Identification of MHC Peptides Using Mass Spectrometry for Neoantigen Discovery and Cancer Vaccine Development

Abstract

Immunotherapy with neoantigens presented by major histocompatibility complex (MHC) is one of the most promising approaches in cancer treatment. Using this approach, cancer vaccines can be designed to target tumor‐specific mutations that are not found in normal tissues. Clinical trials have demonstrated an increased immune response and eradication of tumors after injecting synthetic peptides selected from the immunopeptidome. Although the sequence of MHC binding peptides can be predicted from genome sequencing and prediction algorithms, this approach results in large numbers of predicted peptides, requiring the confirmation by mass spectrometry (MS) analysis. Identification of MHC peptides by direct MS analysis of immunopeptidome is accurate and sensitive, with tens of thousands of unique peptides potentially identified from either cancer cell line or tumor tissue. Peptides with mutations can also be identified with patient‐specific protein databases constructed from genome or transcriptome sequencing data. MS analysis also enables the characterization of the post‐translational modifications (PTMs) of those antigens that cannot be predicted. Moreover, PTMs were found to be more efficient in triggering an immune response. In addition to reviewing recent advances in the identification of neoantigens using MS, the techniques for cancer vaccine candidate selection and formulation, vaccine delivery systems, and the potential for use in combination with other therapeutics are also discussed. It is anticipated that MS‐based techniques will play an important role in future cancer vaccine development. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:110–125, 2021.

Neo-Antigen mRNA Vaccines

“…Efforts have been made to further improve MS by, for example, prefixing it to high pressure liquid chromatography, to ensure higher purity of the samples, or by implementing tandem mass spectrometry, resulting in higher specificity [ 82 ]. Alone, MS does not suffice as a method for neo-antigen identification as it requires a priori knowledge of the potential target, although exceptions can be made for peptides spliced in the proteasome, peptides with post-translational modification (PTM) and peptides from non-coding regions [ 83 ]. However, because of its high sensitivity, accuracy and reproducible qualification and quantification of the HLA peptidome, it makes for a valid approach for neo-antigen validation.…”

“…IP is regarded as highly specific and flexible, allowing HLA-peptide isolation from a range of biological samples upon MAE. Although MAE without IP is a more time- and cost-effective approach, it lacks selectivity, as up to 60% of the eluted peptides can be contaminants [ 83 ]. Lanoix et al [ 90 ] compared both methods and concluded that both resulted in reproducible candidate neo-antigen libraries.…”

Main Strategies for the Identification of Neoantigens

“…Neoantigen candidate selection relies on the spectra of somatic mutations identified by WES/RNA-seq. This approach suffers from a lack of direct experimental evidence of the real presence of predicted epitopes on the cell surface as a complex with MHC molecules [ 153 , 154 ]. Lacking data could be obtained using high-throughput mass spectrometry techniques [ 153 , 154 ] that at present allow us to analyze large amounts of peptides or whole proteins simultaneously.…”

“…This approach suffers from a lack of direct experimental evidence of the real presence of predicted epitopes on the cell surface as a complex with MHC molecules [ 153 , 154 ]. Lacking data could be obtained using high-throughput mass spectrometry techniques [ 153 , 154 ] that at present allow us to analyze large amounts of peptides or whole proteins simultaneously. This review does not aim to give a detailed characterization of MS-based approaches; for a comprehensive review on this topic, the reader could refer to [ 56 , 153 , 154 ].…”

Current Challenges in Vaccinology

“…Genomics is not the only area that has undergone remarkable transformation recently in terms of the technologies and platforms that can be used to design, create, and study vaccines. Examples include the following: mass cytometry, which allows for incredibly complex immunophenotyping (24,25); proteomics and mass spectrometry (26)(27)(28)(29)(30); and metabolomics, which has been closely linked to immunologic function and vaccine response (31)(32)(33). However, in this focused review, we will explore how genomics and recent genomic technologies have impacted vaccine development and may provide solutions to both the long-standing barriers in vaccine design and the new challenges posed by new and re-emerging pathogens of public health importance.…”