Immunogenicity of non-canonical HLA-I tumor ligands identified through proteogenomics

Abstract

Tumor antigens are central to antitumor immunity. Recent evidence suggests that peptides from non-canonical (nonC) aberrantly translated proteins can be presented on HLA-I by tumor cells. Here, we investigated the immunogenicity of nonC tumor HLA-I ligands (nonC-TL) to better understand their contribution to cancer immunosurveillance and their therapeutic applicability. Using proteogenomics, we identified 517 nonC-TL from 9 patients with melanoma, gynecological, and head and neck cancer. We found no recognition of the 507 nonC-TL tested by autologous ex vivo expanded tumor reactive T-cell cultures while the same cultures demonstrated reactivity to mutated, cancer-germline, or melanocyte differentiation antigens. However, in vitro sensitization of donor peripheral blood lymphocytes against 170 selected nonC-TL, led to the identification of T-cell receptors (TCRs) specific to three nonC-TL, two of which mapped to the UTR5 regions of HOXC13 and ZKSCAN1, and one mapping to a non-coding spliced variant of C5orf22C. T cells targeting these nonC-TL recognized cancer cell lines naturally presenting their corresponding antigens. Expression of the three immunogenic nonC-TL was shared across tumor types and barely or not detected in normal cells. Our findings predict a limited contribution of nonC-TL to cancer immunosurveillance but demonstrate they may be attractive novel targets for widely applicable immunotherapies.

What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?

“…Interestingly, peptides derived from noncanonical ORFs are much more abundant in HLA-I datasets compared with HLA-II datasets ( 18 , 34 , 36 , 38 , 39 , 53 , 94 ). HLA-I molecules usually present peptides derived from proteasome-mediated degradation of newly synthesized and other cellular proteins, and HLA-I presentation is tightly linked with protein synthesis and degradation rates.…”

What can Ribo-seq and proteomics tell us about the non-canonical proteome?

“…Interestingly, peptides derived from non-canonical ORFs are much more abundant in HLA-I datasets compared to HLA-II datasets (18,34,36,38,39,53,93). HLA-I molecules usually present peptides derived from proteasome-mediated degradation of newly synthesized and other cellular proteins, and HLA-I presentation is tightly linked with protein synthesis and degradation rates.…”