Proteogenomic Characterization of Head and Neck Squamous Cell Cancer Immunopeptidomes to Detect Non Canonical Protein Targets for Cancer Immunotherapy.

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Publication Date


Publication Title

AAI Annual Meeting; May 6-10; Portland, OR. 2022


oregon; chiles; genomics


  1. Background: Strategies that unleash anticancer immunity are improving outcomes for patients with many types of cancer. However, the targets of anticancer immunity remain largely unidentified. Recently, it was observed that cancer cells translate mRNAs that are not typically expressed by normal cells. Some of the resulting proteins, termed novel unanotated or non canonical proteins, are not expressed in the thymus and are rapidly degraded and preferentially loaded onto MHC class I molecules of cancer cells. In acute myelogenous leukemia (AML) there are a substantial number of these proteins that are common among AML, identifying them as shared tumor antigens. Our group has speculated that by characterizing the peptides bound to HLA of head and neck squamous cell cancer (HNSCC) cell lines we will identify a library of potential HLA-presented non canonical protein epitopes that can be used as immunotherapy targets and to monitor anti-cancer immunity.

Methods: HNSCC cell lines generated at the Earle A. Chiles Research Institute are being characterized by Whole Genome Sequencing, whole transcriptome RNA-Seq and LC-MS/MS of peptides eluted from HLA. The whole transcriptome RNA-Seq will be used to identify non canonical protein spectra from LC-MS/MS analyses.

Results: Preliminary studies identified hundreds of novel immunopeptides per HNSCC cell line. The majority of the identified peptides were predicted as strong or weak binders to the patients’ HLA-I.

Conclusions: Mass spectroscopy is a useful approach to characterize the HLA-presented cancer immunopeptidome. Integration of whole transcriptome RNA-Seq may allow for novel HNSCC peptide identifications that were not discovered by searching against public databases alone.

Clinical Institute



Earle A. Chiles Research Institute




Iwamoto N, Moudgil T, Meng R, Dowdell A, Fass J, Welle J, Rattray R, Cha J, Hilton TL, Paustian C, Bell RB, Laws M, McDonnell G, Bifulco CB, Jensen SM, Hu HM, Urba WJ, Leidner RS, Koguchi Y, Piening B, Shimada T, Fox BA

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