INSERM U1242 Oncogenesis Stress Signaling - SPECIAL SEMINAR - Centre De Lutte Contre Le Cancer Eugène Marquis

Integrative discovery of non-canonical neoantigens: emerging opportunities and challenges for cancer immunotherapy

Dr. Léa PROCHASSON

PharmD and molecular biologist

Curie Institute - PARIS

Unité « Dynamique de l’information Génétique, bases fondamentales et cancer » (UMR3244)

Equipe: ARN non codant, épigénétique et fluidité des génomes

Abstract

The clinical success of cancer immunotherapy relies on the identification of tumour-specific antigens capable of eliciting effective T-cell responses. However, canonical mutation-derived neoantigens remain challenging targets because of their limited immunogenicity, patient specificity, and heterogeneous HLA presentation. In contrast, the non-canonical proteome, generated through the translation of alternative open reading frames (ORFs) within non-coding transcripts, represents a promising and largely unexplored source of tumour antigens.
Here, we developed an integrative pipeline for the discovery and validation of shared non-canonical neoantigens in pancreatic cancer. By combining transcriptome-wide k-mer analysis, ribosome profiling, immunopeptidomics, and functional immunogenicity assays, we identified 14 non-canonical neoantigens across primary and metastatic tumors, presented by several common HLA alleles (HLA-A02:01, -A01:01 and -A*24:02). Their therapeutic potential was further assessed through MHC-binding, T-cell activation, and peptide-specific T-cell receptor (TCR) screening using naïve CD8+ T cells from healthy donors. One candidate successfully passed all validation steps, eliciting a detectable antigen-specific immune response. Importantly, this neoantigen was shared by approximately 20% of patients in our cohort, highlighting its potential as a component of an off-the-shelf multiplex vaccine for pancreatic cancer. Overall, this work establishes a scalable framework for the identification and functional validation of clinically relevant neoantigens beyond the canonical coding genome.