By performing mass spectrometry (MS) to survey peptides eluted from cell lines transduced to express a single HLA-I allele frequently expressed in the US population, and a minigene encoding one of 10 commonly occurring tumor-specific mutations, four HLA-A*11:01- and five HLA-A*03:01-restricted naturally processed neoepitopes were identified. Corresponding HLA-I Tg mice were immunized with MS-defined minimal peptides, and murine TCRs were isolated that were active at nM peptide concentrations and were highly mutation-specific for KRAS G13D, PIK3CA E545K, EGFR L858R, BRAF V600E (HLA- A*11:01), and KRAS G12V, EGFR L858R, BRAF V600E (HLA-A*03:01).

Contributed by Paula Hochman

BACKGROUND: Tumor-specific mutated proteins can create immunogenic non-self, mutation-containing 'neoepitopes' that are attractive targets for adoptive T-cell therapies. To avoid the complexity of defining patient-specific, private neoepitopes, there has been major interest in targeting common shared mutations in driver genes using off-the-shelf T-cell receptors (TCRs) engineered into autologous lymphocytes. However, identifying the precise naturally processed neoepitopes to pursue is a complex and challenging process. One method to definitively demonstrate whether an epitope is presented at the cell surface is to elute peptides bound to a specific major histocompatibility complex (MHC) allele and analyze them by mass spectrometry (MS). These MS data can then be prospectively applied to isolate TCRs specific to the neoepitope. METHODS: We created mono-allelic cell lines expressing one class I HLA allele and one common mutated oncogene in order to eliminate HLA deconvolution requirements and increase the signal of recovered peptides. MHC-bound peptides on the surface of these cell lines were immunoprecipitated, purified, and analyzed using liquid chromatography-tandem mass spectrometry, producing a list of mutation-containing minimal epitopes. To validate the immunogenicity of these neoepitopes, HLA-transgenic mice were vaccinated using the minimal peptides identified by MS in order to generate neoepitope-reactive TCRs. Specificity of these candidate TCRs was confirmed by peptide titration and recognition of transduced targets. RESULTS: We identified precise neoepitopes derived from mutated isoforms of KRAS, EGFR, BRAF, and PIK3CA presented by HLA-A*03:01 and/or HLA-A*11:01 across multiple biological replicates. From our MS data, we were able to successfully isolate murine TCRs that specifically recognize four HLA-A*11:01 restricted neoepitopes (KRAS G13D, PIK3CA E545K, EGFR L858R and BRAF V600E) and three HLA-A*03:01 restricted neoepitopes (KRAS G12V, EGFR L858R and BRAF V600E). CONCLUSIONS: Our data show that an MS approach can be used to demonstrate which shared oncogene-derived neoepitopes are processed and presented by common HLA alleles, and those MS data can rapidly be used to develop TCRs against these common tumor-specific antigens. Although further characterization of these neoepitope-specific murine TCRs is required, ultimately, they have the potential to be used clinically for adoptive cell therapy.

Author Info: (1) Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA catherine.ade@nih.gov. (2) Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA. (3) Cancer Res

Author Info: (1) Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA catherine.ade@nih.gov. (2) Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA. (3) Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. (4) Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA. (5) Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA. (6) Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA. Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA. (7) Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA. Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD, USA. (8) Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA. Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA. (9) Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA. NextCure Inc, Beltsville, MD, USA. (10) Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. (11) Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA.