RESUMEN
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.
RESUMEN
Assembly of TCRalpha and TCRdelta genes from the TCRalpha/delta locus is tightly controlled for the proper generation of alphabeta and gammadelta T cells. Of >100 shared variable gene segments in the TCRalpha/delta locus, only a few are predominantly used for the TCRdelta gene assembly, while most are for TCRalpha. However, the importance and mechanisms of the selective variable gene rearrangement for T cell development are not fully understood. We report herein that the development of a tissue-specific gammadelta T cell population is critically affected by recombination signal sequence-associated restriction on the variable gene usage for TCRdelta assembly. We found that the development of substitute skin gammadelta T cells in mice deficient of the TCRgamma3 gene, which is used in wild-type skin gammadelta T cells, was drastically affected by the strain background. A Vgamma2(+) skin gammadelta T cell population developed in mice of the B6 but not the 129 strain backgrounds, due to a difference in the rearrangement of endogenous Vdelta7(+) TCRdelta genes, which paired with the Vgamma2(+) TCRgamma gene to generate the Vgamma2/Vdelta7(+) skin gammadelta T cell precursors in fetal thymi of the B6 background mice. The defective TCRdelta rearrangement of the 129-"Vdelta7" gene was associated with specific variations in its recombination signal sequence, which renders it poorly compatible for rearrangement to Ddelta genes. These findings provide the first direct evidence that recombination signal sequence-associated restriction on the variable gene usage for TCRalpha/delta gene assembly plays an important role in T cell development.
