Abstract IA01: Cryptic antigens: Novel targets in pancreas cancer

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(18_Suppl_3):Abstract nr IA01.