Neoantigens elicit T cell responses in breast cancer

Abstract Neoantigens are tumor-specific antigens that arise from non-synonymous mutations in tumor cells. However, their effect on the immune responses in tumor microenvironment are still unclear in breast cancer.We performed whole exome and RNA sequencing of 31 fresh breast cancer tissues and neoantigen prediction on the non-synonymous single nucleotide variants (nsSNVs) among exonic mutations. Neoantigen profiles were determined by predictive HLA binding affinity (IC50<500nM) and mRNA expression with a read count≥1. We evaluated the association between neoantigen load and expression levels of immune-related genes. Moreover, using primary tumor cells established from a breast cancer patient with malignant ascites, we tried to induce cytotoxic T lymphocytes (CTLs) by co-culturing neoantigen peptide-pulsed dendritic cells (DCs) and autologous peripheral lymphocytes. The functions of CTLs were examined by cytotoxicity and IFN-γ ELISpot assay.. Neoantigen load ranged from 6 to 440 (mean, 95) and was positively correlated with the total number of nsSNVs. Although no associations between neoantigen load and mRNA expressions of T cell markers were observed, but the co-culture of neoantigen-pulsed DCs and lymphocytes successfully induced CTLs ex vivo. These results suggest that neoantigen analysis may show utility in developing strategies to elicit T cell responses.