Residue substitution enhances the immunogenicity of neoepitopes from gastric cancers

Objective:Neoantigens arising from gene mutations in tumors can induce specific immune responses,and neoantigen-based immunotherapies have been tested in clinical trials.Here,we characterized the efficacy of altered neoepitopes in improving immunogenicity against gastric cancer.Methods:Raw data of whole-exome sequencing derived from a patient with gastric cancer were analyzed using bioinformatics methods to identify neoepitopes.Neoepitopes were modified by P1Y(the first amino acid was replaced by tyrosine)and P2L(the second amino acid was replaced by leucine).T2 binding and stability assays were used to detect the affinities between the neoepitopes and the HLA molecules,as well as the stabilities of complexes.Dendritic cells(DCs)presented with neoepitopes stimulated naïve CD8+T cells to induce specific cytotoxic T lymphocytes.ELISA and carboxyfluorescein succinimidyl ester were used to detect IFN-γand TNF-αlevels,and T cell proliferation.Perforin was detected by flow cytometry.The cytotoxicity of T cells was determined using the lactate dehydrogenase assay.Results:Bioinformatics analysis,T2 binding,and stability assays indicated that residue substitution increased the affinity between neoepitopes and HLA molecules,as well as the stabilities of complexes.DCs presented with altered neoepitopes stimulated CD8+T cells to release more IFN-γand had a greater effect on promoting proliferation than wild-type neoepitopes.CD8+T cells stimulated with altered neoepitopes killed more wild-type neoepitope-pulsed T2 cells than those stimulated with wild-type neoepitopes,by secreting more IFN-γ,TNF-α,and perforin.Conclusions:Altered neoepitopes exhibited greater immunogenicity than wild-type neoepitopes.Residue substitution could be used as a new strategy for immunotherapy to target neoantigens.

Finding neoepitopes in mouse models of personalized cancer immunotherapy

BACKGROUND： Cancer immunotherapy uses one＇s own immune system to fight cancerous cells. As immune system is hard- wired to distinguish self and non-self, cancer immunotherapy is predicted to target cancerous cells specifically, therefore is less toxic than chemotherapy and radiation therapy, two major treatments for cancer. Cancer immunologists have spent decades to search for the specific targets in cancerous cells. METHODS： Due to the recent advances in high throughput sequencing and bioinformatics, evidence has merged that the neoantigens in cancerous cells are probably the cancer-specific targets that lead to the destruction of cancer. We will review the transplantable murine tumor models for cancer immunotherapy and the bioinformatics tools used to navigate mouse genome to identify tumor-rejecting neoantigens. RESULTS： Several groups have independently identified point mutations that can be recognized by T cells of host immune system. It is consistent with the note that the formation ofpeptide-MHC I-TCR complex is critical to activate T cells. Both anchor residue and TCR-facing residue mutations have been reported. While TCR-facing residue mutations may directly activate specific T cells, anchor residue mutations improve the binding of peptides to MHC I molecules, which increases the presentation of peptides and the T cell activation indirectly. CONCLUSIONS： Our work indicates that the affinity of neoepitopes for MHC I is not a predictor for anti-tumor immune responses in mice. Instead differential agretopic index （DAI）, the numerical difference of epitope-MHC I affinities between the mutated and un-mutated sequences is a significant predictor. A similar bioinformatics pipeline has been developed to generate personalized vaccines to treat human ovarian cancer in a Phase I clinical trial.