncHLAp, primarily arising from translation of novel unannotated open reading frames (nuORFs), and a substantial proportion of ncHLAp were shared amongst PDAC patients. We developed a stringent translation-centric pipeline to investigate expression of nuORFs across a range of healthy tissues, including healthy thymus, and found that 500 ncHLAp had no detectable evidence of translation in any healthy tissue investigated. We next investigated the immunogenic potential of both cryptic peptides (ncHLAp) and mutation-derived HLAp using an ex vivo T cell priming and expansion platform. A subset of both mutation-derived HLAp and cancer-restricted ncHLAp harbored robust immunogenicity. We identified T cell receptors (TCRs) specific for cancer-restricted cryptic antigens and performed deep characterization of these TCRs. Finally, we demonstrated that cryptic antigen-specific TCR-redirected T cells (TCR-T) exerted robust cytotoxicity and tumoricidal activity against patient-derived PDAC organoids (both ex vivo and in vivo), underscoring the potential to leverage this novel class of antigens for next generation immune-based therapies. Citation Format: William Freed-Pastor. Cryptic antigens: Novel targets in pancreas cancer abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85 (18Suppl₃): Abstract nr IA01.