To expand the repertoire of verified neoepitope-HLA combinations, particularly those that are shared among patients and tumor types, Gurung, Heidersbach, and Darwish et al. developed a high-throughput discovery pipeline. 47 selected shared cancer mutations and 15 prevalent HLA alleles yielded 24,149 possible neoepitope–HLA combinations, which were then analyzed in an experimental HLA binding assay (TR-FRET) and with NetMHCpan-4.0. Both approaches seemed necessary for comprehensive discovery and identified 844 stable combinations. Proteomic analysis using monoallelic cell lines verified 86 neoepitope–HLA pairs, and in a proof-of-concept, human TCR-engineered T cells were cytotoxic to minigene-expressing cell lines.
Contributed by Ute Burkhardt
ABSTRACT: The broad application of precision cancer immunotherapies is limited by the number of validated neoepitopes that are common among patients or tumor types. To expand the known repertoire of shared neoantigen-human leukocyte antigen (HLA) complexes, we developed a high-throughput platform that coupled an in vitro peptide-HLA binding assay with engineered cellular models expressing individual HLA alleles in combination with a concatenated transgene harboring 47 common cancer neoantigens. From more than 24,000 possible neoepitope-HLA combinations, biochemical and computational assessment yielded 844 unique candidates, of which 86 were verified after immunoprecipitation mass spectrometry analyses of engineered, monoallelic cell lines. To evaluate the potential for immunogenicity, we identified T cell receptors that recognized select neoepitope-HLA pairs and elicited a response after introduction into human T cells. These cellular systems and our data on therapeutically relevant neoepitopes in their HLA contexts will aid researchers studying antigen processing as well as neoepitope targeting therapies.