The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction

Abstract

A challenge in developing personalized cancer immunotherapies is the prediction of putative cancer-specific antigens. Currently, predictive algorithms are used to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid in the selection of putative epitope targets. One drawback of current epitope prediction algorithms is that they are trained on datasets containing biochemical HLA-peptide binding data that may not completely capture the rules associated with endogenous processing and presentation. The field of MS has made great improvements in instrumentation speed and sensitivity, chromatographic resolution, and proteogenomic database search strategies to facilitate the identification of HLA-ligands from a variety of cell types and tumor tissues. As such, these advances have enabled MS profiling of HLA-binding peptides to be a tractable, orthogonal approach to lower throughput biochemical assays for generating comprehensive datasets to train epitope prediction algorithms. In this review, we will highlight the progress made in the field of HLA-ligand profiling enabled by MS and its impact on current and future epitope prediction strategies.

Keywords: cancer; epitope prediction; immunoproteomics; neoantigens; peptidomics.

Figure 1

Development and function of personalized neoantigen vaccines. A) Overview of the epitope selection process in the development of personalized cancer vaccines. Tumor‐specific variants are first identified using whole exome or transcriptome sequencing from the patient's tumor biopsy. The sequence variant containing peptides are ranked by an epitope selection pipeline. The resulting putative neoantigen epitopes could be further prioritized based on T cell response prediction or measurement. Predicted neoantigens containing high confident epitopes are selected for vaccine production. B) Schematic depicting the function of personalized neoantigen vaccines. Predicted neoantigens are administered in combination with adjuvants and/or checkpoint inhibitors to increase the patient's immune response. Upon vaccination, dendritic cells, and/or other antigen presenting cells uptake the neoantigens delivered by a vehicle, such as DNA, RNA, or long peptide form (box 1). After the dendritic cells or other antigen presenting cells process the neoantigens, they can present the resulting epitopes to naïve T cells, which are subsequently activated to become cytotoxic (box 2). These neoantigen‐specific cytotoxic T cells replicate and circulate in the peripheral vascular system (box 3). When these T cells encounter tumor cells presenting the corresponding epitopes, they can identify and eliminate them by cytotoxicity and other immune functions (box 4).

Figure 2

Multi‐allelic and mono‐allelic approaches in HLA ligand profiling. In a multi‐allelic approach, the HLA ligands are co‐immunoprecipitated with HLA heterodimers directly from patient material or cell lines (top). Because these cells naturally expressed multiple HLA alleles, peptides identified from such multi‐allelic approaches must be deconvoluted to assign binding to a specific HLA heterodimer if the HLA types are known. In a mono‐allelic approach, the HLA‐ligands are co‐immunoprecipitated with HLA heterodimers from cell lines genetically modified for expression of only a single HLA allele (bottom). Thus, peptides identified from mono‐allelic approaches do not require deconvolution for HLA heterodimer binding assignments.