ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery

• Published in: Frontiers in immunology Vol. 12; p. 658372
• Main Authors: Finton, Kathryn A. K., Brusniak, Mi-Youn, Jones, Lisa A., Lin, Chenwei, Fioré-Gartland, Andrew J., Brock, Chance, Gafken, Philip R., Strong, Roland K.
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 23.04.2021
• Subjects: Immunology; immunotherapy; ligandome analysis; mass spectrometry; MHC class I; peptide-HLA complex; MHC class I; mass spectrometry; peptide-HLA complex; ligandome analysis; immunotherapy
• ISSN: 1664-3224; 1664-3224
• DOI: 10.3389/fimmu.2021.658372

Conventional immunoprecipitation/mass spectroscopy identification of HLA-restricted peptides remains the purview of specializing laboratories, due to the complexity of the methodology, and requires computational post-analysis to assign peptides to individual alleles when using pan-HLA antibodies. We have addressed these limitations with ARTEMIS: a simple, robust, and flexible platform for peptide discovery across ligandomes, optionally including specific proteins-of-interest, that combines novel, secreted HLA-I discovery reagents spanning multiple alleles, optimized lentiviral transduction, and streamlined affinity-tag purification to improve upon conventional methods. This platform fills a middle ground between existing techniques: sensitive and adaptable, but easy and affordable enough to be widely employed by general laboratories. We used ARTEMIS to catalog allele-specific ligandomes from HEK293 cells for seven classical HLA alleles and compared results across replicates, against computational predictions, and against high-quality conventional datasets. We also applied ARTEMIS to identify potentially useful, novel HLA-restricted peptide targets from oncovirus oncoproteins and tumor-associated antigens.