Scaling measurements of peptide-HLA complex stability using user-defined libraries and mass spectrometry 2310029
Human leukocyte antigen (HLA) class I presents intracellular peptides to the immune system on the cell surface. Since this process is crucial for the recognition of cancer cells and the initiation of anti-tumor immunity, peptides presented by HLA are valuable immunotherapy targets. More stable peptide HLA (pHLA) complexes provoke superior immune responses. However, how peptide sequence motifs contribute to pHLA stability is not well understood. We developed a high-throughput assay to quantify stability of thousands of user-defined pHLA produced in E. coli. Peptide libraries and the desired HLA are produced and form pHLA complexes in E. coli. pHLA are purified and stability is evaluated by treating pHLA with a thermal gradient and recovering only the peptides which remain HLA-bound after heat treatment. Peptide depletion over the temperature range is monitored by quantitative tandem mass tag (TMT) enabled mass spectrometry. Our new E. coli-based method is reliable for assessing pHLA stability. Detected HLA-binding peptides have the expected binding motifs, and stability data strongly correlates with current gold-standard data. We are able to generate large peptide stability datasets (1,800+ peptides) in one scaled experiment — five times larger than currently available datasets. We show that peptide motifs and anchor residue combinations potentially drive pHLA stability. Additionally, peptides were included in user-defined libraries with public immunogenicity annotations. We observed that immunogenic peptides were significantly more stable than non-immunogenic peptides. We generated customizable pHLA stability datasets which show how peptide sequence motifs affect pHLA stability, and may be helpful for improving our mechanistic understanding of pHLA stability. Further, since peptide stability is related to immunogenicity, these large-scale pHLA stability datasets will be useful for improving peptide immunogenicity predictions for the development of immunotherapeutics. NIH R01CA155010, Mark Foundation for Cancer Research, Moderna Classical and Non-Classical Antigen Presenting Cells (APC)