The CT26 model is one of the most widely tested systems for cancer immunotherapy. Over 70% of the CD8+ CTL responses in CT26 tumors are directed against two peptides: SPSYVYHQF (AH1) presented by H-2Ld, or GGPESFYCASW (GSW11) presented by H-2Dd. Both peptides derive from the ecotropic murine leukaemia virus gp70 envelope glycoprotein, which is the highest expressed gene in CT26, and have relative low affinity values for their respective MHC-I. However, there is a lack of knowledge about other CTL specificities in CT26, the relationship between abundance and affinity of such peptides, and their roles in tumor rejection. We identified 96 potential epitopes restricted by MHC-I molecules in BALB/c mice based on previously published immuno-transcriptomic data. We used a mathematical algorithm integrating the peptides relative affinity to MHC-I measured by NetMHC4.0, and their abundance in the proteome, which resulted in a prediction of the likelihood of peptide presentation. Screening was performed in splenocytes from Treg-depleted CT26-challenged mice via IFNγ intracellular cytokine staining and T cell proliferation assays. Our approach led to the identification of a novel CTL specificity restricted by H-2Kd (Kd34), which shows moderate IFNγ responses in splenocytes from mice responding to the therapy. Moreover, using Kd34-specific dextramers, we were able to detect a small population of tumor-infiltrating lymphocytes (TILs) specific for this peptide, with similar phenotypic traits to AH1- and GSW1-specific TILs. The identification of such novel CD8+ T cell specificities will improve the understanding about the relationship between immunodominance and epitope abundance/affinity to better tailor vaccine strategies in cancer.
Human papillomavirus (HPV) infection accounts for 5% cancers worldwide, with cervical carcinoma and squamous cell carcinoma of the head and neck (SCCHN) being most common. HPV can enable immune evasion, with 50% of HPV+SCCHN having reduced pMHC I expression, correlating with fewer tumor infiltrating lymphocytes (TIL) and a worse clinical outcome. Polymorphisms in the endoplasmic reticulum aminopeptidase1 (ERAP1), a key component of antigen processing, trimming N-terminally extended peptides for MHC I, are associated with prognosis and outcome in cervical carcinoma. We have previously demonstrated ERAP1 to be highly polymorphic, forming distinct allotypes with functional differences. Here we investigate the contribution of ERAP1 in the pathogenesis of SCCHN. We identified a number of novel ERAP1 allotype pairs (both chromosomal copies) from HPV+ SCCHN. Assessment of trimming function revealed a range of abilities to generate the model epitope SIINFEHL from individual amino acid or AIVMK precursors. Furthermore, the ability to generate HPV-16 E6/E7 specific epitopes also demonstrated varying trimming phenotypes. Interestingly, the overall ability to generate the final epitopes (model and HPV) in TILLOW patients was poor, whereas TILHIGH patients efficiently generated them. This difference revealed ERAP1 gene sequence and function stratifies with TIL levels and prognosis. These results demonstrate that the successful presentation of HPV-16 E6/E7 epitopes at the cell surface depends on the ERAP1 allotype pairs expressed within an individual. Furthermore, the allotype pairs correlate with levels of tumor infiltrate, suggesting ERAP1 activity as an indicator of prognosis in HPV+ SCCHN patients.
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