Certain phosphorylated
peptides are differentially presented by MHC molecules on
cancer cells characterized by aberrant phosphorylation.
Phosphopeptides presented in complex with the
human leukocyte antigen HLA-A*02:01 provide a stability advantage over their nonphosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether
tumor-associated
phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of
phosphopeptides presented by the prevalent alleles
HLA-A*03:01, -A*11:01, -C*07:01, and - C*07:02.
Methods: We isolated
peptide-MHC complexes by immunoprecipitation from 10 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics datasets to assemble a curated set of
phosphopeptides presented by 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected
phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for
phosphopeptide-specific multimer binding and
cytokine production.
Results: Conclusions:
Phosphopeptides presented by multiple alleles that are differentially expressed on
tumors constitute
tumor-specific
antigens that could be targeted for
cancer immunotherapy, but the immunogenicity of such
phosphopeptides is not a general feature. In particular,
phosphopeptides presented by
HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while
phosphopeptides presented by
HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population,
phosphopeptide-targeted
immunotherapies should be wary of allele-specific differences. What is already known on this topic - Phosphorylated
peptides presented by the common HLA alleles A*02:01 and B*07:02 are differentially expressed by multiple
tumor types, exhibit structural fitness due to phosphorylation, and are targets of healthy donor T cell surveillance, but it is not clear, however, whether such features apply to
phosphopeptides presented by other common HLA alleles. What this study adds - We investigated the
tumor presentation, binding, structural features, and immunogenicity of
phosphopeptides to the prevalent alleles A*03:01, A*11:01, C*07:01, and C*07:02, selected on the basis of their presentation by malignant cells but not normal cells. We found
tumor antigens derived from genetic dependencies in
lymphomas and
leukemias that bind
HLA-A3, -A11, -C7 molecules. While we could detect circulating T cell responses in healthy individuals to A*02:01 and A*11:01
phosphopeptides, we did not find such responses to A*03:01 or C*07:01
phosphopeptides, except when utilizing allogeneic donor T cells, indicating that these
phosphopeptides may not be immunogenic in an autologous setting but can still be targeted by other means. How this study might affect research, practice or policy - An expanded patient population expressing alleles other than A*02:01 can be addressed through the development of
immunotherapies specific for
phosphopeptides profiled in the present work, provided the nuances we describe between alleles are taken into consideration.